Daily Papers

In recent years, diffusion-based models have demonstrated exceptional performance in searching for simultaneously stable, unique, and novel (S.U.N.) crystalline materials. However, most of these models don't have the ability to change the number of atoms in the crystal during the generation process, which limits the variability of model sampling trajectories. In this paper, we demonstrate the severity of this restriction and introduce a simple yet powerful technique, mirage infusion, which enables diffusion models to change the state of the atoms that make up the crystal from existent to non-existent (mirage) and vice versa. We show that this technique improves model quality by up to times2.5 compared to the same model without this modification. The resulting model, Mirage Atom Diffusion (MiAD), is an equivariant joint diffusion model for de novo crystal generation that is capable of altering the number of atoms during the generation process. MiAD achieves an 8.2% S.U.N. rate on the MP-20 dataset, which substantially exceeds existing state-of-the-art approaches. The source code can be found at https://github.com/andrey-okhotin/miad.git{github.com/andrey-okhotin/miad}.

Generative models for crystalline materials often rely on equivariant graph neural networks, which capture geometric structure well but are costly to train and slow to sample. We present Crystalite, a lightweight diffusion Transformer for crystal modeling built around two simple inductive biases. The first is Subatomic Tokenization, a compact chemically structured atom representation that replaces high-dimensional one-hot encodings and is better suited to continuous diffusion. The second is the Geometry Enhancement Module (GEM), which injects periodic minimum-image pair geometry directly into attention through additive geometric biases. Together, these components preserve the simplicity and efficiency of a standard Transformer while making it better matched to the structure of crystalline materials. Crystalite achieves state-of-the-art results on crystal structure prediction benchmarks, and de novo generation performance, attaining the best S.U.N. discovery score among the evaluated baselines while sampling substantially faster than geometry-heavy alternatives.

Generative models for structure-based drug design are often limited to a specific modality, restricting their broader applicability. To address this challenge, we introduce FuncBind, a framework based on computer vision to generate target-conditioned, all-atom molecules across atomic systems. FuncBind uses neural fields to represent molecules as continuous atomic densities and employs score-based generative models with modern architectures adapted from the computer vision literature. This modality-agnostic representation allows a single unified model to be trained on diverse atomic systems, from small to large molecules, and handle variable atom/residue counts, including non-canonical amino acids. FuncBind achieves competitive in silico performance in generating small molecules, macrocyclic peptides, and antibody complementarity-determining region loops, conditioned on target structures. FuncBind also generated in vitro novel antibody binders via de novo redesign of the complementarity-determining region H3 loop of two chosen co-crystal structures. As a final contribution, we introduce a new dataset and benchmark for structure-conditioned macrocyclic peptide generation. The code is available at https://github.com/prescient-design/funcbind.

Unified generation of sequence and structure for scientific data (e.g., materials, molecules, proteins) is a critical task. Existing approaches primarily rely on either autoregressive sequence models or diffusion models, each offering distinct advantages and facing notable limitations. Autoregressive models, such as GPT, Llama, and Phi-4, have demonstrated remarkable success in natural language generation and have been extended to multimodal tasks (e.g., image, video, and audio) using advanced encoders like VQ-VAE to represent complex modalities as discrete sequences. However, their direct application to scientific domains is challenging due to the high precision requirements and the diverse nature of scientific data. On the other hand, diffusion models excel at generating high-dimensional scientific data, such as protein, molecule, and material structures, with remarkable accuracy. Yet, their inability to effectively model sequences limits their potential as general-purpose multimodal foundation models. To address these challenges, we propose UniGenX, a unified framework that combines autoregressive next-token prediction with conditional diffusion models. This integration leverages the strengths of autoregressive models to ease the training of conditional diffusion models, while diffusion-based generative heads enhance the precision of autoregressive predictions. We validate the effectiveness of UniGenX on material and small molecule generation tasks, achieving a significant leap in state-of-the-art performance for material crystal structure prediction and establishing new state-of-the-art results for small molecule structure prediction, de novo design, and conditional generation. Notably, UniGenX demonstrates significant improvements, especially in handling long sequences for complex structures, showcasing its efficacy as a versatile tool for scientific data generation.

Inverse design of solid-state materials with desired properties represents a formidable challenge in materials science. Although recent generative models have demonstrated potential, their adoption has been hindered by limitations such as inefficiency, architectural constraints and restricted open-source availability. The representation of crystal structures using the SLICES (Simplified Line-Input Crystal-Encoding System) notation as a string of characters enables the use of state-of-the-art natural language processing models, such as Transformers, for crystal design. Drawing inspiration from the success of GPT models in generating coherent text, we trained a generative Transformer on the next-token prediction task to generate solid-state materials with targeted properties. We demonstrate MatterGPT's capability to generate de novo crystal structures with targeted single properties, including both lattice-insensitive (formation energy) and lattice-sensitive (band gap) properties. Furthermore, we extend MatterGPT to simultaneously target multiple properties, addressing the complex challenge of multi-objective inverse design of crystals. Our approach showcases high validity, uniqueness, and novelty in generated structures, as well as the ability to generate materials with properties beyond the training data distribution. This work represents a significant step forward in computational materials discovery, offering a powerful and open tool for designing materials with tailored properties for various applications in energy, electronics, and beyond.

The generation of plausible crystal structures is often the first step in predicting the structure and properties of a material from its chemical composition. Quickly generating and predicting inorganic crystal structures is important for the discovery of new materials, which can target applications such as energy or electronic devices. However, most current methods for crystal structure prediction are computationally expensive, slowing the pace of innovation. Seeding structure prediction algorithms with quality generated candidates can overcome a major bottleneck. Here, we introduce CrystaLLM, a methodology for the versatile generation of crystal structures, based on the autoregressive large language modeling (LLM) of the Crystallographic Information File (CIF) format. Trained on millions of CIF files, CrystaLLM focuses on modeling crystal structures through text. CrystaLLM can produce plausible crystal structures for a wide range of inorganic compounds unseen in training, as demonstrated by ab initio simulations. The integration with predictors of formation energy permits the use of a Monte Carlo Tree Search algorithm to improve the generation of meaningful structures. Our approach challenges conventional representations of crystals, and demonstrates the potential of LLMs for learning effective 'world models' of crystal chemistry, which will lead to accelerated discovery and innovation in materials science.

Crystal structure generation is a foundational challenge in materials discovery, particularly in designing functional inorganic crystalline materials with desired properties. Most existing diffusion-based generative models for crystals rely on complex, hand-crafted priors and modular architectures to separately model atom types, atomic positions, and lattice parameters. These methods often require customized diffusion processes and conditional denoising, which can introduce additional model complexities and inconsistencies. Here we introduce DiffCrysGen, a fully data-driven, score-based diffusion model that jointly learns the distribution of all structural components in crystalline materials. With crystal structure representation as unified 2D matrices, DiffCrysGen bypasses the need for task-specific priors or decoupled modules, enabling end-to-end generation of atom types, fractional coordinates, and lattice parameters within a single framework. Our model learns crystallographic symmetry and chemical validity directly from large-scale datasets, allowing it to scale to complex materials discovery tasks. As a demonstration, we applied DiffCrysGen to the design of rare-earth-free magnetic materials with high saturation magnetization, showing its effectiveness in generating stable, diverse, and property-aligned candidates for sustainable magnet applications.

Generative models trained at scale can now produce text, video, and more recently, scientific data such as crystal structures. In applications of generative approaches to materials science, and in particular to crystal structures, the guidance from the domain expert in the form of high-level instructions can be essential for an automated system to output candidate crystals that are viable for downstream research. In this work, we formulate end-to-end language-to-structure generation as a multi-objective optimization problem, and propose Generative Hierarchical Materials Search (GenMS) for controllable generation of crystal structures. GenMS consists of (1) a language model that takes high-level natural language as input and generates intermediate textual information about a crystal (e.g., chemical formulae), and (2) a diffusion model that takes intermediate information as input and generates low-level continuous value crystal structures. GenMS additionally uses a graph neural network to predict properties (e.g., formation energy) from the generated crystal structures. During inference, GenMS leverages all three components to conduct a forward tree search over the space of possible structures. Experiments show that GenMS outperforms other alternatives of directly using language models to generate structures both in satisfying user request and in generating low-energy structures. We confirm that GenMS is able to generate common crystal structures such as double perovskites, or spinels, solely from natural language input, and hence can form the foundation for more complex structure generation in near future.

The design of functional materials with desired properties is essential in driving technological advances in areas like energy storage, catalysis, and carbon capture. Generative models provide a new paradigm for materials design by directly generating entirely novel materials given desired property constraints. Despite recent progress, current generative models have low success rate in proposing stable crystals, or can only satisfy a very limited set of property constraints. Here, we present MatterGen, a model that generates stable, diverse inorganic materials across the periodic table and can further be fine-tuned to steer the generation towards a broad range of property constraints. To enable this, we introduce a new diffusion-based generative process that produces crystalline structures by gradually refining atom types, coordinates, and the periodic lattice. We further introduce adapter modules to enable fine-tuning towards any given property constraints with a labeled dataset. Compared to prior generative models, structures produced by MatterGen are more than twice as likely to be novel and stable, and more than 15 times closer to the local energy minimum. After fine-tuning, MatterGen successfully generates stable, novel materials with desired chemistry, symmetry, as well as mechanical, electronic and magnetic properties. Finally, we demonstrate multi-property materials design capabilities by proposing structures that have both high magnetic density and a chemical composition with low supply-chain risk. We believe that the quality of generated materials and the breadth of MatterGen's capabilities represent a major advancement towards creating a universal generative model for materials design.

Crystalline materials often exhibit a high level of symmetry. However, most generative models do not account for symmetry, but rather model each atom without any constraints on its position or element. We propose a generative model, Wyckoff Diffusion (WyckoffDiff), which generates symmetry-based descriptions of crystals. This is enabled by considering a crystal structure representation that encodes all symmetry, and we design a novel neural network architecture which enables using this representation inside a discrete generative model framework. In addition to respecting symmetry by construction, the discrete nature of our model enables fast generation. We additionally present a new metric, Fr\'echet Wrenformer Distance, which captures the symmetry aspects of the materials generated, and we benchmark WyckoffDiff against recently proposed generative models for crystal generation. Code is available online at https://github.com/httk/wyckoffdiff

Accelerating material discovery holds the potential to greatly help mitigate the climate crisis. Discovering new solid-state materials such as electrocatalysts, super-ionic conductors or photovoltaic materials can have a crucial impact, for instance, in improving the efficiency of renewable energy production and storage. In this paper, we introduce Crystal-GFN, a generative model of crystal structures that sequentially samples structural properties of crystalline materials, namely the space group, composition and lattice parameters. This domain-inspired approach enables the flexible incorporation of physical and structural hard constraints, as well as the use of any available predictive model of a desired physicochemical property as an objective function. To design stable materials, one must target the candidates with the lowest formation energy. Here, we use as objective the formation energy per atom of a crystal structure predicted by a new proxy machine learning model trained on MatBench. The results demonstrate that Crystal-GFN is able to sample highly diverse crystals with low (median -3.1 eV/atom) predicted formation energy.

Generative models trained on internet-scale data are capable of generating novel and realistic texts, images, and videos. A natural next question is whether these models can advance science, for example by generating novel stable materials. Traditionally, models with explicit structures (e.g., graphs) have been used in modeling structural relationships in scientific data (e.g., atoms and bonds in crystals), but generating structures can be difficult to scale to large and complex systems. Another challenge in generating materials is the mismatch between standard generative modeling metrics and downstream applications. For instance, common metrics such as the reconstruction error do not correlate well with the downstream goal of discovering stable materials. In this work, we tackle the scalability challenge by developing a unified crystal representation that can represent any crystal structure (UniMat), followed by training a diffusion probabilistic model on these UniMat representations. Our empirical results suggest that despite the lack of explicit structure modeling, UniMat can generate high fidelity crystal structures from larger and more complex chemical systems, outperforming previous graph-based approaches under various generative modeling metrics. To better connect the generation quality of materials to downstream applications, such as discovering novel stable materials, we propose additional metrics for evaluating generative models of materials, including per-composition formation energy and stability with respect to convex hulls through decomposition energy from Density Function Theory (DFT). Lastly, we show that conditional generation with UniMat can scale to previously established crystal datasets with up to millions of crystals structures, outperforming random structure search (the current leading method for structure discovery) in discovering new stable materials.

We present CrystalDiT, a diffusion transformer for crystal structure generation that achieves state-of-the-art performance by challenging the trend of architectural complexity. Instead of intricate, multi-stream designs, CrystalDiT employs a unified transformer that imposes a powerful inductive bias: treating lattice and atomic properties as a single, interdependent system. Combined with a periodic table-based atomic representation and a balanced training strategy, our approach achieves 9.62% SUN (Stable, Unique, Novel) rate on MP-20, substantially outperforming recent methods including FlowMM (4.38%) and MatterGen (3.42%). Notably, CrystalDiT generates 63.28% unique and novel structures while maintaining comparable stability rates, demonstrating that architectural simplicity can be more effective than complexity for materials discovery. Our results suggest that in data-limited scientific domains, carefully designed simple architectures outperform sophisticated alternatives that are prone to overfitting.

Generative machine learning (ML) models hold great promise for accelerating materials discovery through the inverse design of inorganic crystals, enabling an unprecedented exploration of chemical space. Yet, the lack of standardized evaluation frameworks makes it challenging to evaluate, compare, and further develop these ML models meaningfully. In this work, we introduce LeMat-GenBench, a unified benchmark for generative models of crystalline materials, supported by a set of evaluation metrics designed to better inform model development and downstream applications. We release both an open-source evaluation suite and a public leaderboard on Hugging Face, and benchmark 12 recent generative models. Results reveal that an increase in stability leads to a decrease in novelty and diversity on average, with no model excelling across all dimensions. Altogether, LeMat-GenBench establishes a reproducible and extensible foundation for fair model comparison and aims to guide the development of more reliable, discovery-oriented generative models for crystalline materials.

Discovering novel materials is critical for technological advancements such as solar cells, batteries, and carbon capture. However, the development of new materials is constrained by a slow and expensive trial-and-error process. To accelerate this pipeline, we introduce PLaID++, a Large Language Model (LLM) fine-tuned for stable and property-guided crystal generation. We fine-tune Qwen-2.5 7B to generate crystal structures using a novel Wyckoff-based text representation. We show that generation can be effectively guided with a reinforcement learning technique based on Direct Preference Optimization (DPO), with sampled structures categorized by their stability, novelty, and space group. By encoding symmetry constraints directly into text and guiding model outputs towards desirable chemical space, PLaID++ generates structures that are thermodynamically stable, unique, and novel at a sim50\% greater rate than prior methods and conditionally generates structures with desired space group properties. Our experiments highlight the effectiveness of iterative DPO, achieving sim115\% and sim50\% improvements in unconditional and space group conditioned generation, respectively, compared to fine-tuning alone. Our work demonstrates the potential of adapting post-training techniques from natural language processing to materials design, paving the way for targeted and efficient discovery of novel materials.

