Daily Papers

Shortcut models represent a promising, non-adversarial paradigm for generative modeling, uniquely supporting one-step, few-step, and multi-step sampling from a single trained network. However, their widespread adoption has been stymied by critical performance bottlenecks. This paper tackles the five core issues that held shortcut models back: (1) the hidden flaw of compounding guidance, which we are the first to formalize, causing severe image artifacts; (2) inflexible fixed guidance that restricts inference-time control; (3) a pervasive frequency bias driven by a reliance on low-level distances in the direct domain, which biases reconstructions toward low frequencies; (4) divergent self-consistency arising from a conflict with EMA training; and (5) curvy flow trajectories that impede convergence. To address these challenges, we introduce iSM, a unified training framework that systematically resolves each limitation. Our framework is built on four key improvements: Intrinsic Guidance provides explicit, dynamic control over guidance strength, resolving both compounding guidance and inflexibility. A Multi-Level Wavelet Loss mitigates frequency bias to restore high-frequency details. Scaling Optimal Transport (sOT) reduces training variance and learns straighter, more stable generative paths. Finally, a Twin EMA strategy reconciles training stability with self-consistency. Extensive experiments on ImageNet 256 x 256 demonstrate that our approach yields substantial FID improvements over baseline shortcut models across one-step, few-step, and multi-step generation, making shortcut models a viable and competitive class of generative models.

In many domains, autoregressive models can attain high likelihood on the task of predicting the next observation. However, this maximum-likelihood (MLE) objective does not necessarily match a downstream use-case of autoregressively generating high-quality sequences. The MLE objective weights sequences proportionally to their frequency under the data distribution, with no guidance for the model's behaviour out of distribution (OOD): leading to compounding error during autoregressive generation. In order to address this compounding error problem, we formulate sequence generation as an imitation learning (IL) problem. This allows us to minimize a variety of divergences between the distribution of sequences generated by an autoregressive model and sequences from a dataset, including divergences with weight on OOD generated sequences. The IL framework also allows us to incorporate backtracking by introducing a backspace action into the generation process. This further mitigates the compounding error problem by allowing the model to revert a sampled token if it takes the sequence OOD. Our resulting method, SequenceMatch, can be implemented without adversarial training or major architectural changes. We identify the SequenceMatch-chi^2 divergence as a more suitable training objective for autoregressive models which are used for generation. We show that empirically, SequenceMatch training leads to improvements over MLE on text generation with language models.

The study demonstrates the capabilities of a vector-based approach for calculating stoichiometric coefficients in chemical equations, using black powder as an illustrative example. A method is proposed for selecting and constraining intermediate interactions between reactants, as well as for identifying final products. It is shown that even a small number of components can lead to a large number of final and intermediate products. Through concrete calculations, a correlation is established between the number of possible chemical equations and the number of reactants. A methodology is proposed for computing all possible chemical equations within a reaction system for arbitrary component ratios, enabling the derivation of all feasible chemical reactions. Additionally, a method is developed for calculating the chemical composition for a fixed set of reactants, allowing for the evaluation of the set of products resulting from all possible chemical interactions given a specified initial composition.

In a compound AI system, components such as an LLM call, a retriever, a code interpreter, or tools are interconnected. The system's behavior is primarily driven by parameters such as instructions or tool definitions. Recent advancements enable end-to-end optimization of these parameters using an LLM. Notably, leveraging an LLM as an optimizer is particularly efficient because it avoids gradient computation and can generate complex code and instructions. This paper presents a survey of the principles and emerging trends in LLM-based optimization of compound AI systems. It covers archetypes of compound AI systems, approaches to LLM-based end-to-end optimization, and insights into future directions and broader impacts. Importantly, this survey uses concepts from program analysis to provide a unified view of how an LLM optimizer is prompted to optimize a compound AI system. The exhaustive list of paper is provided at https://github.com/linyuhongg/LLM-based-Optimization-of-Compound-AI-Systems.