In this work, we introduce PhononBench, the first large-scale benchmark for dynamical stability in AI-generated crystals. Leveraging the recently developed MatterSim interatomic potential, which achieves DFT-level accuracy in phonon predictions across more than 10,000 materials, PhononBench enables efficient large-scale phonon calculations and dynamical-stability analysis for 108,843 crystal structures generated by six leading crystal generation models. PhononBench reveals a widespread limitation of current generative models in ensuring dynamical stability: the average dynamical-stability rate across all generated structures is only 25.83%, with the top-performing model, MatterGen, reaching just 41.0%. Further case studies show that in property-targeted generation-illustrated here by band-gap conditioning with MatterGen--the dynamical-stability rate remains as low as 23.5% even at the optimal band-gap condition of 0.5 eV. In space-group-controlled generation, higher-symmetry crystals exhibit better stability (e.g., cubic systems achieve rates up to 49.2%), yet the average stability across all controlled generations is still only 34.4%. An important additional outcome of this study is the identification of 28,119 crystal structures that are phonon-stable across the entire Brillouin zone, providing a substantial pool of reliable candidates for future materials exploration. By establishing the first large-scale dynamical-stability benchmark, this work systematically highlights the current limitations of crystal generation models and offers essential evaluation criteria and guidance for their future development toward the design and discovery of physically viable materials. All model-generated crystal structures, phonon calculation results, and the high-throughput evaluation workflows developed in PhononBench will be openly released at https://github.com/xqh19970407/PhononBench

Self-supervised neural language models have recently achieved unprecedented success, from natural language processing to learning the languages of biological sequences and organic molecules. These models have demonstrated superior performance in the generation, structure classification, and functional predictions for proteins and molecules with learned representations. However, most of the masking-based pre-trained language models are not designed for generative design, and their black-box nature makes it difficult to interpret their design logic. Here we propose BLMM Crystal Transformer, a neural network based probabilistic generative model for generative and tinkering design of inorganic materials. Our model is built on the blank filling language model for text generation and has demonstrated unique advantages in learning the "materials grammars" together with high-quality generation, interpretability, and data efficiency. It can generate chemically valid materials compositions with as high as 89.7\% charge neutrality and 84.8\% balanced electronegativity, which are more than 4 and 8 times higher compared to a pseudo random sampling baseline. The probabilistic generation process of BLMM allows it to recommend tinkering operations based on learned materials chemistry and makes it useful for materials doping. Combined with the TCSP crysal structure prediction algorithm, We have applied our model to discover a set of new materials as validated using DFT calculations. Our work thus brings the unsupervised transformer language models based generative artificial intelligence to inorganic materials. A user-friendly web app has been developed for computational materials doping and can be accessed freely at www.materialsatlas.org/blmtinker.

Generative models for materials, especially inorganic crystals, hold potential to transform the theoretical prediction of novel compounds and structures. Advancement in this field depends critically on robust benchmarks and minimal, information-rich datasets that enable meaningful model evaluation. This paper critically examines common datasets and reported metrics for a crystal structure prediction taskx2014generating the most likely structures given the chemical composition of a material. We focus on three key issues: First, materials datasets should contain unique crystal structures; for example, we show that the widely-utilized carbon-24 dataset only contains approx40% unique structures. Second, materials datasets should not be split randomly if polymorphs of many different compositions are numerous, which we find to be the case for the perov-5 dataset. Third, benchmarks can mislead if used uncritically, e.g., reporting a match rate metric without considering the structural variety exhibited by identical building blocks. To address these oft-overlooked issues, we introduce several fixes. We provide revised versions of the carbon-24 dataset: one with duplicates removed, one deduplicated and split by number of atoms N, and two containing only identical structures but with different unit cells. We also propose a new split for the perov-5 dataset which ensures polymorphs are grouped within each split subset, setting a more sensible standard for benchmarking model performance. Finally, we present METRe and cRMSE, new model evaluation metrics that can correct existing issues with the match rate metric.

Crystals are the foundation of numerous scientific and industrial applications. While various learning-based approaches have been proposed for crystal generation, existing methods seldom consider the space group constraint which is crucial in describing the geometry of crystals and closely relevant to many desirable properties. However, considering space group constraint is challenging owing to its diverse and nontrivial forms. In this paper, we reduce the space group constraint into an equivalent formulation that is more tractable to be handcrafted into the generation process. In particular, we translate the space group constraint into two parts: the basis constraint of the invariant logarithmic space of the lattice matrix and the Wyckoff position constraint of the fractional coordinates. Upon the derived constraints, we then propose DiffCSP++, a novel diffusion model that has enhanced a previous work DiffCSP by further taking space group constraint into account. Experiments on several popular datasets verify the benefit of the involvement of the space group constraint, and show that our DiffCSP++ achieves promising performance on crystal structure prediction, ab initio crystal generation and controllable generation with customized space groups.

Material discovery is a critical area of research with the potential to revolutionize various fields, including carbon capture, renewable energy, and electronics. However, the immense scale of the chemical space makes it challenging to explore all possible materials experimentally. In this paper, we introduce FlowLLM, a novel generative model that combines large language models (LLMs) and Riemannian flow matching (RFM) to design novel crystalline materials. FlowLLM first fine-tunes an LLM to learn an effective base distribution of meta-stable crystals in a text representation. After converting to a graph representation, the RFM model takes samples from the LLM and iteratively refines the coordinates and lattice parameters. Our approach significantly outperforms state-of-the-art methods, increasing the generation rate of stable materials by over three times and increasing the rate for stable, unique, and novel crystals by sim50% - a huge improvement on a difficult problem. Additionally, the crystals generated by FlowLLM are much closer to their relaxed state when compared with another leading model, significantly reducing post-hoc computational cost.

Accelerated materials discovery is an urgent demand to drive advancements in fields such as energy conversion, storage, and catalysis. Property-directed generative design has emerged as a transformative approach for rapidly discovering new functional inorganic materials with multiple desired properties within vast and complex search spaces. However, this approach faces two primary challenges: data scarcity for functional properties and the multi-objective optimization required to balance competing tasks. Here, we present a multi-property-directed generative framework designed to overcome these limitations and enhance site symmetry-compliant crystal generation beyond P1 (translational) symmetry. By incorporating Wyckoff-position-based data augmentation and transfer learning, our framework effectively handles sparse and small functional datasets, enabling the generation of new stable materials simultaneously conditioned on targeted space group, band gap, and formation energy. Using this approach, we identified previously unknown thermodynamically and lattice-dynamically stable semiconductors in tetragonal, trigonal, and cubic systems, with bandgaps ranging from 0.13 to 2.20 eV, as validated by density functional theory (DFT) calculations. Additionally, we assessed their thermoelectric descriptors using DFT, indicating their potential suitability for thermoelectric applications. We believe our integrated framework represents a significant step forward in generative design of inorganic materials.

De novo design seeks to generate molecules with required property profiles by virtual design-make-test cycles. With the emergence of deep learning and neural generative models in many application areas, models for molecular design based on neural networks appeared recently and show promising results. However, the new models have not been profiled on consistent tasks, and comparative studies to well-established algorithms have only seldom been performed. To standardize the assessment of both classical and neural models for de novo molecular design, we propose an evaluation framework, GuacaMol, based on a suite of standardized benchmarks. The benchmark tasks encompass measuring the fidelity of the models to reproduce the property distribution of the training sets, the ability to generate novel molecules, the exploration and exploitation of chemical space, and a variety of single and multi-objective optimization tasks. The benchmarking open-source Python code, and a leaderboard can be found on https://benevolent.ai/guacamol

Generative modeling of crystal data distribution is an important yet challenging task due to the unique periodic physical symmetry of crystals. Diffusion-based methods have shown early promise in modeling crystal distribution. More recently, Bayesian Flow Networks were introduced to aggregate noisy latent variables, resulting in a variance-reduced parameter space that has been shown to be advantageous for modeling Euclidean data distributions with structural constraints (Song et al., 2023). Inspired by this, we seek to unlock its potential for modeling variables located in non-Euclidean manifolds e.g. those within crystal structures, by overcoming challenging theoretical issues. We introduce CrysBFN, a novel crystal generation method by proposing a periodic Bayesian flow, which essentially differs from the original Gaussian-based BFN by exhibiting non-monotonic entropy dynamics. To successfully realize the concept of periodic Bayesian flow, CrysBFN integrates a new entropy conditioning mechanism and empirically demonstrates its significance compared to time-conditioning. Extensive experiments over both crystal ab initio generation and crystal structure prediction tasks demonstrate the superiority of CrysBFN, which consistently achieves new state-of-the-art on all benchmarks. Surprisingly, we found that CrysBFN enjoys a significant improvement in sampling efficiency, e.g., ~100x speedup 10 v.s. 2000 steps network forwards) compared with previous diffusion-based methods on MP-20 dataset. Code is available at https://github.com/wu-han-lin/CrysBFN.

Designing metal-organic frameworks (MOFs) with novel chemistries is a longstanding challenge due to their large combinatorial space and complex 3D arrangements of the building blocks. While recent deep generative models have enabled scalable MOF generation, they assume (1) a fixed set of building blocks and (2) known local 3D coordinates of building blocks. However, this limits their ability to (1) design novel MOFs and (2) generate the structure using novel building blocks. We propose a two-stage MOF generation framework that overcomes these limitations by modeling both chemical and geometric degrees of freedom. First, we train an SMILES-based autoregressive model to generate metal and organic building blocks, paired with a cheminformatics toolkit for 3D structure initialization. Second, we introduce a flow matching model that predicts translations, rotations, and torsional angles to assemble the blocks into valid 3D frameworks. Our experiments demonstrate improved reconstruction accuracy, the generation of valid, novel, and unique MOFs, and the ability to create novel building blocks. Our code is available at https://github.com/nayoung10/MOFFlow-2.

Artificial intelligence (AI)-driven methods can vastly improve the historically costly drug design process, with various generative models already in widespread use. Generative models for de novo drug design, in particular, focus on the creation of novel biological compounds entirely from scratch, representing a promising future direction. Rapid development in the field, combined with the inherent complexity of the drug design process, creates a difficult landscape for new researchers to enter. In this survey, we organize de novo drug design into two overarching themes: small molecule and protein generation. Within each theme, we identify a variety of subtasks and applications, highlighting important datasets, benchmarks, and model architectures and comparing the performance of top models. We take a broad approach to AI-driven drug design, allowing for both micro-level comparisons of various methods within each subtask and macro-level observations across different fields. We discuss parallel challenges and approaches between the two applications and highlight future directions for AI-driven de novo drug design as a whole. An organized repository of all covered sources is available at https://github.com/gersteinlab/GenAI4Drug.

Generative models have recently shown great promise for accelerating the design and discovery of new functional materials. Conditional generation enhances this capacity by allowing inverse design, where specific desired properties can be requested during the generation process. However, conditioning of transformer-based approaches, in particular, is constrained by discrete tokenisation schemes and the risk of catastrophic forgetting during fine-tuning. This work introduces CrystaLLM-π (property injection), a conditional autoregressive framework that integrates continuous property representations directly into the transformer's attention mechanism. Two architectures, Property-Key-Value (PKV) Prefix attention and PKV Residual attention, are presented. These methods bypass inefficient sequence-level tokenisation and preserve foundational knowledge from unsupervised pre-training on Crystallographic Information Files (CIFs) as textual input. We establish the efficacy of these mechanisms through systematic robustness studies and evaluate the framework's versatility across two distinct tasks. First, for structure recovery, the model processes high-dimensional, heterogeneous X-ray diffraction patterns, achieving structural accuracy competitive with specialised models and demonstrating applications to experimental structure recovery and polymorph differentiation. Second, for materials discovery, the model is fine-tuned on a specialised photovoltaic dataset to generate novel, stable candidates validated by Density Functional Theory (DFT). It implicitly learns to target optimal band gap regions for high photovoltaic efficiency, demonstrating a capability to map complex structure-property relationships. CrystaLLM-π provides a unified, flexible, and computationally efficient framework for inverse materials design.

Crystal symmetry plays a fundamental role in determining its physical, chemical, and electronic properties such as electrical and thermal conductivity, optical and polarization behavior, and mechanical strength. Almost all known crystalline materials have internal symmetry. However, this is often inadequately addressed by existing generative models, making the consistent generation of stable and symmetrically valid crystal structures a significant challenge. We introduce WyFormer, a generative model that directly tackles this by formally conditioning on space group symmetry. It achieves this by using Wyckoff positions as the basis for an elegant, compressed, and discrete structure representation. To model the distribution, we develop a permutation-invariant autoregressive model based on the Transformer encoder and an absence of positional encoding. Extensive experimentation demonstrates WyFormer's compelling combination of attributes: it achieves best-in-class symmetry-conditioned generation, incorporates a physics-motivated inductive bias, produces structures with competitive stability, predicts material properties with competitive accuracy even without atomic coordinates, and exhibits unparalleled inference speed.

Crystalline materials are a fundamental component in next-generation technologies, yet modeling their distribution presents unique computational challenges. Of the plausible arrangements of atoms in a periodic lattice only a vanishingly small percentage are thermodynamically stable, which is a key indicator of the materials that can be experimentally realized. Two fundamental tasks in this area are to (a) predict the stable crystal structure of a known composition of elements and (b) propose novel compositions along with their stable structures. We present FlowMM, a pair of generative models that achieve state-of-the-art performance on both tasks while being more efficient and more flexible than competing methods. We generalize Riemannian Flow Matching to suit the symmetries inherent to crystals: translation, rotation, permutation, and periodic boundary conditions. Our framework enables the freedom to choose the flow base distributions, drastically simplifying the problem of learning crystal structures compared with diffusion models. In addition to standard benchmarks, we validate FlowMM's generated structures with quantum chemistry calculations, demonstrating that it is about 3x more efficient, in terms of integration steps, at finding stable materials compared to previous open methods.

Generative models have advanced significantly in sampling material systems with continuous variables, such as atomistic structures. However, their application to discrete variables, like atom types or spin states, remains underexplored. In this work, we introduce a Boltzmann generator built on discrete flow matching, specifically tailored for systems with discrete phase-space coordinates (e.g., the Ising model or crystalline compounds). This approach enables a single model to sample free energy surfaces over a wide temperature range with minimal training overhead. In addition, the model generation is scalable to larger lattice sizes than those in the training set. We demonstrate the effectiveness of our approach on the 2D Ising model, showing efficient and reliable free energy sampling. This framework provides a scalable and computationally efficient solution for discrete coordinate systems and can be extended to sample the alchemical degrees of freedom in crystalline compounds.

Designing de novo proteins beyond those found in nature holds significant promise for advancements in both scientific and engineering applications. Current methodologies for protein design often rely on AI-based models, such as surrogate models that address end-to-end problems by linking protein structure to material properties or vice versa. However, these models frequently focus on specific material objectives or structural properties, limiting their flexibility when incorporating out-of-domain knowledge into the design process or comprehensive data analysis is required. In this study, we introduce ProtAgents, a platform for de novo protein design based on Large Language Models (LLMs), where multiple AI agents with distinct capabilities collaboratively address complex tasks within a dynamic environment. The versatility in agent development allows for expertise in diverse domains, including knowledge retrieval, protein structure analysis, physics-based simulations, and results analysis. The dynamic collaboration between agents, empowered by LLMs, provides a versatile approach to tackling protein design and analysis problems, as demonstrated through diverse examples in this study. The problems of interest encompass designing new proteins, analyzing protein structures and obtaining new first-principles data -- natural vibrational frequencies -- via physics simulations. The concerted effort of the system allows for powerful automated and synergistic design of de novo proteins with targeted mechanical properties. The flexibility in designing the agents, on one hand, and their capacity in autonomous collaboration through the dynamic LLM-based multi-agent environment on the other hand, unleashes great potentials of LLMs in addressing multi-objective materials problems and opens up new avenues for autonomous materials discovery and design.

Crystal Structure Prediction (CSP) is crucial in various scientific disciplines. While CSP can be addressed by employing currently-prevailing generative models (e.g. diffusion models), this task encounters unique challenges owing to the symmetric geometry of crystal structures -- the invariance of translation, rotation, and periodicity. To incorporate the above symmetries, this paper proposes DiffCSP, a novel diffusion model to learn the structure distribution from stable crystals. To be specific, DiffCSP jointly generates the lattice and atom coordinates for each crystal by employing a periodic-E(3)-equivariant denoising model, to better model the crystal geometry. Notably, different from related equivariant generative approaches, DiffCSP leverages fractional coordinates other than Cartesian coordinates to represent crystals, remarkably promoting the diffusion and the generation process of atom positions. Extensive experiments verify that our DiffCSP significantly outperforms existing CSP methods, with a much lower computation cost in contrast to DFT-based methods. Moreover, the superiority of DiffCSP is also observed when it is extended for ab initio crystal generation.

De novo 3D molecule generation is a pivotal task in drug discovery. However, many recent geometric generative models struggle to produce high-quality 3D structures, even if they maintain 2D validity and topological stability. To tackle this issue and enhance the learning of effective molecular generation dynamics, we present Megalodon-a family of scalable transformer models. These models are enhanced with basic equivariant layers and trained using a joint continuous and discrete denoising co-design objective. We assess Megalodon's performance on established molecule generation benchmarks and introduce new 3D structure benchmarks that evaluate a model's capability to generate realistic molecular structures, particularly focusing on energetics. We show that Megalodon achieves state-of-the-art results in 3D molecule generation, conditional structure generation, and structure energy benchmarks using diffusion and flow matching. Furthermore, doubling the number of parameters in Megalodon to 40M significantly enhances its performance, generating up to 49x more valid large molecules and achieving energy levels that are 2-10x lower than those of the best prior generative models.

Recently, 3D generative models have shown promising performances in structure-based drug design by learning to generate ligands given target binding sites. However, only modeling the target-ligand distribution can hardly fulfill one of the main goals in drug discovery -- designing novel ligands with desired properties, e.g., high binding affinity, easily synthesizable, etc. This challenge becomes particularly pronounced when the target-ligand pairs used for training do not align with these desired properties. Moreover, most existing methods aim at solving de novo design task, while many generative scenarios requiring flexible controllability, such as R-group optimization and scaffold hopping, have received little attention. In this work, we propose DecompOpt, a structure-based molecular optimization method based on a controllable and decomposed diffusion model. DecompOpt presents a new generation paradigm which combines optimization with conditional diffusion models to achieve desired properties while adhering to the molecular grammar. Additionally, DecompOpt offers a unified framework covering both de novo design and controllable generation. To achieve so, ligands are decomposed into substructures which allows fine-grained control and local optimization. Experiments show that DecompOpt can efficiently generate molecules with improved properties than strong de novo baselines, and demonstrate great potential in controllable generation tasks.

High throughput experimentation tools, machine learning (ML) methods, and open material databases are radically changing the way new materials are discovered. From the experimentally driven approach in the past, we are moving quickly towards the artificial intelligence (AI) driven approach, realizing the 'inverse design' capabilities that allow the discovery of new materials given the desired properties. This review aims to discuss different principles of AI-driven generative models that are applicable for materials discovery, including different materials representations available for this purpose. We will also highlight specific applications of generative models in designing new catalysts, semiconductors, polymers, or crystals while addressing challenges such as data scarcity, computational cost, interpretability, synthesizability, and dataset biases. Emerging approaches to overcome limitations and integrate AI with experimental workflows will be discussed, including multimodal models, physics informed architectures, and closed-loop discovery systems. This review aims to provide insights for researchers aiming to harness AI's transformative potential in accelerating materials discovery for sustainability, healthcare, and energy innovation.

Developing accurate, transferable and computationally inexpensive machine learning models can rapidly accelerate the discovery and development of new materials. Some of the major challenges involved in developing such models are, (i) limited availability of materials data as compared to other fields, (ii) lack of universal descriptor of materials to predict its various properties. The limited availability of materials data can be addressed through transfer learning, while the generic representation was recently addressed by Xie and Grossman [1], where they developed a crystal graph convolutional neural network (CGCNN) that provides a unified representation of crystals. In this work, we develop a new model (MT-CGCNN) by integrating CGCNN with transfer learning based on multi-task (MT) learning. We demonstrate the effectiveness of MT-CGCNN by simultaneous prediction of various material properties such as Formation Energy, Band Gap and Fermi Energy for a wide range of inorganic crystals (46774 materials). MT-CGCNN is able to reduce the test error when employed on correlated properties by upto 8%. The model prediction has lower test error compared to CGCNN, even when the training data is reduced by 10%. We also demonstrate our model's better performance through prediction of end user scenario related to metal/non-metal classification. These results encourage further development of machine learning approaches which leverage multi-task learning to address the aforementioned challenges in the discovery of new materials. We make MT-CGCNN's source code available to encourage reproducible research.

Materials identification and structural understanding from powder X-ray diffraction (PXRD) data is a long-standing challenge in materials science, fundamental to discovering and characterizing novel materials. A prerequisite for full structure solution is the accurate determination of the crystal lattice, including lattice parameters and crystallographic symmetries. Traditional methods for this are iterative and typically require expert input, and while existing deep learning approaches have shown promise, a robust, single-shot method for comprehensive lattice determination from experimental data remains a key goal. Here, we introduce AlphaDiffract, a deep learning framework that achieves state-of-the-art performance in predicting the crystal system, space group, and lattice parameters directly from PXRD patterns. AlphaDiffract utilizes a 1D adaptation of the ConvNeXt architecture, a modern convolutional neural network that integrates key design principles from transformers, coupled with dedicated prediction heads for each crystallographic property. The model is trained on the largest-to-date physics-based dataset of over 31 million simulated diffraction patterns, generated by augmenting 312,267 curated structures from the ICSD and Materials Project databases. Crucially, it demonstrates strong generalization to experimental data, achieving 81.7% crystal system accuracy and 66.2% space group accuracy on the RRUFF dataset while additionally predicting all six lattice parameters. By providing a unified model for rapid and accurate lattice determination from PXRD data, AlphaDiffract represents a significant step forward in leveraging deep learning for high-throughput materials discovery.

We apply preference learning to the task of language model-guided design of novel structural alloys. In contrast to prior work that focuses on generating stable inorganic crystals, our approach targets the synthesizeability of a specific structural class: BCC/B2 superalloys, an underexplored family of materials with potential applications in extreme environments. Using three open-weight models (LLaMA-3.1, Gemma-2, and OLMo-2), we demonstrate that language models can be optimized for multiple design objectives using a single, unified reward signal through Direct Preference Optimization (DPO). Unlike prior approaches that rely on heuristic or human-in-the-loop feedback (costly), our reward signal is derived from thermodynamic phase calculations, offering a scientifically grounded criterion for model tuning. To our knowledge, this is the first demonstration of preference-tuning a language model using physics-grounded feedback for structural alloy design. The resulting framework is general and extensible, providing a path forward for intelligent design-space exploration across a range of physical science domains.

Generating the periodic structure of stable materials is a long-standing challenge for the material design community. This task is difficult because stable materials only exist in a low-dimensional subspace of all possible periodic arrangements of atoms: 1) the coordinates must lie in the local energy minimum defined by quantum mechanics, and 2) global stability also requires the structure to follow the complex, yet specific bonding preferences between different atom types. Existing methods fail to incorporate these factors and often lack proper invariances. We propose a Crystal Diffusion Variational Autoencoder (CDVAE) that captures the physical inductive bias of material stability. By learning from the data distribution of stable materials, the decoder generates materials in a diffusion process that moves atomic coordinates towards a lower energy state and updates atom types to satisfy bonding preferences between neighbors. Our model also explicitly encodes interactions across periodic boundaries and respects permutation, translation, rotation, and periodic invariances. We significantly outperform past methods in three tasks: 1) reconstructing the input structure, 2) generating valid, diverse, and realistic materials, and 3) generating materials that optimize a specific property. We also provide several standard datasets and evaluation metrics for the broader machine learning community.

In the realm of digital creativity, our potential to craft intricate 3D worlds from imagination is often hampered by the limitations of existing digital tools, which demand extensive expertise and efforts. To narrow this disparity, we introduce CLAY, a 3D geometry and material generator designed to effortlessly transform human imagination into intricate 3D digital structures. CLAY supports classic text or image inputs as well as 3D-aware controls from diverse primitives (multi-view images, voxels, bounding boxes, point clouds, implicit representations, etc). At its core is a large-scale generative model composed of a multi-resolution Variational Autoencoder (VAE) and a minimalistic latent Diffusion Transformer (DiT), to extract rich 3D priors directly from a diverse range of 3D geometries. Specifically, it adopts neural fields to represent continuous and complete surfaces and uses a geometry generative module with pure transformer blocks in latent space. We present a progressive training scheme to train CLAY on an ultra large 3D model dataset obtained through a carefully designed processing pipeline, resulting in a 3D native geometry generator with 1.5 billion parameters. For appearance generation, CLAY sets out to produce physically-based rendering (PBR) textures by employing a multi-view material diffusion model that can generate 2K resolution textures with diffuse, roughness, and metallic modalities. We demonstrate using CLAY for a range of controllable 3D asset creations, from sketchy conceptual designs to production ready assets with intricate details. Even first time users can easily use CLAY to bring their vivid 3D imaginations to life, unleashing unlimited creativity.

Matbench Discovery simulates the deployment of machine learning (ML) energy models in a high-throughput search for stable inorganic crystals. We address the disconnect between (i) thermodynamic stability and formation energy and (ii) in-domain vs out-of-distribution performance. Alongside this paper, we publish a Python package to aid with future model submissions and a growing online leaderboard with further insights into trade-offs between various performance metrics. To answer the question which ML methodology performs best at materials discovery, our initial release explores a variety of models including random forests, graph neural networks (GNN), one-shot predictors, iterative Bayesian optimizers and universal interatomic potentials (UIP). Ranked best-to-worst by their test set F1 score on thermodynamic stability prediction, we find CHGNet > M3GNet > MACE > ALIGNN > MEGNet > CGCNN > CGCNN+P > Wrenformer > BOWSR > Voronoi tessellation fingerprints with random forest. The top 3 models are UIPs, the winning methodology for ML-guided materials discovery, achieving F1 scores of ~0.6 for crystal stability classification and discovery acceleration factors (DAF) of up to 5x on the first 10k most stable predictions compared to dummy selection from our test set. We also highlight a sharp disconnect between commonly used global regression metrics and more task-relevant classification metrics. Accurate regressors are susceptible to unexpectedly high false-positive rates if those accurate predictions lie close to the decision boundary at 0 eV/atom above the convex hull where most materials are. Our results highlight the need to focus on classification metrics that actually correlate with improved stability hit rate.

Deep generative models have recently achieved superior performance in 3D molecule generation. Most of them first generate atoms and then add chemical bonds based on the generated atoms in a post-processing manner. However, there might be no corresponding bond solution for the temporally generated atoms as their locations are generated without considering potential bonds. We define this problem as the atom-bond inconsistency problem and claim it is the main reason for current approaches to generating unrealistic 3D molecules. To overcome this problem, we propose a new diffusion model called MolDiff which can generate atoms and bonds simultaneously while still maintaining their consistency by explicitly modeling the dependence between their relationships. We evaluated the generation ability of our proposed model and the quality of the generated molecules using criteria related to both geometry and chemical properties. The empirical studies showed that our model outperforms previous approaches, achieving a three-fold improvement in success rate and generating molecules with significantly better quality.

De novo drug design requires simultaneously generating novel molecules outside of training data and predicting their target properties, making it a hard task for generative models. To address this, we propose Joint Transformer that combines a Transformer decoder, Transformer encoder, and a predictor in a joint generative model with shared weights. We formulate a probabilistic black-box optimization algorithm that employs Joint Transformer to generate novel molecules with improved target properties and outperforms other SMILES-based optimization methods in de novo drug design.

Crystal structures are characterized by atomic bases within a primitive unit cell that repeats along a regular lattice throughout 3D space. The periodic and infinite nature of crystals poses unique challenges for geometric graph representation learning. Specifically, constructing graphs that effectively capture the complete geometric information of crystals and handle chiral crystals remains an unsolved and challenging problem. In this paper, we introduce a novel approach that utilizes the periodic patterns of unit cells to establish the lattice-based representation for each atom, enabling efficient and expressive graph representations of crystals. Furthermore, we propose ComFormer, a SE(3) transformer designed specifically for crystalline materials. ComFormer includes two variants; namely, iComFormer that employs invariant geometric descriptors of Euclidean distances and angles, and eComFormer that utilizes equivariant vector representations. Experimental results demonstrate the state-of-the-art predictive accuracy of ComFormer variants on various tasks across three widely-used crystal benchmarks. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

Advances in generative artificial intelligence are transforming how metal-organic frameworks (MOFs) are designed and discovered. This Perspective introduces the shift from laborious enumeration of MOF candidates to generative approaches that can autonomously propose and synthesize in the laboratory new porous reticular structures on demand. We outline the progress of employing deep learning models, such as variational autoencoders, diffusion models, and large language model-based agents, that are fueled by the growing amount of available data from the MOF community and suggest novel crystalline materials designs. These generative tools can be combined with high-throughput computational screening and even automated experiments to form accelerated, closed-loop discovery pipelines. The result is a new paradigm for reticular chemistry in which AI algorithms more efficiently direct the search for high-performance MOF materials for clean air and energy applications. Finally, we highlight remaining challenges such as synthetic feasibility, dataset diversity, and the need for further integration of domain knowledge.

In this paper, we push the boundaries of fine-grained 3D generation into truly creative territory. Current methods either lack intricate details or simply mimic existing objects -- we enable both. By lifting 2D fine-grained understanding into 3D through multi-view diffusion and modeling part latents as continuous distributions, we unlock the ability to generate entirely new, yet plausible parts through interpolation and sampling. A self-supervised feature consistency loss further ensures stable generation of these unseen parts. The result is the first system capable of creating novel 3D objects with species-specific details that transcend existing examples. While we demonstrate our approach on birds, the underlying framework extends beyond things that can chirp! Code will be released at https://github.com/kamwoh/chirpy3d.