This paper investigates the extent to which pretrained German BERT encodes knowledge of noun compound semantics. We comprehensively vary combinations of target tokens, layers, and cased vs. uncased models, and evaluate them by predicting the compositionality of 868 gold standard compounds. Looking at representational patterns within the transformer architecture, we observe trends comparable to equivalent prior work on English, with compositionality information most easily recoverable in the early layers. However, our strongest results clearly lag behind those reported for English, suggesting an inherently more difficult task in German. This may be due to the higher productivity of compounding in German than in English and the associated increase in constituent-level ambiguity, including in our target compound set.

Guidance is a crucial technique for extracting the best performance out of image-generating diffusion models. Traditionally, a constant guidance weight has been applied throughout the sampling chain of an image. We show that guidance is clearly harmful toward the beginning of the chain (high noise levels), largely unnecessary toward the end (low noise levels), and only beneficial in the middle. We thus restrict it to a specific range of noise levels, improving both the inference speed and result quality. This limited guidance interval improves the record FID in ImageNet-512 significantly, from 1.81 to 1.40. We show that it is quantitatively and qualitatively beneficial across different sampler parameters, network architectures, and datasets, including the large-scale setting of Stable Diffusion XL. We thus suggest exposing the guidance interval as a hyperparameter in all diffusion models that use guidance.

Multi-component compounding is a prevalent phenomenon in Sanskrit, and understanding the implicit structure of a compound's components is crucial for deciphering its meaning. Earlier approaches in Sanskrit have focused on binary compounds and neglected the multi-component compound setting. This work introduces the novel task of nested compound type identification (NeCTI), which aims to identify nested spans of a multi-component compound and decode the implicit semantic relations between them. To the best of our knowledge, this is the first attempt in the field of lexical semantics to propose this task. We present 2 newly annotated datasets including an out-of-domain dataset for this task. We also benchmark these datasets by exploring the efficacy of the standard problem formulations such as nested named entity recognition, constituency parsing and seq2seq, etc. We present a novel framework named DepNeCTI: Dependency-based Nested Compound Type Identifier that surpasses the performance of the best baseline with an average absolute improvement of 13.1 points F1-score in terms of Labeled Span Score (LSS) and a 5-fold enhancement in inference efficiency. In line with the previous findings in the binary Sanskrit compound identification task, context provides benefits for the NeCTI task. The codebase and datasets are publicly available at: https://github.com/yaswanth-iitkgp/DepNeCTI

Structure-Based molecule optimization (SBMO) aims to optimize molecules with both continuous coordinates and discrete types against protein targets. A promising direction is to exert gradient guidance on generative models given its remarkable success in images, but it is challenging to guide discrete data and risks inconsistencies between modalities. To this end, we leverage a continuous and differentiable space derived through Bayesian inference, presenting Molecule Joint Optimization (MolJO), the gradient-based SBMO framework that facilitates joint guidance signals across different modalities while preserving SE(3)-equivariance. We introduce a novel backward correction strategy that optimizes within a sliding window of the past histories, allowing for a seamless trade-off between explore-and-exploit during optimization. MolJO achieves state-of-the-art performance on CrossDocked2020 benchmark (Success Rate 51.3%, Vina Dock -9.05 and SA 0.78), more than 4x improvement in Success Rate compared to the gradient-based counterpart, and 2x "Me-Better" Ratio as much as 3D baselines. Furthermore, we extend MolJO to a wide range of optimization settings, including multi-objective optimization and challenging tasks in drug design such as R-group optimization and scaffold hopping, further underscoring its versatility. Code is available at https://github.com/AlgoMole/MolCRAFT.

To enhance large language models (LLMs) for chemistry problem solving, several LLM-based agents augmented with tools have been proposed, such as ChemCrow and Coscientist. However, their evaluations are narrow in scope, leaving a large gap in understanding the benefits of tools across diverse chemistry tasks. To bridge this gap, we develop ChemAgent, an enhanced chemistry agent over ChemCrow, and conduct a comprehensive evaluation of its performance on both specialized chemistry tasks and general chemistry questions. Surprisingly, ChemAgent does not consistently outperform its base LLMs without tools. Our error analysis with a chemistry expert suggests that: For specialized chemistry tasks, such as synthesis prediction, we should augment agents with specialized tools; however, for general chemistry questions like those in exams, agents' ability to reason correctly with chemistry knowledge matters more, and tool augmentation does not always help.