Diffusion- and flow-based generative models have recently demonstrated strong performance in protein backbone generation tasks, offering unprecedented capabilities for de novo protein design. However, while achieving notable performance in generation quality, these models are limited by their generating speed, often requiring hundreds of iterative steps in the reverse-diffusion process. This computational bottleneck limits their practical utility in large-scale protein discovery, where thousands to millions of candidate structures are needed. To address this challenge, we explore the techniques of score distillation, which has shown great success in reducing the number of sampling steps in the vision domain while maintaining high generation quality. However, a straightforward adaptation of these methods results in unacceptably low designability. Through extensive study, we have identified how to appropriately adapt Score identity Distillation (SiD), a state-of-the-art score distillation strategy, to train few-step protein backbone generators which significantly reduce sampling time, while maintaining comparable performance to their pretrained teacher model. In particular, multistep generation combined with inference time noise modulation is key to the success. We demonstrate that our distilled few-step generators achieve more than a 20-fold improvement in sampling speed, while achieving similar levels of designability, diversity, and novelty as the Proteina teacher model. This reduction in inference cost enables large-scale in silico protein design, thereby bringing diffusion-based models closer to real-world protein engineering applications. The PyTorch implementation is available at https://github.com/LY-Xie/SiD_Protein

Cryo-electron microscopy (cryo-EM) is a technique for reconstructing the 3-dimensional (3D) structure of biomolecules (especially large protein complexes and molecular assemblies). As the resolution increases to the near-atomic scale, building protein structures de novo from cryo-EM maps becomes possible. Recently, recognition-based de novo building methods have shown the potential to streamline this process. However, it cannot build a complete structure due to the low signal-to-noise ratio (SNR) problem. At the same time, AlphaFold has led to a great breakthrough in predicting protein structures. This has inspired us to combine fragment recognition and structure prediction methods to build a complete structure. In this paper, we propose a new method named FFF that bridges protein structure prediction and protein structure recognition with flexible fitting. First, a multi-level recognition network is used to capture various structural features from the input 3D cryo-EM map. Next, protein structural fragments are generated using pseudo peptide vectors and a protein sequence alignment method based on these extracted features. Finally, a complete structural model is constructed using the predicted protein fragments via flexible fitting. Based on our benchmark tests, FFF outperforms the baseline methods for building complete protein structures.

Most 3D generation research focuses on up-projecting 2D foundation models into the 3D space, either by minimizing 2D Score Distillation Sampling (SDS) loss or fine-tuning on multi-view datasets. Without explicit 3D priors, these methods often lead to geometric anomalies and multi-view inconsistency. Recently, researchers have attempted to improve the genuineness of 3D objects by directly training on 3D datasets, albeit at the cost of low-quality texture generation due to the limited texture diversity in 3D datasets. To harness the advantages of both approaches, we propose Bidirectional Diffusion(BiDiff), a unified framework that incorporates both a 3D and a 2D diffusion process, to preserve both 3D fidelity and 2D texture richness, respectively. Moreover, as a simple combination may yield inconsistent generation results, we further bridge them with novel bidirectional guidance. In addition, our method can be used as an initialization of optimization-based models to further improve the quality of 3D model and efficiency of optimization, reducing the generation process from 3.4 hours to 20 minutes. Experimental results have shown that our model achieves high-quality, diverse, and scalable 3D generation. Project website: https://bidiff.github.io/.

Crystal structure determination from powder diffraction patterns is a complex challenge in materials science, often requiring extensive expertise and computational resources. This study introduces DiffractGPT, a generative pre-trained transformer model designed to predict atomic structures directly from X-ray diffraction (XRD) patterns. By capturing the intricate relationships between diffraction patterns and crystal structures, DiffractGPT enables fast and accurate inverse design. Trained on thousands of atomic structures and their simulated XRD patterns from the JARVIS-DFT dataset, we evaluate the model across three scenarios: (1) without chemical information, (2) with a list of elements, and (3) with an explicit chemical formula. The results demonstrate that incorporating chemical information significantly enhances prediction accuracy. Additionally, the training process is straightforward and fast, bridging gaps between computational, data science, and experimental communities. This work represents a significant advancement in automating crystal structure determination, offering a robust tool for data-driven materials discovery and design.

Recent advances in synthetic methods enable designing subunits that self-assemble into structures with well-defined sizes and architectures, but yields are frequently suppressed by the formation of off-target metastable structures. Increasing the complexity (number of distinct inter-subunit interaction types) can inhibit off-target structures, but leads to slower kinetics and higher synthesis costs. Here, we use icosahedral shells formed of programmable triangular subunits as a model system, and identify design principles that produce the highest target yield at the lowest complexity. We use a symmetry-based construction to create a range of design complexities, starting from the maximal symmetry Caspar-Klug assembly up to the fully addressable, zero-symmetry assembly. Kinetic Monte Carlo simulations reveal that the most prominent defects leading to off-target assemblies are a class of disclinations. We derive symmetry-based rules for identifying the optimal (lowest-complexity, highest-symmetry) design that inhibits these disclinations, leading to robust, high-fidelity assembly of targets with arbitrarily large sizes. Optimal complexity varies non-monotonically with target size, with `magic' sizes appearing for high-symmetry designs in which symmetry axes do not intersect vertices of the triangular net. The optimal designs at magic sizes require 12 times fewer inequivalent interaction-types than the (minimal symmetry) fully addressable construction.

Proteins are dynamic molecular machines whose biological functions, spanning enzymatic catalysis, signal transduction, and structural adaptation, are intrinsically linked to their motions. Designing proteins with targeted dynamic properties, however, remains a challenge due to the complex, degenerate relationships between sequence, structure, and molecular motion. Here, we introduce VibeGen, a generative AI framework that enables end-to-end de novo protein design conditioned on normal mode vibrations. VibeGen employs an agentic dual-model architecture, comprising a protein designer that generates sequence candidates based on specified vibrational modes and a protein predictor that evaluates their dynamic accuracy. This approach synergizes diversity, accuracy, and novelty during the design process. Via full-atom molecular simulations as direct validation, we demonstrate that the designed proteins accurately reproduce the prescribed normal mode amplitudes across the backbone while adopting various stable, functionally relevant structures. Notably, generated sequences are de novo, exhibiting no significant similarity to natural proteins, thereby expanding the accessible protein space beyond evolutionary constraints. Our work integrates protein dynamics into generative protein design, and establishes a direct, bidirectional link between sequence and vibrational behavior, unlocking new pathways for engineering biomolecules with tailored dynamical and functional properties. This framework holds broad implications for the rational design of flexible enzymes, dynamic scaffolds, and biomaterials, paving the way toward dynamics-informed AI-driven protein engineering.

We propose Ambient Dataloops, an iterative framework for refining datasets that makes it easier for diffusion models to learn the underlying data distribution. Modern datasets contain samples of highly varying quality, and training directly on such heterogeneous data often yields suboptimal models. We propose a dataset-model co-evolution process; at each iteration of our method, the dataset becomes progressively higher quality, and the model improves accordingly. To avoid destructive self-consuming loops, at each generation, we treat the synthetically improved samples as noisy, but at a slightly lower noisy level than the previous iteration, and we use Ambient Diffusion techniques for learning under corruption. Empirically, Ambient Dataloops achieve state-of-the-art performance in unconditional and text-conditional image generation and de novo protein design. We further provide a theoretical justification for the proposed framework that captures the benefits of the data looping procedure.

We introduce StableMaterials, a novel approach for generating photorealistic physical-based rendering (PBR) materials that integrate semi-supervised learning with Latent Diffusion Models (LDMs). Our method employs adversarial training to distill knowledge from existing large-scale image generation models, minimizing the reliance on annotated data and enhancing the diversity in generation. This distillation approach aligns the distribution of the generated materials with that of image textures from an SDXL model, enabling the generation of novel materials that are not present in the initial training dataset. Furthermore, we employ a diffusion-based refiner model to improve the visual quality of the samples and achieve high-resolution generation. Finally, we distill a latent consistency model for fast generation in just four steps and propose a new tileability technique that removes visual artifacts typically associated with fewer diffusion steps. We detail the architecture and training process of StableMaterials, the integration of semi-supervised training within existing LDM frameworks and show the advantages of our approach. Comparative evaluations with state-of-the-art methods show the effectiveness of StableMaterials, highlighting its potential applications in computer graphics and beyond. StableMaterials is publicly available at https://gvecchio.com/stablematerials.

3D molecule generation is crucial for drug discovery and material design. While prior efforts focus on 3D diffusion models for their benefits in modeling continuous 3D conformers, they overlook the advantages of 1D SELFIES-based Language Models (LMs), which can generate 100% valid molecules and leverage the billion-scale 1D molecule datasets. To combine these advantages for 3D molecule generation, we propose a foundation model -- NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation. NExT-Mol uses an extensively pretrained molecule LM for 1D molecule generation, and subsequently predicts the generated molecule's 3D conformers with a 3D diffusion model. We enhance NExT-Mol's performance by scaling up the LM's model size, refining the diffusion neural architecture, and applying 1D to 3D transfer learning. Notably, our 1D molecule LM significantly outperforms baselines in distributional similarity while ensuring validity, and our 3D diffusion model achieves leading performances in conformer prediction. Given these improvements in 1D and 3D modeling, NExT-Mol achieves a 26% relative improvement in 3D FCD for de novo 3D generation on GEOM-DRUGS, and a 13% average relative gain for conditional 3D generation on QM9-2014. Our codes and pretrained checkpoints are available at https://github.com/acharkq/NExT-Mol.

Recently, 3D generation methods have shown their powerful ability to automate 3D model creation. However, most 3D generation methods only rely on an input image or a text prompt to generate a 3D model, which lacks the control of each component of the generated 3D model. Any modifications of the input image lead to an entire regeneration of the 3D models. In this paper, we introduce a new method called CMD that generates a 3D model from an input image while enabling flexible local editing of each component of the 3D model. In CMD, we formulate the 3D generation as a conditional multiview diffusion model, which takes the existing or known parts as conditions and generates the edited or added components. This conditional multiview diffusion model not only allows the generation of 3D models part by part but also enables local editing of 3D models according to the local revision of the input image without changing other 3D parts. Extensive experiments are conducted to demonstrate that CMD decomposes a complex 3D generation task into multiple components, improving the generation quality. Meanwhile, CMD enables efficient and flexible local editing of a 3D model by just editing one rendered image.

Deep generative diffusion models are a promising avenue for 3D de novo molecular design in materials science and drug discovery. However, their utility is still limited by suboptimal performance on large molecular structures and limited training data. To address this gap, we explore the design space of E(3)-equivariant diffusion models, focusing on previously unexplored areas. Our extensive comparative analysis evaluates the interplay between continuous and discrete state spaces. From this investigation, we present the EQGAT-diff model, which consistently outperforms established models for the QM9 and GEOM-Drugs datasets. Significantly, EQGAT-diff takes continuous atom positions, while chemical elements and bond types are categorical and uses time-dependent loss weighting, substantially increasing training convergence, the quality of generated samples, and inference time. We also showcase that including chemically motivated additional features like hybridization states in the diffusion process enhances the validity of generated molecules. To further strengthen the applicability of diffusion models to limited training data, we investigate the transferability of EQGAT-diff trained on the large PubChem3D dataset with implicit hydrogen atoms to target different data distributions. Fine-tuning EQGAT-diff for just a few iterations shows an efficient distribution shift, further improving performance throughout data sets. Finally, we test our model on the Crossdocked data set for structure-based de novo ligand generation, underlining the importance of our findings showing state-of-the-art performance on Vina docking scores.

In this report, we present Hunyuan3D 2.5, a robust suite of 3D diffusion models aimed at generating high-fidelity and detailed textured 3D assets. Hunyuan3D 2.5 follows two-stages pipeline of its previous version Hunyuan3D 2.0, while demonstrating substantial advancements in both shape and texture generation. In terms of shape generation, we introduce a new shape foundation model -- LATTICE, which is trained with scaled high-quality datasets, model-size, and compute. Our largest model reaches 10B parameters and generates sharp and detailed 3D shape with precise image-3D following while keeping mesh surface clean and smooth, significantly closing the gap between generated and handcrafted 3D shapes. In terms of texture generation, it is upgraded with phyiscal-based rendering (PBR) via a novel multi-view architecture extended from Hunyuan3D 2.0 Paint model. Our extensive evaluation shows that Hunyuan3D 2.5 significantly outperforms previous methods in both shape and end-to-end texture generation.

Materials synthesis is vital for innovations such as energy storage, catalysis, electronics, and biomedical devices. Yet, the process relies heavily on empirical, trial-and-error methods guided by expert intuition. Our work aims to support the materials science community by providing a practical, data-driven resource. We have curated a comprehensive dataset of 17K expert-verified synthesis recipes from open-access literature, which forms the basis of our newly developed benchmark, AlchemyBench. AlchemyBench offers an end-to-end framework that supports research in large language models applied to synthesis prediction. It encompasses key tasks, including raw materials and equipment prediction, synthesis procedure generation, and characterization outcome forecasting. We propose an LLM-as-a-Judge framework that leverages large language models for automated evaluation, demonstrating strong statistical agreement with expert assessments. Overall, our contributions offer a supportive foundation for exploring the capabilities of LLMs in predicting and guiding materials synthesis, ultimately paving the way for more efficient experimental design and accelerated innovation in materials science.

Predicting physical properties of materials from their crystal structures is a fundamental problem in materials science. In peripheral areas such as the prediction of molecular properties, fully connected attention networks have been shown to be successful. However, unlike these finite atom arrangements, crystal structures are infinitely repeating, periodic arrangements of atoms, whose fully connected attention results in infinitely connected attention. In this work, we show that this infinitely connected attention can lead to a computationally tractable formulation, interpreted as neural potential summation, that performs infinite interatomic potential summations in a deeply learned feature space. We then propose a simple yet effective Transformer-based encoder architecture for crystal structures called Crystalformer. Compared to an existing Transformer-based model, the proposed model requires only 29.4% of the number of parameters, with minimal modifications to the original Transformer architecture. Despite the architectural simplicity, the proposed method outperforms state-of-the-art methods for various property regression tasks on the Materials Project and JARVIS-DFT datasets.

We introduce DreamCraft3D++, an extension of DreamCraft3D that enables efficient high-quality generation of complex 3D assets. DreamCraft3D++ inherits the multi-stage generation process of DreamCraft3D, but replaces the time-consuming geometry sculpting optimization with a feed-forward multi-plane based reconstruction model, speeding up the process by 1000x. For texture refinement, we propose a training-free IP-Adapter module that is conditioned on the enhanced multi-view images to enhance texture and geometry consistency, providing a 4x faster alternative to DreamCraft3D's DreamBooth fine-tuning. Experiments on diverse datasets demonstrate DreamCraft3D++'s ability to generate creative 3D assets with intricate geometry and realistic 360{\deg} textures, outperforming state-of-the-art image-to-3D methods in quality and speed. The full implementation will be open-sourced to enable new possibilities in 3D content creation.

Discovering novel drug candidate molecules is one of the most fundamental and critical steps in drug development. Generative deep learning models, which create synthetic data given a probability distribution, offer a high potential for designing de novo molecules. However, to be utilisable in real life drug development pipelines, these models should be able to design drug like and target centric molecules. In this study, we propose an end to end generative system, DrugGEN, for the de novo design of drug candidate molecules that interact with intended target proteins. The proposed method represents molecules as graphs and processes them via a generative adversarial network comprising graph transformer layers. The system is trained using a large dataset of drug like compounds and target specific bioactive molecules to design effective inhibitory molecules against the AKT1 protein, which is critically important in developing treatments for various types of cancer. We conducted molecular docking and dynamics to assess the target centric generation performance of the model, as well as attention score visualisation to examine model interpretability. In parallel, selected compounds were chemically synthesised and evaluated in the context of in vitro enzymatic assays, which identified two bioactive molecules that inhibited AKT1 at low micromolar concentrations. These results indicate that DrugGEN's de novo molecules have a high potential for interacting with the AKT1 protein at the level of its native ligands. Using the open access DrugGEN codebase, it is possible to easily train models for other druggable proteins, given a dataset of experimentally known bioactive molecules.

Deep generative models have shown promise for modeling metal-organic frameworks (MOFs), but existing approaches (1) rely on coarse-grained representations that assume fixed bond lengths and angles, and (2) neglect the MOF-adsorbate interactions, which are critical for downstream applications. We introduce AtomMOF, a scalable flow-based model built on an all-atom Diffusion Transformer that maps 2D molecular graphs of building blocks and adsorbates directly to equilibrium 3D structures without imposing structural constraints. We further present scaling laws for porous crystal generation, indicating predictable performance gains with increased model capacity, and introduce Feynman-Kac steering guided by machine-learned interatomic potentials to improve geometric validity and sampling stability. On the (MOF-only) BW dataset, AtomMOF increases the match rate by 35.00% and reduces RMSD by 32.64%. On the ODAC25 dataset (MOF-adsorbate), AtomMOF is substantially more sample-efficient than grand canonical Monte Carlo in recovering adsorption configurations and can identify candidates with lower adsorption energies than the reference dataset. Code is available at https://github.com/nayoung10/AtomMOF.

We present DreamCraft3D, a hierarchical 3D content generation method that produces high-fidelity and coherent 3D objects. We tackle the problem by leveraging a 2D reference image to guide the stages of geometry sculpting and texture boosting. A central focus of this work is to address the consistency issue that existing works encounter. To sculpt geometries that render coherently, we perform score distillation sampling via a view-dependent diffusion model. This 3D prior, alongside several training strategies, prioritizes the geometry consistency but compromises the texture fidelity. We further propose Bootstrapped Score Distillation to specifically boost the texture. We train a personalized diffusion model, Dreambooth, on the augmented renderings of the scene, imbuing it with 3D knowledge of the scene being optimized. The score distillation from this 3D-aware diffusion prior provides view-consistent guidance for the scene. Notably, through an alternating optimization of the diffusion prior and 3D scene representation, we achieve mutually reinforcing improvements: the optimized 3D scene aids in training the scene-specific diffusion model, which offers increasingly view-consistent guidance for 3D optimization. The optimization is thus bootstrapped and leads to substantial texture boosting. With tailored 3D priors throughout the hierarchical generation, DreamCraft3D generates coherent 3D objects with photorealistic renderings, advancing the state-of-the-art in 3D content generation. Code available at https://github.com/deepseek-ai/DreamCraft3D.

Materials discovery requires navigating vast chemical and structural spaces while satisfying multiple, often conflicting, objectives. We present LLM-guided Evolution for MAterials design (LLEMA), a unified framework that couples the scientific knowledge embedded in large language models with chemistry-informed evolutionary rules and memory-based refinement. At each iteration, an LLM proposes crystallographically specified candidates under explicit property constraints; a surrogate-augmented oracle estimates physicochemical properties; and a multi-objective scorer updates success/failure memories to guide subsequent generations. Evaluated on 14 realistic tasks spanning electronics, energy, coatings, optics, and aerospace, LLEMA discovers candidates that are chemically plausible, thermodynamically stable, and property-aligned, achieving higher hit-rates and stronger Pareto fronts than generative and LLM-only baselines. Ablation studies confirm the importance of rule-guided generation, memory-based refinement, and surrogate prediction. By enforcing synthesizability and multi-objective trade-offs, LLEMA delivers a principled pathway to accelerate practical materials discovery. Code: https://github.com/scientific-discovery/LLEMA

With the growing availability of data within various scientific domains, generative models hold enormous potential to accelerate scientific discovery. They harness powerful representations learned from datasets to speed up the formulation of novel hypotheses with the potential to impact material discovery broadly. We present the Generative Toolkit for Scientific Discovery (GT4SD). This extensible open-source library enables scientists, developers, and researchers to train and use state-of-the-art generative models to accelerate scientific discovery focused on material design.

Exploratory synthesis efforts for iron-based superconductors (FeSC) have been driven by hopes of improving superconducting critical temperatures (TCs), providing high-quality samples for in-depth studies of intrinsic properties, and exploring potential superconductivity in similar families of materials. This manuscript summarizes the synthesis routes that are used for producing FeSC and their undoped parents, in single crystal and polycrystalline forms. A few of the materials challenges are summarized.

Recent work has shown the potential of graph neural networks to efficiently predict material properties, enabling high-throughput screening of materials. Training these models, however, often requires large quantities of labelled data, obtained via costly methods such as ab initio calculations or experimental evaluation. By leveraging a series of material-specific transformations, we introduce CrystalCLR, a framework for constrastive learning of representations with crystal graph neural networks. With the addition of a novel loss function, our framework is able to learn representations competitive with engineered fingerprinting methods. We also demonstrate that via model finetuning, contrastive pretraining can improve the performance of graph neural networks for prediction of material properties and significantly outperform traditional ML models that use engineered fingerprints. Lastly, we observe that CrystalCLR produces material representations that form clusters by compound class.

Powder X-ray diffraction (XRD) is a foundational technique for characterizing crystalline materials. However, the reliable interpretation of XRD patterns, particularly in multiphase systems, remains a manual and expertise-demanding task. As a characterization method that only provides structural information, multiple reference phases can often be fit to a single pattern, leading to potential misinterpretation when alternative solutions are overlooked. To ease humans' efforts and address the challenge, we introduce Dara (Data-driven Automated Rietveld Analysis), a framework designed to automate the robust identification and refinement of multiple phases from powder XRD data. Dara performs an exhaustive tree search over all plausible phase combinations within a given chemical space and validates each hypothesis using a robust Rietveld refinement routine (BGMN). Key features include structural database filtering, automatic clustering of isostructural phases during tree expansion, peak-matching-based scoring to identify promising phases for refinement. When ambiguity exists, Dara generates multiple hypothesis which can then be decided between by human experts or with further characteriztion tools. By enhancing the reliability and accuracy of phase identification, Dara enables scalable analysis of realistic complex XRD patterns and provides a foundation for integration into multimodal characterization workflows, moving toward fully self-driving materials discovery.

Strategies for the generation of periodic discrete structures with identical two-point correlation are developed. Starting from a pair of root structures, which are not related by translation, phase inversion or axis reflections, child structures of arbitrary resolution (i.e., pixel or voxel numbers) and number of phases (i.e., material phases/species) can be generated by means of trivial embedding based phase extension, application of kernels and/or phase coalescence, such that the generated structures inherit the two-point-correlation equivalence. Proofs of the inheritance property are provided by means of the Discrete Fourier Transform theory. A Python 3 implementation of the results is offered by the authors through the Github repository https://github.com/DataAnalyticsEngineering/EQ2PC in order to make the provided results reproducible and useful for all interested readers. Examples for the generation of structures are demonstrated, together with applications in the homogenization theory of periodic media.

Recent advances in deep learning inspired neural network-based approaches to computational materials discovery (CMD). A plethora of problems in this field involve finding materials that optimize a target property. Nevertheless, the increasingly popular generative modeling methods are ineffective at boldly exploring attractive regions of the materials space due to their maximum likelihood training. In this work, we offer an alternative CMD technique based on offline model-based optimization (MBO) that fuses direct optimization of a target material property into generation. To that end, we introduce a domain-specific model, dubbed CliqueFlowmer, that incorporates recent advances of clique-based MBO into transformer and flow generation. We validate CliqueFlowmer's optimization abilities and show that materials it produces strongly outperform those provided by generative baselines. To enable employment of CliqueFlowmer in specialized materials optimization problems and support interdisciplinary research, we open-source our code at https://github.com/znowu/CliqueFlowmer.

While generative artificial intelligence has advanced significantly across text, image, audio, and video domains, 3D generation remains comparatively underdeveloped due to fundamental challenges such as data scarcity, algorithmic limitations, and ecosystem fragmentation. To this end, we present Step1X-3D, an open framework addressing these challenges through: (1) a rigorous data curation pipeline processing >5M assets to create a 2M high-quality dataset with standardized geometric and textural properties; (2) a two-stage 3D-native architecture combining a hybrid VAE-DiT geometry generator with an diffusion-based texture synthesis module; and (3) the full open-source release of models, training code, and adaptation modules. For geometry generation, the hybrid VAE-DiT component produces TSDF representations by employing perceiver-based latent encoding with sharp edge sampling for detail preservation. The diffusion-based texture synthesis module then ensures cross-view consistency through geometric conditioning and latent-space synchronization. Benchmark results demonstrate state-of-the-art performance that exceeds existing open-source methods, while also achieving competitive quality with proprietary solutions. Notably, the framework uniquely bridges the 2D and 3D generation paradigms by supporting direct transfer of 2D control techniques~(e.g., LoRA) to 3D synthesis. By simultaneously advancing data quality, algorithmic fidelity, and reproducibility, Step1X-3D aims to establish new standards for open research in controllable 3D asset generation.

Optimization of atomic structures presents a challenging problem, due to their highly rough and non-convex energy landscape, with wide applications in the fields of drug design, materials discovery, and mechanics. Here, we present a graph reinforcement learning approach, StriderNET, that learns a policy to displace the atoms towards low energy configurations. We evaluate the performance of StriderNET on three complex atomic systems, namely, binary Lennard-Jones particles, calcium silicate hydrates gel, and disordered silicon. We show that StriderNET outperforms all classical optimization algorithms and enables the discovery of a lower energy minimum. In addition, StriderNET exhibits a higher rate of reaching minima with energies, as confirmed by the average over multiple realizations. Finally, we show that StriderNET exhibits inductivity to unseen system sizes that are an order of magnitude different from the training system.

Recently, diffusion- and flow-based generative models of protein structures have emerged as a powerful tool for de novo protein design. Here, we develop Proteina, a new large-scale flow-based protein backbone generator that utilizes hierarchical fold class labels for conditioning and relies on a tailored scalable transformer architecture with up to 5x as many parameters as previous models. To meaningfully quantify performance, we introduce a new set of metrics that directly measure the distributional similarity of generated proteins with reference sets, complementing existing metrics. We further explore scaling training data to millions of synthetic protein structures and explore improved training and sampling recipes adapted to protein backbone generation. This includes fine-tuning strategies like LoRA for protein backbones, new guidance methods like classifier-free guidance and autoguidance for protein backbones, and new adjusted training objectives. Proteina achieves state-of-the-art performance on de novo protein backbone design and produces diverse and designable proteins at unprecedented length, up to 800 residues. The hierarchical conditioning offers novel control, enabling high-level secondary-structure guidance as well as low-level fold-specific generation.

Designing de-novo molecules with desired property profiles requires efficient exploration of the vast chemical space ranging from 10^{23} to 10^{60} possible synthesizable candidates. While various deep generative models have been developed to design small molecules using diverse input representations, Molecular Large Language Models (Mol-LLMs) based on string representations have emerged as a scalable approach capable of exploring billions of molecules. However, there remains limited understanding regarding how standard language modeling practices such as textual representations, tokenization strategies, model size, and dataset scale impact molecular generation performance. In this work, we systematically investigate these critical aspects by introducing NovoMolGen, a family of transformer-based foundation models pretrained on 1.5 billion molecules for de-novo molecule generation. Through extensive empirical analyses, we identify a weak correlation between performance metrics measured during pretraining and actual downstream performance, revealing important distinctions between molecular and general NLP training dynamics. NovoMolGen establishes new state-of-the-art results, substantially outperforming prior Mol-LLMs and specialized generative models in both unconstrained and goal-directed molecular generation tasks, thus providing a robust foundation for advancing efficient and effective molecular modeling strategies.

Reducing hallucination of Large Language Models (LLMs) is imperative for use in the sciences where reproducibility is crucial. However, LLMs inherently lack long-term memory, making it a nontrivial, ad hoc, and inevitably biased task to fine-tune them on domain-specific literature and data. Here we introduce LLaMP, a multimodal retrieval-augmented generation (RAG) framework of multiple data-aware reasoning-and-acting (ReAct) agents that dynamically interact with computational and experimental data on Materials Project (MP). Without fine-tuning, LLaMP demonstrates an ability to comprehend and integrate various modalities of materials science concepts, fetch relevant data stores on the fly, process higher-order data (such as crystal structures and elastic tensors), and summarize multi-step procedures for solid-state synthesis. We show that LLaMP effectively corrects errors in GPT-3.5's intrinsic knowledge, reducing a 5.21% MAPE on frequently-documented bandgaps and a significant 1103.54% MAPE on formation energies -- errors that GPT-3.5 seems to derive from mixed data sources. Additionally, LLaMP substantially reduces the hallucinated volumetric strain in a diamond cubic silicon structure from 66.3% to 0. The proposed framework offers an intuitive and nearly hallucination-free approach to exploring materials informatics and establishes a pathway for knowledge distillation and fine-tuning other language models. We envision the framework as a valuable component for scientific hypotheses and a foundation for future autonomous laboratories where multiple LLM agents communicate and cooperate with robotics to drive material synthesis and chemical reactions without hard-coded human logic and intervention.

We develop a multi-step workflow for the discovery of conventional superconductors, starting with a Bardeen Cooper Schrieffer inspired pre-screening of 1736 materials with high Debye temperature and electronic density of states. Next, we perform electron-phonon coupling calculations for 1058 of them to establish a large and systematic database of BCS superconducting properties. Using the McMillan-Allen-Dynes formula, we identify 105 dynamically stable materials with transition temperatures, Tc>5 K. Additionally, we analyze trends in our dataset and individual materials including MoN, VC, VTe, KB6, Ru3NbC, V3Pt, ScN, LaN2, RuO2, and TaC. We demonstrate that deep-learning(DL) models can predict superconductor properties faster than direct first principles computations. Notably, we find that by predicting the Eliashberg function as an intermediate quantity, we can improve model performance versus a direct DL prediction of Tc. We apply the trained models on the crystallographic open database and pre-screen candidates for further DFT calculations.