Compound AI systems that combine multiple LLM calls, such as self-refine and multi-agent-debate, achieve strong performance on many AI tasks. We address a core question in optimizing compound systems: for each LLM call or module in the system, how should one decide which LLM to use? We show that these LLM choices have a large effect on quality, but the search space is exponential. We propose LLMSelector, an efficient framework for model selection in compound systems, which leverages two key empirical insights: (i) end-to-end performance is often monotonic in how well each module performs, with all other modules held fixed, and (ii) per-module performance can be estimated accurately by an LLM. Building upon these insights, LLMSelector iteratively selects one module and allocates to it the model with the highest module-wise performance, as estimated by an LLM, until no further gain is possible. LLMSelector is applicable to any compound system with a bounded number of modules, and its number of API calls scales linearly with the number of modules, achieving high-quality model allocation both empirically and theoretically. Experiments with popular compound systems such as multi-agent debate and self-refine using LLMs such as GPT-4o, Claude 3.5 Sonnet and Gemini 1.5 show that LLMSelector confers 5%-70% accuracy gains compared to using the same LLM for all modules.

Classifier guidance is a recently introduced method to trade off mode coverage and sample fidelity in conditional diffusion models post training, in the same spirit as low temperature sampling or truncation in other types of generative models. Classifier guidance combines the score estimate of a diffusion model with the gradient of an image classifier and thereby requires training an image classifier separate from the diffusion model. It also raises the question of whether guidance can be performed without a classifier. We show that guidance can be indeed performed by a pure generative model without such a classifier: in what we call classifier-free guidance, we jointly train a conditional and an unconditional diffusion model, and we combine the resulting conditional and unconditional score estimates to attain a trade-off between sample quality and diversity similar to that obtained using classifier guidance.

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

A ChatGPT-like system for drug compounds could be a game-changer in pharmaceutical research, accelerating drug discovery, enhancing our understanding of structure-activity relationships, guiding lead optimization, aiding drug repurposing, reducing the failure rate, and streamlining clinical trials. In this work, we make an initial attempt towards enabling ChatGPT-like capabilities on drug molecule graphs, by developing a prototype system DrugChat. DrugChat works in a similar way as ChatGPT. Users upload a compound molecule graph and ask various questions about this compound. DrugChat will answer these questions in a multi-turn, interactive manner. The DrugChat system consists of a graph neural network (GNN), a large language model (LLM), and an adaptor. The GNN takes a compound molecule graph as input and learns a representation for this graph. The adaptor transforms the graph representation produced by the GNN into another representation that is acceptable to the LLM. The LLM takes the compound representation transformed by the adaptor and users' questions about this compound as inputs and generates answers. All these components are trained end-to-end. To train DrugChat, we collected instruction tuning datasets which contain 10,834 drug compounds and 143,517 question-answer pairs. The code and data is available at https://github.com/UCSD-AI4H/drugchat

It is imperative for Large language models (LLMs) to follow instructions with elaborate requirements (i.e. Complex Instructions Following). Yet, it remains under-explored how to enhance the ability of LLMs to follow complex instructions with multiple constraints. To bridge the gap, we initially study what training data is effective in enhancing complex constraints following abilities. We found that training LLMs with instructions containing multiple constraints enhances their understanding of complex instructions, especially those with lower complexity levels. The improvement can even generalize to compositions of out-of-domain constraints. Additionally, we further propose methods addressing how to obtain and utilize the effective training data. Finally, we conduct extensive experiments to prove the effectiveness of our methods in terms of overall performance and training efficiency. We also demonstrate that our methods improve models' ability to follow instructions generally and generalize effectively across out-of-domain, in-domain, and adversarial settings, while maintaining general capabilities.