Materials discovery and development are critical for addressing global challenges. Yet, the exponential growth in materials science literature comprising vast amounts of textual data has created significant bottlenecks in knowledge extraction, synthesis, and scientific reasoning. Large Language Models (LLMs) offer unprecedented opportunities to accelerate materials research through automated analysis and prediction. Still, their effective deployment requires domain-specific adaptation for understanding and solving domain-relevant tasks. Here, we present LLaMat, a family of foundational models for materials science developed through continued pretraining of LLaMA models on an extensive corpus of materials literature and crystallographic data. Through systematic evaluation, we demonstrate that LLaMat excels in materials-specific NLP and structured information extraction while maintaining general linguistic capabilities. The specialized LLaMat-CIF variant demonstrates unprecedented capabilities in crystal structure generation, predicting stable crystals with high coverage across the periodic table. Intriguingly, despite LLaMA-3's superior performance in comparison to LLaMA-2, we observe that LLaMat-2 demonstrates unexpectedly enhanced domain-specific performance across diverse materials science tasks, including structured information extraction from text and tables, more particularly in crystal structure generation, a potential adaptation rigidity in overtrained LLMs. Altogether, the present work demonstrates the effectiveness of domain adaptation towards developing practically deployable LLM copilots for materials research. Beyond materials science, our findings reveal important considerations for domain adaptation of LLMs, such as model selection, training methodology, and domain-specific performance, which may influence the development of specialized scientific AI systems.

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

2D diffusion model, which often contains unwanted baked-in shading effects and results in unrealistic rendering effects in the downstream applications. Generating Physically Based Rendering (PBR) materials instead of just RGB textures would be a promising solution. However, directly distilling the PBR material parameters from 2D diffusion models still suffers from incorrect material decomposition, such as baked-in shading effects in albedo. We introduce DreamMat, an innovative approach to resolve the aforementioned problem, to generate high-quality PBR materials from text descriptions. We find out that the main reason for the incorrect material distillation is that large-scale 2D diffusion models are only trained to generate final shading colors, resulting in insufficient constraints on material decomposition during distillation. To tackle this problem, we first finetune a new light-aware 2D diffusion model to condition on a given lighting environment and generate the shading results on this specific lighting condition. Then, by applying the same environment lights in the material distillation, DreamMat can generate high-quality PBR materials that are not only consistent with the given geometry but also free from any baked-in shading effects in albedo. Extensive experiments demonstrate that the materials produced through our methods exhibit greater visual appeal to users and achieve significantly superior rendering quality compared to baseline methods, which are preferable for downstream tasks such as game and film production.

Most deep neural networks are trained under fixed network architectures and require retraining when the architecture changes. If expanding the network's size is needed, it is necessary to retrain from scratch, which is expensive. To avoid this, one can grow from a small network by adding random weights over time to gradually achieve the target network size. However, this naive approach falls short in practice as it brings too much noise to the growing process. Prior work tackled this issue by leveraging the already learned weights and training data for generating new weights through conducting a computationally expensive analysis step. In this paper, we introduce MixtureGrowth, a new approach to growing networks that circumvents the initialization overhead in prior work. Before growing, each layer in our model is generated with a linear combination of parameter templates. Newly grown layer weights are generated by using a new linear combination of existing templates for a layer. On one hand, these templates are already trained for the task, providing a strong initialization. On the other, the new coefficients provide flexibility for the added layer weights to learn something new. We show that our approach boosts top-1 accuracy over the state-of-the-art by 2-2.5% on CIFAR-100 and ImageNet datasets, while achieving comparable performance with fewer FLOPs to a larger network trained from scratch. Code is available at https://github.com/chaudatascience/mixturegrowth.

3D generation has seen remarkable progress in recent years. Existing techniques, such as score distillation methods, produce notable results but require extensive per-scene optimization, impacting time efficiency. Alternatively, reconstruction-based approaches prioritize efficiency but compromise quality due to their limited handling of uncertainty. We introduce GECO, a novel method for high-quality 3D generative modeling that operates within a second. Our approach addresses the prevalent issues of uncertainty and inefficiency in current methods through a two-stage approach. In the initial stage, we train a single-step multi-view generative model with score distillation. Then, a second-stage distillation is applied to address the challenge of view inconsistency from the multi-view prediction. This two-stage process ensures a balanced approach to 3D generation, optimizing both quality and efficiency. Our comprehensive experiments demonstrate that GECO achieves high-quality image-to-3D generation with an unprecedented level of efficiency.

Single image-to-3D generation is pivotal for crafting controllable 3D assets. Given its underconstrained nature, we leverage geometric priors from a 3D novel view generation diffusion model and appearance priors from a 2D image generation method to guide the optimization process. We note that a disparity exists between the training datasets of 2D and 3D diffusion models, leading to their outputs showing marked differences in appearance. Specifically, 2D models tend to deliver more detailed visuals, whereas 3D models produce consistent yet over-smooth results across different views. Hence, we optimize a set of 3D Gaussians using 3D priors in spatial domain to ensure geometric consistency, while exploiting 2D priors in the frequency domain through Fourier transform for higher visual quality. This 2D-3D hybrid Fourier Score Distillation objective function (dubbed hy-FSD), can be integrated into existing 3D generation methods, yielding significant performance improvements. With this technique, we further develop an image-to-3D generation pipeline to create high-quality 3D objects within one minute, named Fourier123. Extensive experiments demonstrate that Fourier123 excels in efficient generation with rapid convergence speed and visual-friendly generation results.

Generating new molecules is fundamental to advancing critical applications such as drug discovery and material synthesis. Flows can generate molecules effectively by inverting the encoding process, however, existing flow models either require artifactual dequantization or specific node/edge orderings, lack desiderata such as permutation invariance, or induce discrepancy between the encoding and the decoding steps that necessitates post hoc validity correction. We circumvent these issues with novel continuous normalizing E(3)-equivariant flows, based on a system of node ODEs coupled as a graph PDE, that repeatedly reconcile locally toward globally aligned densities. Our models can be cast as message-passing temporal networks, and result in superlative performance on the tasks of density estimation and molecular generation. In particular, our generated samples achieve state-of-the-art on both the standard QM9 and ZINC250K benchmarks.

The ability to generate 3D multiphase microstructures on-demand with targeted attributes can greatly accelerate the design of advanced materials. Here, we present a conditional latent diffusion model (LDM) framework that rapidly synthesizes high-fidelity 3D multiphase microstructures tailored to user specifications. Using this approach, we generate diverse two-phase and three-phase microstructures at high resolution (volumes of 128 times 128 times 64 voxels, representing >10^6 voxels each) within seconds, overcoming the scalability and time limitations of traditional simulation-based methods. Key design features, such as desired volume fractions and tortuosities, are incorporated as controllable inputs to guide the generative process, ensuring that the output structures meet prescribed statistical and topological targets. Moreover, the framework predicts corresponding manufacturing (processing) parameters for each generated microstructure, helping to bridge the gap between digital microstructure design and experimental fabrication. While demonstrated on organic photovoltaic (OPV) active-layer morphologies, the flexible architecture of our approach makes it readily adaptable to other material systems and microstructure datasets. By combining computational efficiency, adaptability, and experimental relevance, this framework addresses major limitations of existing methods and offers a powerful tool for accelerated materials discovery.

Generating novel molecules with higher properties than the training space, namely the out-of-distribution generation, is important for {de~novo} drug design. However, it is not easy for distribution learning-based models, for example diffusion models, to solve this challenge as these methods are designed to fit the distribution of training data as close as possible. In this paper, we show that Bayesian flow network is capable of effortlessly generating high quality out-of-distribution samples that meet several scenarios. We introduce a semi-autoregressive training/sampling method that helps to enhance the model performance and surpass the state-of-the-art models.

In 3D modeling, designers often use an existing 3D model as a reference to create new ones. This practice has inspired the development of Phidias, a novel generative model that uses diffusion for reference-augmented 3D generation. Given an image, our method leverages a retrieved or user-provided 3D reference model to guide the generation process, thereby enhancing the generation quality, generalization ability, and controllability. Our model integrates three key components: 1) meta-ControlNet that dynamically modulates the conditioning strength, 2) dynamic reference routing that mitigates misalignment between the input image and 3D reference, and 3) self-reference augmentations that enable self-supervised training with a progressive curriculum. Collectively, these designs result in a clear improvement over existing methods. Phidias establishes a unified framework for 3D generation using text, image, and 3D conditions with versatile applications.

We propose fine-tuning large language models for generation of stable materials. While unorthodox, fine-tuning large language models on text-encoded atomistic data is simple to implement yet reliable, with around 90% of sampled structures obeying physical constraints on atom positions and charges. Using energy above hull calculations from both learned ML potentials and gold-standard DFT calculations, we show that our strongest model (fine-tuned LLaMA-2 70B) can generate materials predicted to be metastable at about twice the rate (49% vs 28%) of CDVAE, a competing diffusion model. Because of text prompting's inherent flexibility, our models can simultaneously be used for unconditional generation of stable material, infilling of partial structures and text-conditional generation. Finally, we show that language models' ability to capture key symmetries of crystal structures improves with model scale, suggesting that the biases of pretrained LLMs are surprisingly well-suited for atomistic data.

Many environmental remediation and energy applications (conversion and storage) for sustainability need design and development of green novel materials. Discovery processes of such novel materials are time taking and cumbersome due to large number of possible combinations and permutations of materials structures. Often theoretical studies based on Density Functional Theory (DFT) and other theories, coupled with Simulations are conducted to narrow down sample space of candidate materials, before conducting laboratory-based synthesis and analytical process. With the emergence of artificial intelligence (AI), AI techniques are being tried in this process too to ease out simulation time and cost. However tremendous values of previously published research from various parts of the world are still left as labor-intensive manual effort and discretion of individual researcher and prone to human omissions. AIMS-EREA is our novel framework to blend best of breed of Material Science theory with power of Generative AI to give best impact and smooth and quickest discovery of material for sustainability. This also helps to eliminate the possibility of production of hazardous residues and bye-products of the reactions. AIMS-EREA uses all available resources -- Predictive and Analytical AI on large collection of chemical databases along with automated intelligent assimilation of deep materials knowledge from previously published research works through Generative AI. We demonstrate use of our own novel framework with an example, how this framework can be successfully applied to achieve desired success in development of thermoelectric material for waste heat conversion.

This paper introduces diffusion protein language model (DPLM), a versatile protein language model that demonstrates strong generative and predictive capabilities for protein sequences. We first pre-train scalable DPLMs from evolutionary-scale protein sequences within a generative self-supervised discrete diffusion probabilistic framework, which generalizes language modeling for proteins in a principled way. After pre-training, DPLM exhibits the ability to generate structurally plausible, novel, and diverse protein sequences for unconditional generation. We further demonstrate the proposed diffusion generative pre-training makes DPLM possess a better understanding of proteins, making it a superior representation learner, which can be fine-tuned for various predictive tasks, comparing favorably to ESM2 (Lin et al., 2022). Moreover, DPLM can be tailored for various needs, which showcases its prowess of conditional generation in several ways: (1) conditioning on partial peptide sequences, e.g., generating scaffolds for functional motifs with high success rate; (2) incorporating other modalities as conditioner, e.g., structure-conditioned generation for inverse folding; and (3) steering sequence generation towards desired properties, e.g., satisfying specified secondary structures, through a plug-and-play classifier guidance. Code is released at https://github.com/bytedance/dplm.

In real-world scenarios, extensive manual annotation for continual learning is impractical due to prohibitive costs. Although prior arts, influenced by large-scale webly supervised training, suggest leveraging web-scraped data in continual learning, this poses challenges such as data imbalance, usage restrictions, and privacy concerns. Addressing the risks of continual webly supervised training, we present an online continual learning framework - Generative Name only Continual Learning (G-NoCL). The proposed G-NoCL uses a set of generators G along with the learner. When encountering new concepts (i.e., classes), G-NoCL employs the novel sample complexity-guided data ensembling technique DIverSity and COmplexity enhancing ensemBlER (DISCOBER) to optimally sample training data from generated data. Through extensive experimentation, we demonstrate superior performance of DISCOBER in G-NoCL online CL benchmarks, covering both In-Distribution (ID) and Out-of-Distribution (OOD) generalization evaluations, compared to naive generator-ensembling, web-supervised, and manually annotated data.

Recent advances in generative AI have unveiled significant potential for the creation of 3D content. However, current methods either apply a pre-trained 2D diffusion model with the time-consuming score distillation sampling (SDS), or a direct 3D diffusion model trained on limited 3D data losing generation diversity. In this work, we approach the problem by employing a multi-view 2.5D diffusion fine-tuned from a pre-trained 2D diffusion model. The multi-view 2.5D diffusion directly models the structural distribution of 3D data, while still maintaining the strong generalization ability of the original 2D diffusion model, filling the gap between 2D diffusion-based and direct 3D diffusion-based methods for 3D content generation. During inference, multi-view normal maps are generated using the 2.5D diffusion, and a novel differentiable rasterization scheme is introduced to fuse the almost consistent multi-view normal maps into a consistent 3D model. We further design a normal-conditioned multi-view image generation module for fast appearance generation given the 3D geometry. Our method is a one-pass diffusion process and does not require any SDS optimization as post-processing. We demonstrate through extensive experiments that, our direct 2.5D generation with the specially-designed fusion scheme can achieve diverse, mode-seeking-free, and high-fidelity 3D content generation in only 10 seconds. Project page: https://nju-3dv.github.io/projects/direct25.

The detection and classification of exfoliated two-dimensional (2D) material flakes from optical microscope images can be automated using computer vision algorithms. This has the potential to increase the accuracy and objectivity of classification and the efficiency of sample fabrication, and it allows for large-scale data collection. Existing algorithms often exhibit challenges in identifying low-contrast materials and typically require large amounts of training data. Here, we present a deep learning model, called MaskTerial, that uses an instance segmentation network to reliably identify 2D material flakes. The model is extensively pre-trained using a synthetic data generator, that generates realistic microscopy images from unlabeled data. This results in a model that can to quickly adapt to new materials with as little as 5 to 10 images. Furthermore, an uncertainty estimation model is used to finally classify the predictions based on optical contrast. We evaluate our method on eight different datasets comprising five different 2D materials and demonstrate significant improvements over existing techniques in the detection of low-contrast materials such as hexagonal boron nitride.

Text-to-3D generation has recently seen significant progress. To enhance its practicality in real-world applications, it is crucial to generate multiple independent objects with interactions, similar to layer-compositing in 2D image editing. However, existing text-to-3D methods struggle with this task, as they are designed to generate either non-independent objects or independent objects lacking spatially plausible interactions. Addressing this, we propose DreamDissector, a text-to-3D method capable of generating multiple independent objects with interactions. DreamDissector accepts a multi-object text-to-3D NeRF as input and produces independent textured meshes. To achieve this, we introduce the Neural Category Field (NeCF) for disentangling the input NeRF. Additionally, we present the Category Score Distillation Sampling (CSDS), facilitated by a Deep Concept Mining (DCM) module, to tackle the concept gap issue in diffusion models. By leveraging NeCF and CSDS, we can effectively derive sub-NeRFs from the original scene. Further refinement enhances geometry and texture. Our experimental results validate the effectiveness of DreamDissector, providing users with novel means to control 3D synthesis at the object level and potentially opening avenues for various creative applications in the future.