As large language models (LLMs) become increasingly advanced, their ability to exhibit compositional generalization -- the capacity to combine learned skills in novel ways not encountered during training -- has garnered significant attention. This type of generalization, particularly in scenarios beyond training data, is also of great interest in the study of AI safety and alignment. A recent study introduced the SKILL-MIX evaluation, where models are tasked with composing a short paragraph demonstrating the use of a specified k-tuple of language skills. While small models struggled with composing even with k=3, larger models like GPT-4 performed reasonably well with k=5 and 6. In this paper, we employ a setup akin to SKILL-MIX to evaluate the capacity of smaller models to learn compositional generalization from examples. Utilizing a diverse set of language skills -- including rhetorical, literary, reasoning, theory of mind, and common sense -- GPT-4 was used to generate text samples that exhibit random subsets of k skills. Subsequent fine-tuning of 7B and 13B parameter models on these combined skill texts, for increasing values of k, revealed the following findings: (1) Training on combinations of k=2 and 3 skills results in noticeable improvements in the ability to compose texts with k=4 and 5 skills, despite models never having seen such examples during training. (2) When skill categories are split into training and held-out groups, models significantly improve at composing texts with held-out skills during testing despite having only seen training skills during fine-tuning, illustrating the efficacy of the training approach even with previously unseen skills. This study also suggests that incorporating skill-rich (potentially synthetic) text into training can substantially enhance the compositional capabilities of models.

The interdiffusion coefficients are estimated either following the Wagner's method expressed with respect to the composition (mol or atomic fraction) normalized variable after considering the molar volume variation or the den Broeder's method expressed with respect to the concentration (composition divided by the molar volume) normalized variable. On the other hand, the relations for estimation of the intrinsic diffusion coefficients of components as established by van Loo and integrated diffusion coefficients in a phase with narrow homogeneity range as established by Wagner are currently available with respect to the composition normalized variable only. In this study, we have first derived the relation proposed by den Broeder following the line of treatment proposed by Wagner. Further, the relations for estimation of the intrinsic diffusion coefficients of the components and integrated interdiffusion coefficient are established with respect to the concentration normalized variable, which were not available earlier. The veracity of these methods is examined based on the estimation of data in Ni-Pd, Ni-Al and Cu-Sn systems. Our analysis indicates that both the approaches are logically correct and there is small difference in the estimated data in these systems although a higher difference could be found in other systems. The integrated interdiffusion coefficients with respect to the concentration (or concentration normalized variable) can only be estimated considering the ideal molar volume variation. This might be drawback in certain practical systems.

Classifier-free Guidance (CFG) is a widely used technique in modern diffusion models for enhancing sample quality and prompt adherence. However, through an empirical analysis on Gaussian mixture modeling with a closed-form solution, we observe a discrepancy between the suboptimal results produced by CFG and the ground truth. The model's excessive reliance on these suboptimal predictions often leads to semantic incoherence and low-quality outputs. To address this issue, we first empirically demonstrate that the model's suboptimal predictions can be effectively refined using sub-networks of the model itself. Building on this insight, we propose S^2-Guidance, a novel method that leverages stochastic block-dropping during the forward process to construct stochastic sub-networks, effectively guiding the model away from potential low-quality predictions and toward high-quality outputs. Extensive qualitative and quantitative experiments on text-to-image and text-to-video generation tasks demonstrate that S^2-Guidance delivers superior performance, consistently surpassing CFG and other advanced guidance strategies. Our code will be released.