Recent advancements in diffusion techniques have propelled image and video generation to unprece- dented levels of quality, significantly accelerating the deployment and application of generative AI. However, 3D shape generation technology has so far lagged behind, constrained by limitations in 3D data scale, complexity of 3D data process- ing, and insufficient exploration of advanced tech- niques in the 3D domain. Current approaches to 3D shape generation face substantial challenges in terms of output quality, generalization capa- bility, and alignment with input conditions. We present TripoSG, a new streamlined shape diffu- sion paradigm capable of generating high-fidelity 3D meshes with precise correspondence to input images. Specifically, we propose: 1) A large-scale rectified flow transformer for 3D shape generation, achieving state-of-the-art fidelity through training on extensive, high-quality data. 2) A hybrid supervised training strategy combining SDF, normal, and eikonal losses for 3D VAE, achieving high- quality 3D reconstruction performance. 3) A data processing pipeline to generate 2 million high- quality 3D samples, highlighting the crucial rules for data quality and quantity in training 3D gen- erative models. Through comprehensive experi- ments, we have validated the effectiveness of each component in our new framework. The seamless integration of these parts has enabled TripoSG to achieve state-of-the-art performance in 3D shape generation. The resulting 3D shapes exhibit en- hanced detail due to high-resolution capabilities and demonstrate exceptional fidelity to input im- ages. Moreover, TripoSG demonstrates improved versatility in generating 3D models from diverse image styles and contents, showcasing strong gen- eralization capabilities. To foster progress and innovation in the field of 3D generation, we will make our model publicly available.

Recent years have witnessed remarkable advances in artificial intelligence generated content(AIGC), with diverse input modalities, e.g., text, image, video, audio and 3D. The 3D is the most close visual modality to real-world 3D environment and carries enormous knowledge. The 3D content generation shows both academic and practical values while also presenting formidable technical challenges. This review aims to consolidate developments within the burgeoning domain of 3D content generation. Specifically, a new taxonomy is proposed that categorizes existing approaches into three types: 3D native generative methods, 2D prior-based 3D generative methods, and hybrid 3D generative methods. The survey covers approximately 60 papers spanning the major techniques. Besides, we discuss limitations of current 3D content generation techniques, and point out open challenges as well as promising directions for future work. Accompanied with this survey, we have established a project website where the resources on 3D content generation research are provided. The project page is available at https://github.com/hitcslj/Awesome-AIGC-3D.

Generative models for 3D object synthesis have seen significant advancements with the incorporation of prior knowledge distilled from 2D diffusion models. Nevertheless, challenges persist in the form of multi-view geometric inconsistencies and slow generation speeds within the existing 3D synthesis frameworks. This can be attributed to two factors: firstly, the deficiency of abundant geometric a priori knowledge in optimization, and secondly, the entanglement issue between geometry and texture in conventional 3D generation methods.In response, we introduce MetaDreammer, a two-stage optimization approach that leverages rich 2D and 3D prior knowledge. In the first stage, our emphasis is on optimizing the geometric representation to ensure multi-view consistency and accuracy of 3D objects. In the second stage, we concentrate on fine-tuning the geometry and optimizing the texture, thereby achieving a more refined 3D object. Through leveraging 2D and 3D prior knowledge in two stages, respectively, we effectively mitigate the interdependence between geometry and texture. MetaDreamer establishes clear optimization objectives for each stage, resulting in significant time savings in the 3D generation process. Ultimately, MetaDreamer can generate high-quality 3D objects based on textual prompts within 20 minutes, and to the best of our knowledge, it is the most efficient text-to-3D generation method. Furthermore, we introduce image control into the process, enhancing the controllability of 3D generation. Extensive empirical evidence confirms that our method is not only highly efficient but also achieves a quality level that is at the forefront of current state-of-the-art 3D generation techniques.

DreamFusion has recently demonstrated the utility of a pre-trained text-to-image diffusion model to optimize Neural Radiance Fields (NeRF), achieving remarkable text-to-3D synthesis results. However, the method has two inherent limitations: (a) extremely slow optimization of NeRF and (b) low-resolution image space supervision on NeRF, leading to low-quality 3D models with a long processing time. In this paper, we address these limitations by utilizing a two-stage optimization framework. First, we obtain a coarse model using a low-resolution diffusion prior and accelerate with a sparse 3D hash grid structure. Using the coarse representation as the initialization, we further optimize a textured 3D mesh model with an efficient differentiable renderer interacting with a high-resolution latent diffusion model. Our method, dubbed Magic3D, can create high quality 3D mesh models in 40 minutes, which is 2x faster than DreamFusion (reportedly taking 1.5 hours on average), while also achieving higher resolution. User studies show 61.7% raters to prefer our approach over DreamFusion. Together with the image-conditioned generation capabilities, we provide users with new ways to control 3D synthesis, opening up new avenues to various creative applications.

In this report, we introduce UltraShape 1.0, a scalable 3D diffusion framework for high-fidelity 3D geometry generation. The proposed approach adopts a two-stage generation pipeline: a coarse global structure is first synthesized and then refined to produce detailed, high-quality geometry. To support reliable 3D generation, we develop a comprehensive data processing pipeline that includes a novel watertight processing method and high-quality data filtering. This pipeline improves the geometric quality of publicly available 3D datasets by removing low-quality samples, filling holes, and thickening thin structures, while preserving fine-grained geometric details. To enable fine-grained geometry refinement, we decouple spatial localization from geometric detail synthesis in the diffusion process. We achieve this by performing voxel-based refinement at fixed spatial locations, where voxel queries derived from coarse geometry provide explicit positional anchors encoded via RoPE, allowing the diffusion model to focus on synthesizing local geometric details within a reduced, structured solution space. Our model is trained exclusively on publicly available 3D datasets, achieving strong geometric quality despite limited training resources. Extensive evaluations demonstrate that UltraShape 1.0 performs competitively with existing open-source methods in both data processing quality and geometry generation. All code and trained models will be released to support future research.

Computational materials discovery is limited by the high cost of first-principles calculations. Machine learning (ML) potentials that predict energies from crystal structures are promising, but existing methods face computational bottlenecks. Steerable graph neural networks (GNNs) encode geometry with spherical harmonics, respecting atomic symmetries -- permutation, rotation, and translation -- for physically realistic predictions. Yet maintaining equivariance is difficult: activation functions must be modified, and each layer must handle multiple data types for different harmonic orders. We present Facet, a GNN architecture for efficient ML potentials, developed through systematic analysis of steerable GNNs. Our innovations include replacing expensive multi-layer perceptrons (MLPs) for interatomic distances with splines, which match performance while cutting computational and memory demands. We also introduce a general-purpose equivariant layer that mixes node information via spherical grid projection followed by standard MLPs -- faster than tensor products and more expressive than linear or gate layers. On the MPTrj dataset, Facet matches leading models with far fewer parameters and under 10% of their training compute. On a crystal relaxation task, it runs twice as fast as MACE models. We further show SevenNet-0's parameters can be reduced by over 25% with no accuracy loss. These techniques enable more than 10x faster training of large-scale foundation models for ML potentials, potentially reshaping computational materials discovery.

The most widely used method for obtaining high-quality two-dimensional materials is through mechanical exfoliation of bulk crystals. Manual identification of suitable flakes from the resulting random distribution of crystal thicknesses and sizes on a substrate is a time-consuming, tedious task. Here, we present a platform for fully automated scanning, detection, and classification of two-dimensional materials, the source code of which we make openly available. Our platform is designed to be accurate, reliable, fast, and versatile in integrating new materials, making it suitable for everyday laboratory work. The implementation allows fully automated scanning and analysis of wafers with an average inference time of 100 ms for images of 2.3 Mpixels. The developed detection algorithm is based on a combination of the flakes' optical contrast toward the substrate and their geometric shape. We demonstrate that it is able to detect the majority of exfoliated flakes of various materials, with an average recall (AR50) between 67% and 89%. We also show that the algorithm can be trained with as few as five flakes of a given material, which we demonstrate for the examples of few-layer graphene, WSe_2, MoSe_2, CrI_3, 1T-TaS_2 and hexagonal BN. Our platform has been tested over a two-year period, during which more than 10^6 images of multiple different materials were acquired by over 30 individual researchers.

3D modeling is moving from virtual to physical. Existing 3D generation primarily emphasizes geometries and textures while neglecting physical-grounded modeling. Consequently, despite the rapid development of 3D generative models, the synthesized 3D assets often overlook rich and important physical properties, hampering their real-world application in physical domains like simulation and embodied AI. As an initial attempt to address this challenge, we propose PhysX, an end-to-end paradigm for physical-grounded 3D asset generation. 1) To bridge the critical gap in physics-annotated 3D datasets, we present PhysXNet - the first physics-grounded 3D dataset systematically annotated across five foundational dimensions: absolute scale, material, affordance, kinematics, and function description. In particular, we devise a scalable human-in-the-loop annotation pipeline based on vision-language models, which enables efficient creation of physics-first assets from raw 3D assets.2) Furthermore, we propose PhysXGen, a feed-forward framework for physics-grounded image-to-3D asset generation, injecting physical knowledge into the pre-trained 3D structural space. Specifically, PhysXGen employs a dual-branch architecture to explicitly model the latent correlations between 3D structures and physical properties, thereby producing 3D assets with plausible physical predictions while preserving the native geometry quality. Extensive experiments validate the superior performance and promising generalization capability of our framework. All the code, data, and models will be released to facilitate future research in generative physical AI.

Automatic 3D content creation has gained increasing attention recently, due to its potential in various applications such as video games, film industry, and AR/VR. Recent advancements in diffusion models and multimodal models have notably improved the quality and efficiency of 3D object generation given a single RGB image. However, 3D objects generated even by state-of-the-art methods are still unsatisfactory compared to human-created assets. Considering only textures instead of materials makes these methods encounter challenges in photo-realistic rendering, relighting, and flexible appearance editing. And they also suffer from severe misalignment between geometry and high-frequency texture details. In this work, we propose a novel approach to boost the quality of generated 3D objects from the perspective of Physics-Based Rendering (PBR) materials. By analyzing the components of PBR materials, we choose to consider albedo, roughness, metalness, and bump maps. For albedo and bump maps, we leverage Stable Diffusion fine-tuned on synthetic data to extract these values, with novel usages of these fine-tuned models to obtain 3D consistent albedo UV and bump UV for generated objects. In terms of roughness and metalness maps, we adopt a semi-automatic process to provide room for interactive adjustment, which we believe is more practical. Extensive experiments demonstrate that our model is generally beneficial for various state-of-the-art generation methods, significantly boosting the quality and realism of their generated 3D objects, with natural relighting effects and substantially improved geometry.

Molecular ferroelectric materials have attracted widespread attention due to their abundant chemical diversity, structural tunability, low synthesis temperature, and high flexibility. Meanwhile, the integration of molecular ferroelectric materials and Si is still challenging, while the fundamental understanding of the ferroelectric switching process is still lacking. Herein, we have successfully synthesized the imidazole perchlorate (ImClO4) single crystals and a series of high-quality highly-oriented thin films on a Si substrate. A high inverse piezoelectric coefficient (55.7 pm/V) is demonstrated for the thin films. Two types of domain bands can be observed (in the size of a few microns): type-I band tilts ~60{\deg} with respect to the horizontal axis, while the type-II band is perpendicular to the horizontal axis. Most of the domain walls (DWs) are 180{\deg} DWs for the two bands, while some 109{\deg} DWs can also be observed. Interestingly, the DWs in type-I band are curved, charged domain walls; while the 180{\deg} DWs in type-II band are straight, noncharged domain walls. After applying +20 V for 5 s through a PFM tip, the 180{\deg} DWs in type-I band shrink first, then disconnect from the band boundary, forming a needle-like domain with a size of ~100 nm. The needle-like domain will extend toward the band boundary after an inverse bias is applied (-20 V), and expand along the band boundary after touching the boundary. Whereas for the type-II domain band, the 180{\deg} DWs are more mobile than the 109{\deg} domain walls, which displaces ~500 nm after applying +20 V. While such displacement is much shorter after the application of a negative bias for the same duration, starting from the positively poled sample. We hope to spur further interest in the on-chip design of the molecular ferroelectrics based electronic devices.

Generative machine learning models can potentially provide direct access to novel and relevant portions of the full chemical space, overcoming the cost of systematic sampling. However, the training of these models generally requires a large amount of data, often precluding the use of expensive high-level ab initio simulations for this task. The generation of coordination compounds of Dy with large magnetic anisotropy represents a topical example, where multireference simulations of large molecules are necessary to perform reliable predictions. Here, we show that a semi-supervised chemically-inspired training-by-proxy of generative variational autoencoders can reduce the cost associated with building a training set from multireference simulations by two orders of magnitude. We illustrate the power of this approach by generating 100s of new organic ligands for Dy(III) pentagonal bipyramidal complexes exhibiting record values of magnetic anisotropy, while starting from datasets as small as 1k multireference calculations. This work thus paves the way to the computational generation of molecules as complex coordination compounds with target electronic and magnetic properties.

The annotation (assigning structural chemical identities) of MS/MS spectra remains a significant challenge due to the enormous molecular diversity in biological samples and the limited scope of reference databases. Currently, the vast majority of spectral measurements remain in the "dark chemical space" without structural annotations. To improve annotation, we propose MADGEN (Mass-spec Attends to De Novo Molecular GENeration), a scaffold-based method for de novo molecular structure generation guided by mass spectrometry data. MADGEN operates in two stages: scaffold retrieval and spectra-conditioned molecular generation starting with the scaffold. In the first stage, given an MS/MS spectrum, we formulate scaffold retrieval as a ranking problem and employ contrastive learning to align mass spectra with candidate molecular scaffolds. In the second stage, starting from the retrieved scaffold, we employ the MS/MS spectrum to guide an attention-based generative model to generate the final molecule. Our approach constrains the molecular generation search space, reducing its complexity and improving generation accuracy. We evaluate MADGEN on three datasets (NIST23, CANOPUS, and MassSpecGym) and evaluate MADGEN's performance with a predictive scaffold retriever and with an oracle retriever. We demonstrate the effectiveness of using attention to integrate spectral information throughout the generation process to achieve strong results with the oracle retriever.

Modularization is a cornerstone of computer science, abstracting complex functions into atomic building blocks. In this paper, we introduce a new level of modularization by abstracting generative models into atomic generative modules. Analogous to fractals in mathematics, our method constructs a new type of generative model by recursively invoking atomic generative modules, resulting in self-similar fractal architectures that we call fractal generative models. As a running example, we instantiate our fractal framework using autoregressive models as the atomic generative modules and examine it on the challenging task of pixel-by-pixel image generation, demonstrating strong performance in both likelihood estimation and generation quality. We hope this work could open a new paradigm in generative modeling and provide a fertile ground for future research. Code is available at https://github.com/LTH14/fractalgen.

Leveraging new data sources is a key step in accelerating the pace of materials design and discovery. To complement the strides in synthesis planning driven by historical, experimental, and computed data, we present an automated method for connecting scientific literature to synthesis insights. Starting from natural language text, we apply word embeddings from language models, which are fed into a named entity recognition model, upon which a conditional variational autoencoder is trained to generate syntheses for arbitrary materials. We show the potential of this technique by predicting precursors for two perovskite materials, using only training data published over a decade prior to their first reported syntheses. We demonstrate that the model learns representations of materials corresponding to synthesis-related properties, and that the model's behavior complements existing thermodynamic knowledge. Finally, we apply the model to perform synthesizability screening for proposed novel perovskite compounds.

The development of accurate and efficient machine learning models for predicting the structure and properties of molecular crystals has been hindered by the scarcity of publicly available datasets of structures with property labels. To address this challenge, we introduce the Open Molecular Crystals 2025 (OMC25) dataset, a collection of over 27 million molecular crystal structures containing 12 elements and up to 300 atoms in the unit cell. The dataset was generated from dispersion-inclusive density functional theory (DFT) relaxation trajectories of over 230,000 randomly generated molecular crystal structures of around 50,000 organic molecules. OMC25 comprises diverse chemical compounds capable of forming different intermolecular interactions and a wide range of crystal packing motifs. We provide detailed information on the dataset's construction, composition, structure, and properties. To demonstrate the quality and use cases of OMC25, we further trained and evaluated state-of-the-art open-source machine learning interatomic potentials. By making this dataset publicly available, we aim to accelerate the development of more accurate and efficient machine learning models for molecular crystals.

Inspired by the principle of deliberate practice in human learning, we propose Deliberate Practice for Synthetic Data Generation (DP), a novel framework that improves sample efficiency through dynamic synthetic data generation. Prior work has shown that scaling synthetic data is inherently challenging, as naively adding new data leads to diminishing returns. To address this, pruning has been identified as a key mechanism for improving scaling, enabling models to focus on the most informative synthetic samples. Rather than generating a large dataset and pruning it afterward, DP efficiently approximates the direct generation of informative samples. We theoretically show how training on challenging, informative examples improves scaling laws and empirically validate that DP achieves better scaling performance with significantly fewer training samples and iterations. On ImageNet-100, DP generates 3.4x fewer samples and requires six times fewer iterations, while on ImageNet-1k, it generates 8x fewer samples with a 30 percent reduction in iterations, all while achieving superior performance compared to prior work.

Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointly with the underlying amino acid sequence. This is challenging, for instance, because the model must reason over side chains that change in length during generation. We introduce La-Proteina for atomistic protein design based on a novel partially latent protein representation: coarse backbone structure is modeled explicitly, while sequence and atomistic details are captured via per-residue latent variables of fixed dimensionality, thereby effectively side-stepping challenges of explicit side-chain representations. Flow matching in this partially latent space then models the joint distribution over sequences and full-atom structures. La-Proteina achieves state-of-the-art performance on multiple generation benchmarks, including all-atom co-designability, diversity, and structural validity, as confirmed through detailed structural analyses and evaluations. Notably, La-Proteina also surpasses previous models in atomistic motif scaffolding performance, unlocking critical atomistic structure-conditioned protein design tasks. Moreover, La-Proteina is able to generate co-designable proteins of up to 800 residues, a regime where most baselines collapse and fail to produce valid samples, demonstrating La-Proteina's scalability and robustness.

Denoising diffusion models have shown great potential in multiple research areas. Existing diffusion-based generative methods on de novo 3D molecule generation face two major challenges. Since majority heavy atoms in molecules allow connections to multiple atoms through single bonds, solely using pair-wise distance to model molecule geometries is insufficient. Therefore, the first one involves proposing an effective neural network as the denoising kernel that is capable to capture complex multi-body interatomic relationships and learn high-quality features. Due to the discrete nature of graphs, mainstream diffusion-based methods for molecules heavily rely on predefined rules and generate edges in an indirect manner. The second challenge involves accommodating molecule generation to diffusion and accurately predicting the existence of bonds. In our research, we view the iterative way of updating molecule conformations in diffusion process is consistent with molecular dynamics and introduce a novel molecule generation method named Geometric-Facilitated Molecular Diffusion (GFMDiff). For the first challenge, we introduce a Dual-Track Transformer Network (DTN) to fully excevate global spatial relationships and learn high quality representations which contribute to accurate predictions of features and geometries. As for the second challenge, we design Geometric-Facilitated Loss (GFLoss) which intervenes the formation of bonds during the training period, instead of directly embedding edges into the latent space. Comprehensive experiments on current benchmarks demonstrate the superiority of GFMDiff.

3D object generation has undergone significant advancements, yielding high-quality results. However, fall short of achieving precise user control, often yielding results that do not align with user expectations, thus limiting their applicability. User-envisioning 3D object generation faces significant challenges in realizing its concepts using current generative models due to limited interaction capabilities. Existing methods mainly offer two approaches: (i) interpreting textual instructions with constrained controllability, or (ii) reconstructing 3D objects from 2D images. Both of them limit customization to the confines of the 2D reference and potentially introduce undesirable artifacts during the 3D lifting process, restricting the scope for direct and versatile 3D modifications. In this work, we introduce Interactive3D, an innovative framework for interactive 3D generation that grants users precise control over the generative process through extensive 3D interaction capabilities. Interactive3D is constructed in two cascading stages, utilizing distinct 3D representations. The first stage employs Gaussian Splatting for direct user interaction, allowing modifications and guidance of the generative direction at any intermediate step through (i) Adding and Removing components, (ii) Deformable and Rigid Dragging, (iii) Geometric Transformations, and (iv) Semantic Editing. Subsequently, the Gaussian splats are transformed into InstantNGP. We introduce a novel (v) Interactive Hash Refinement module to further add details and extract the geometry in the second stage. Our experiments demonstrate that Interactive3D markedly improves the controllability and quality of 3D generation. Our project webpage is available at https://interactive-3d.github.io/.

The reliability with Machine Learning (ML) techniques in novel materials discovery often depend on the quality of the dataset, in addition to the relevant features used in describing the material. In this regard, the current study presents and validates a newly processed materials dataset that can be utilized for benchmark ML analysis, as it relates to the prediction and classification of deterministic target properties. Originally, the dataset was extracted from the Open Quantum Materials Database (OQMD) and contains a robust 16,323 samples of ABX3 inorganic perovskite structures. The dataset is tabular in form and is preprocessed to include sixty-one generalized input features that broadly describes the physicochemical, stability/geometrical, and Density Functional Theory (DFT) target properties associated with the elemental ionic sites in a three-dimensional ABX3 polyhedral. For validation, four different ML models are employed to predict three distinctive target properties, namely: formation energy, energy band gap, and crystal system. On experimentation, the best accuracy measurements are reported at 0.013 eV/atom MAE, 0.216 eV MAE, and 85% F1, corresponding to the formation energy prediction, band gap prediction and crystal system multi-classification, respectively. Moreover, the realized results are compared with previous literature and as such, affirms the resourcefulness of the current dataset for future benchmark materials analysis via ML techniques. The preprocessed dataset and source codes are openly available to download from github.com/chenebuah/ML_abx3_dataset.

We introduce InVirtuoGen, a discrete flow generative model for fragmented SMILES for de novo and fragment-constrained generation, and target-property/lead optimization of small molecules. The model learns to transform a uniform source over all possible tokens into the data distribution. Unlike masked models, its training loss accounts for predictions on all sequence positions at every denoising step, shifting the generation paradigm from completion to refinement, and decoupling the number of sampling steps from the sequence length. For de novo generation, InVirtuoGen achieves a stronger quality-diversity pareto frontier than prior fragment-based models and competitive performance on fragment-constrained tasks. For property and lead optimization, we propose a hybrid scheme that combines a genetic algorithm with a Proximal Property Optimization fine-tuning strategy adapted to discrete flows. Our approach sets a new state-of-the-art on the Practical Molecular Optimization benchmark, measured by top-10 AUC across tasks, and yields higher docking scores in lead optimization than previous baselines. InVirtuoGen thus establishes a versatile generative foundation for drug discovery, from early hit finding to multi-objective lead optimization. We further contribute to open science by releasing pretrained checkpoints and code, making our results fully reproduciblehttps://github.com/invirtuolabs/InVirtuoGen_results.

We present a learning-based system for rapid mass-scale material synthesis that is useful for novice and expert users alike. The user preferences are learned via Gaussian Process Regression and can be easily sampled for new recommendations. Typically, each recommendation takes 40-60 seconds to render with global illumination, which makes this process impracticable for real-world workflows. Our neural network eliminates this bottleneck by providing high-quality image predictions in real time, after which it is possible to pick the desired materials from a gallery and assign them to a scene in an intuitive manner. Workflow timings against Disney's "principled" shader reveal that our system scales well with the number of sought materials, thus empowering even novice users to generate hundreds of high-quality material models without any expertise in material modeling. Similarly, expert users experience a significant decrease in the total modeling time when populating a scene with materials. Furthermore, our proposed solution also offers controllable recommendations and a novel latent space variant generation step to enable the real-time fine-tuning of materials without requiring any domain expertise.

Synthesizability remains a critical bottleneck in generative molecular design. While recent advances have addressed synthesizability in 2D graphs, extending these constraints to 3D for geometry-based conditional generation remains largely unexplored. In this work, we present SynCoGen (Synthesizable Co-Generation), a single framework that combines simultaneous masked graph diffusion and flow matching for synthesizable 3D molecule generation. SynCoGen samples from the joint distribution of molecular building blocks, chemical reactions, and atomic coordinates. To train the model, we curated SynSpace, a dataset family containing over 1.2M synthesis-aware building block graphs and 7.5M conformers. SynCoGen achieves state-of-the-art performance in unconditional small molecule graph and conformer co-generation. For protein ligand generation in drug discovery, the amortized model delivers superior performance in both molecular linker design and pharmacophore-conditioned generation across diverse targets without relying on any scoring functions. Overall, this multimodal non-autoregressive formulation represents a foundation for a range of molecular design applications, including analog expansion, lead optimization, and direct de novo design.

Perovskite solar cells (PSCs) have rapidly emerged as a leading contender in next-generation photovoltaic technologies, owing to their exceptional power conversion efficiencies and advantageous material properties. Despite these advances, challenges such as long-term stability, environmental sustainability, and scalable manufacturing continue to hinder their commercialization. Precursor additive engineering has shown promise in addressing these issues by enhancing both the performance and durability of PSCs. However, the explosive growth of scientific literature and the complex interplay of materials, processes, and device architectures make it increasingly difficult for researchers to efficiently access, organize, and utilize domain knowledge in this rapidly evolving field. To address this gap, we introduce Perovskite-R1, a specialized large language model (LLM) with advanced reasoning capabilities tailored for the discovery and design of PSC precursor additives. By systematically mining and curating 1,232 high-quality scientific publications and integrating a comprehensive library of 33,269 candidate materials, we constructed a domain-specific instruction-tuning dataset using automated question-answer generation and chain-of-thought reasoning. Fine-tuning the QwQ-32B model on this dataset resulted in Perovskite-R1, which can intelligently synthesize literature insights and generate innovative and practical solutions for defect passivation and the selection of precursor additives. Experimental validation of several model-proposed strategies confirms their effectiveness in improving material stability and performance. Our work demonstrates the potential of domain-adapted LLMs in accelerating materials discovery and provides a closed-loop framework for intelligent, data-driven advancements in perovskite photovoltaic research.

Scientific researchers frequently use the in situ synchrotron high-energy powder X-ray diffraction (XRD) technique to examine the crystallographic structures of materials in functional devices such as rechargeable battery materials. We propose a method for identifying artifacts in experimental XRD images. The proposed method uses deep learning convolutional neural network architectures, such as tunable U-Nets to identify the artifacts. In particular, the predicted artifacts are evaluated against the corresponding ground truth (manually implemented) using the overall true positive rate or recall. The result demonstrates that the U-Nets can consistently produce great recall performance at 92.4% on the test dataset, which is not included in the training, with a 34% reduction in average false positives in comparison to the conventional method. The U-Nets also reduce the time required to identify and separate artifacts by more than 50%. Furthermore, the exclusion of the artifacts shows major changes in the integrated 1D XRD pattern, enhancing further analysis of the post-processing XRD data.

Large language models have demonstrated remarkable reasoning capabilities across diverse natural language tasks. However, comparable breakthroughs in scientific discovery are more limited, because understanding complex physical phenomena demands multifaceted representations far beyond language alone. A compelling example is the design of functional materials such as MOFs-critical for a range of impactful applications like carbon capture and hydrogen storage. Navigating their vast and intricate design space in language-based representations interpretable by LLMs is challenging due to the numerous possible three-dimensional atomic arrangements and strict reticular rules of coordination geometry and topology. Despite promising early results in LLM-assisted discovery for simpler materials systems, MOF design remains heavily reliant on tacit human expertise rarely codified in textual information alone. To overcome this barrier, we introduce L2M3OF, the first multimodal LLM for MOFs. L2M3OF integrates crystal representation learning with language understanding to process structural, textual, and knowledge modalities jointly. L2M3OF employs a pre-trained crystal encoder with a lightweight projection layer to compress structural information into a token space, enabling efficient alignment with language instructions. To facilitate training and evaluation, we curate a structure-property-knowledge database of crystalline materials and benchmark L2M3OF against state-of-the-art closed-source LLMs such as GPT-5, Gemini-2.5-Pro and DeepSeek-R1. Experiments show that L2M3OF outperforms leading text-based closed-source LLMs in property prediction and knowledge generation tasks, despite using far fewer parameters. These results highlight the importance of multimodal approaches for porous material understanding and establish L2M3OF as a foundation for next-generation AI systems in materials discovery.

Benefiting from the rapid development of 2D diffusion models, 3D content creation has made significant progress recently. One promising solution involves the fine-tuning of pre-trained 2D diffusion models to harness their capacity for producing multi-view images, which are then lifted into accurate 3D models via methods like fast-NeRFs or large reconstruction models. However, as inconsistency still exists and limited generated resolution, the generation results of such methods still lack intricate textures and complex geometries. To solve this problem, we propose Magic-Boost, a multi-view conditioned diffusion model that significantly refines coarse generative results through a brief period of SDS optimization (sim15min). Compared to the previous text or single image based diffusion models, Magic-Boost exhibits a robust capability to generate images with high consistency from pseudo synthesized multi-view images. It provides precise SDS guidance that well aligns with the identity of the input images, enriching the local detail in both geometry and texture of the initial generative results. Extensive experiments show Magic-Boost greatly enhances the coarse inputs and generates high-quality 3D assets with rich geometric and textural details. (Project Page: https://magic-research.github.io/magic-boost/)