This paper studies the problem of solving complex chemistry problems with large language models (LLMs). Despite the extensive general knowledge in LLMs (such as GPT-4), they struggle with chemistry reasoning that requires faithful grounded reasoning with diverse chemical knowledge and an integrative understanding of chemical interactions. We propose InstructChem, a new structured reasoning approach that substantially boosts the LLMs' chemical reasoning capabilities. InstructChem explicitly decomposes the reasoning into three critical phrases, including chemical formulae generation by LLMs that offers the basis for subsequent grounded reasoning, step-by-step reasoning that makes multi-step derivations with the identified formulae for a preliminary answer, and iterative review-and-refinement that steers LLMs to progressively revise the previous phases for increasing confidence, leading to the final high-confidence answer. We conduct extensive experiments on four different chemistry challenges, including quantum chemistry, quantum mechanics, physical chemistry, and chemistry kinetics. Our approach significantly enhances GPT-4 on chemistry reasoning, yielding an 8% average absolute improvement and a 30% peak improvement. We further use the generated reasoning by GPT-4 to fine-tune smaller LMs (e.g., Vicuna) and observe strong improvement of the smaller LMs. This validates our approach and enables LLMs to generate high-quality reasoning.

We consider the task of text generation in language models with constraints specified in natural language. To this end, we first create a challenging benchmark Cognac that provides as input to the model a topic with example text, along with a constraint on text to be avoided. Unlike prior work, our benchmark contains knowledge-intensive constraints sourced from databases like Wordnet and Wikidata, which allows for straightforward evaluation while striking a balance between broad attribute-level and narrow lexical-level controls. We find that even state-of-the-art language models like GPT-3 fail often on this task, and propose a solution to leverage a language model's own internal knowledge to guide generation. Our method, called CognacGen, first queries the language model to generate guidance terms for a specified topic or constraint, and uses the guidance to modify the model's token generation probabilities. We propose three forms of guidance (binary verifier, top-k tokens, textual example), and employ prefix-tuning approaches to distill the guidance to tackle diverse natural language constraints. Through extensive empirical evaluations, we demonstrate that CognacGen can successfully generalize to unseen instructions and outperform competitive baselines in generating constraint conforming text.

State-of-the-art machine learning methods exhibit limited compositional generalization. At the same time, there is a lack of realistic benchmarks that comprehensively measure this ability, which makes it challenging to find and evaluate improvements. We introduce a novel method to systematically construct such benchmarks by maximizing compound divergence while guaranteeing a small atom divergence between train and test sets, and we quantitatively compare this method to other approaches for creating compositional generalization benchmarks. We present a large and realistic natural language question answering dataset that is constructed according to this method, and we use it to analyze the compositional generalization ability of three machine learning architectures. We find that they fail to generalize compositionally and that there is a surprisingly strong negative correlation between compound divergence and accuracy. We also demonstrate how our method can be used to create new compositionality benchmarks on top of the existing SCAN dataset, which confirms these findings.

AI is undergoing a paradigm shift, with breakthroughs achieved by systems orchestrating multiple large language models (LLMs) and other complex components. As a result, developing principled and automated optimization methods for compound AI systems is one of the most important new challenges. Neural networks faced a similar challenge in its early days until backpropagation and automatic differentiation transformed the field by making optimization turn-key. Inspired by this, we introduce TextGrad, a powerful framework performing automatic ``differentiation'' via text. TextGrad backpropagates textual feedback provided by LLMs to improve individual components of a compound AI system. In our framework, LLMs provide rich, general, natural language suggestions to optimize variables in computation graphs, ranging from code snippets to molecular structures. TextGrad follows PyTorch's syntax and abstraction and is flexible and easy-to-use. It works out-of-the-box for a variety of tasks, where the users only provide the objective function without tuning components or prompts of the framework. We showcase TextGrad's effectiveness and generality across a diverse range of applications, from question answering and molecule optimization to radiotherapy treatment planning. Without modifying the framework, TextGrad improves the zero-shot accuracy of GPT-4o in Google-Proof Question Answering from 51% to 55%, yields 20% relative performance gain in optimizing LeetCode-Hard coding problem solutions, improves prompts for reasoning, designs new druglike small molecules with desirable in silico binding, and designs radiation oncology treatment plans with high specificity. TextGrad lays a foundation to accelerate the development of the next-generation of AI systems.

Despite their ability to understand chemical knowledge, large language models (LLMs) remain limited in their capacity to propose novel molecules with desired functions (e.g., drug-like properties). In addition, the molecules that LLMs propose can often be challenging to make, and are almost never compatible with automated synthesis approaches. To better enable the discovery of functional small molecules, LLMs need to learn a new molecular language that is more effective in predicting properties and inherently synced with automated synthesis technology. Current molecule LLMs are limited by representing molecules based on atoms. In this paper, we argue that just like tokenizing texts into meaning-bearing (sub-)word tokens instead of characters, molecules should be tokenized at the level of functional building blocks, i.e., parts of molecules that bring unique functions and serve as effective building blocks for real-world automated laboratory synthesis. This motivates us to propose mCLM, a modular Chemical-Language Model that comprises a bilingual language model that understands both natural language descriptions of functions and molecular blocks. mCLM front-loads synthesizability considerations while improving the predicted functions of molecules in a principled manner. mCLM, with only 3B parameters, achieves improvements in synthetic accessibility relative to 7 other leading generative AI methods including GPT-5. When tested on 122 out-of-distribution medicines using only building blocks/tokens that are compatible with automated modular synthesis, mCLM outperforms all baselines in property scores and synthetic accessibility. mCLM can also reason on multiple functions and iteratively self-improve to rescue drug candidates that failed late in clinical trials ("fallen angels").

Large pretrained models such as GPT-3 have had tremendous impact on modern natural language processing by leveraging self-supervised learning to learn salient representations that can be used to readily finetune on a wide variety of downstream tasks. We investigate the possibility of transferring such advances to molecular machine learning by building a chemical foundation model, ChemBERTa-2, using the language of SMILES. While labeled data for molecular prediction tasks is typically scarce, libraries of SMILES strings are readily available. In this work, we build upon ChemBERTa by optimizing the pretraining process. We compare multi-task and self-supervised pretraining by varying hyperparameters and pretraining dataset size, up to 77M compounds from PubChem. To our knowledge, the 77M set constitutes one of the largest datasets used for molecular pretraining to date. We find that with these pretraining improvements, we are competitive with existing state-of-the-art architectures on the MoleculeNet benchmark suite. We analyze the degree to which improvements in pretraining translate to improvement on downstream tasks.

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.

Combination therapies have become the standard of care for diseases such as cancer, tuberculosis, malaria and HIV. However, the combinatorial set of available multi-drug treatments creates a challenge in identifying effective combination therapies available in a situation. To assist medical professionals in identifying beneficial drug-combinations, we construct an expert-annotated dataset for extracting information about the efficacy of drug combinations from the scientific literature. Beyond its practical utility, the dataset also presents a unique NLP challenge, as the first relation extraction dataset consisting of variable-length relations. Furthermore, the relations in this dataset predominantly require language understanding beyond the sentence level, adding to the challenge of this task. We provide a promising baseline model and identify clear areas for further improvement. We release our dataset, code, and baseline models publicly to encourage the NLP community to participate in this task.

Classifier-free guidance (CFG) has become the standard method for enhancing the quality of conditional diffusion models. However, employing CFG requires either training an unconditional model alongside the main diffusion model or modifying the training procedure by periodically inserting a null condition. There is also no clear extension of CFG to unconditional models. In this paper, we revisit the core principles of CFG and introduce a new method, independent condition guidance (ICG), which provides the benefits of CFG without the need for any special training procedures. Our approach streamlines the training process of conditional diffusion models and can also be applied during inference on any pre-trained conditional model. Additionally, by leveraging the time-step information encoded in all diffusion networks, we propose an extension of CFG, called time-step guidance (TSG), which can be applied to any diffusion model, including unconditional ones. Our guidance techniques are easy to implement and have the same sampling cost as CFG. Through extensive experiments, we demonstrate that ICG matches the performance of standard CFG across various conditional diffusion models. Moreover, we show that TSG improves generation quality in a manner similar to CFG, without relying on any conditional information.

Recent advancements in large language models (LLMs) and AI systems have led to a paradigm shift in the design and optimization of complex AI workflows. By integrating multiple components, compound AI systems have become increasingly adept at performing sophisticated tasks. However, as these systems grow in complexity, new challenges arise in optimizing not only individual components but also their interactions. While traditional optimization methods such as supervised fine-tuning (SFT) and reinforcement learning (RL) remain foundational, the rise of natural language feedback introduces promising new approaches, especially for optimizing non-differentiable systems. This paper provides a systematic review of recent progress in optimizing compound AI systems, encompassing both numerical and language-based techniques. We formalize the notion of compound AI system optimization, classify existing methods along several key dimensions, and highlight open research challenges and future directions in this rapidly evolving field. A list of surveyed papers is publicly available at https://github.com/MiuLab/AISysOpt-Survey.

Instruction following is one of the fundamental capabilities of large language models (LLMs). As the ability of LLMs is constantly improving, they have been increasingly applied to deal with complex human instructions in real-world scenarios. Therefore, how to evaluate the ability of complex instruction-following of LLMs has become a critical research problem. Existing benchmarks mainly focus on modeling different types of constraints in human instructions while neglecting the composition of different constraints, which is an indispensable constituent in complex instructions. To this end, we propose ComplexBench, a benchmark for comprehensively evaluating the ability of LLMs to follow complex instructions composed of multiple constraints. We propose a hierarchical taxonomy for complex instructions, including 4 constraint types, 19 constraint dimensions, and 4 composition types, and manually collect a high-quality dataset accordingly. To make the evaluation reliable, we augment LLM-based evaluators with rules to effectively verify whether generated texts can satisfy each constraint and composition. Furthermore, we obtain the final evaluation score based on the dependency structure determined by different composition types. ComplexBench identifies significant deficiencies in existing LLMs when dealing with complex instructions with multiple constraints composition.

We present MixtureVitae, an open-access pretraining corpus built to minimize legal risk while providing strong model performance. MixtureVitae follows a risk-mitigated sourcing strategy that combines public-domain and permissively licensed text (e.g., CC-BY/Apache) with carefully justified low-risk additions (e.g., government works and EU TDM-eligible sources), alongside targeted instruction, reasoning and synthetic data with documented provenance. We detail a transparent, multi-stage pipeline for license-aware filtering, safety and quality screening, and domain-aware mixing, and we release the dataset and curation recipes to support reproducible research. In controlled experiments using the open-sci-ref training protocol (fixed architectures at 130M/400M/1.3B/1.7B parameters; training budgets of 50B and 300B tokens), models trained on MixtureVitae consistently outperform other permissive datasets across a suite of standard benchmarks, and at the 1.7B/300B setting they surpass FineWeb-Edu and approach DCLM in the later stages of training. Performance is particularly strong on math/code and competitive on QA tasks. These results demonstrate that permissive-first, risk-mitigated data provides a practical and legally mitigated foundation for training capable LLMs, reducing reliance on indiscriminate web scraping without sacrificing competitiveness. Code: https://github.com/ontocord/mixturevitae

While many languages possess processes of joining two or more words to create compound words, previous studies have been typically limited only to languages with excessively productive compound formation (e.g., German, Dutch) and there is no public dataset containing compound and non-compound words across a large number of languages. In this work, we systematically study decompounding, the task of splitting compound words into their constituents, at a wide scale. We first address the data gap by introducing a dataset of 255k compound and non-compound words across 56 diverse languages obtained from Wiktionary. We then use this dataset to evaluate an array of Large Language Models (LLMs) on the decompounding task. We find that LLMs perform poorly, especially on words which are tokenized unfavorably by subword tokenization. We thus introduce a novel methodology to train dedicated models for decompounding. The proposed two-stage procedure relies on a fully self-supervised objective in the first stage, while the second, supervised learning stage optionally fine-tunes the model on the annotated Wiktionary data. Our self-supervised models outperform the prior best unsupervised decompounding models by 13.9% accuracy on average. Our fine-tuned models outperform all prior (language-specific) decompounding tools. Furthermore, we use our models to leverage decompounding during the creation of a subword tokenizer, which we refer to as CompoundPiece. CompoundPiece tokenizes compound words more favorably on average, leading to improved performance on decompounding over an otherwise equivalent model using SentencePiece tokenization.

The simplified molecular-input line-entry system (SMILES) is the most popular representation of chemical compounds. Therefore, many SMILES-based molecular property prediction models have been developed. In particular, transformer-based models show promising performance because the model utilizes a massive chemical dataset for self-supervised learning. However, there is no transformer-based model to overcome the inherent limitations of SMILES, which result from the generation process of SMILES. In this study, we grammatically parsed SMILES to obtain connectivity between substructures and their type, which is called the grammatical knowledge of SMILES. First, we pretrained the transformers with substructural tokens, which were parsed from SMILES. Then, we used the training strategy 'same compound model' to better understand SMILES grammar. In addition, we injected knowledge of connectivity and type into the transformer with knowledge adapters. As a result, our representation model outperformed previous compound representations for the prediction of molecular properties. Finally, we analyzed the attention of the transformer model and adapters, demonstrating that the proposed model understands the grammar of SMILES.

Modern neural networks are often trained on massive datasets that are web scraped with minimal human inspection. As a result of this insecure curation pipeline, an adversary can poison or backdoor the resulting model by uploading malicious data to the internet and waiting for a victim to scrape and train on it. Existing approaches for creating poisons and backdoors start with randomly sampled clean data, called base samples, and then modify those samples to craft poisons. However, some base samples may be significantly more amenable to poisoning than others. As a result, we may be able to craft more potent poisons by carefully choosing the base samples. In this work, we use guided diffusion to synthesize base samples from scratch that lead to significantly more potent poisons and backdoors than previous state-of-the-art attacks. Our Guided Diffusion Poisoning (GDP) base samples can be combined with any downstream poisoning or backdoor attack to boost its effectiveness. Our implementation code is publicly available at: https://github.com/hsouri/GDP .

Diffusion models deliver high quality in image synthesis but remain expensive during training and inference. Recent works have leveraged the inherent redundancy in visual content to make training more affordable by training only on a subset of visual information. While these methods were successful in providing cheaper and more effective training, sparsely trained diffusion models struggle in inference. This is due to their lacking response to Classifier-free Guidance (CFG) leading to underwhelming performance during inference. To overcome this, we propose Sparse Guidance (SG). Instead of using conditional dropout as a signal to guide diffusion models, SG uses token-level sparsity. As a result, SG preserves the high-variance of the conditional prediction better, achieving good quality and high variance outputs. Leveraging token-level sparsity at inference, SG improves fidelity at lower compute, achieving 1.58 FID on the commonly used ImageNet-256 benchmark with 25% fewer FLOPs, and yields up to 58% FLOP savings at matched baseline quality. To demonstrate the effectiveness of Sparse Guidance, we train a 2.5B text-to-image diffusion model using training time sparsity and leverage SG during inference. SG achieves improvements in composition and human preference score while increasing throughput at the same time.

We present a new financial domain large language model, InvestLM, tuned on LLaMA-65B (Touvron et al., 2023), using a carefully curated instruction dataset related to financial investment. Inspired by less-is-more-for-alignment (Zhou et al., 2023), we manually curate a small yet diverse instruction dataset, covering a wide range of financial related topics, from Chartered Financial Analyst (CFA) exam questions to SEC filings to Stackexchange quantitative finance discussions. InvestLM shows strong capabilities in understanding financial text and provides helpful responses to investment related questions. Financial experts, including hedge fund managers and research analysts, rate InvestLM's response as comparable to those of state-of-the-art commercial models (GPT-3.5, GPT-4 and Claude-2). Zero-shot evaluation on a set of financial NLP benchmarks demonstrates strong generalizability. From a research perspective, this work suggests that a high-quality domain specific LLM can be tuned using a small set of carefully curated instructions on a well-trained foundation model, which is consistent with the Superficial Alignment Hypothesis (Zhou et al., 2023). From a practical perspective, this work develops a state-of-the-art financial domain LLM with superior capability in understanding financial texts and providing helpful investment advice, potentially enhancing the work efficiency of financial professionals. We release the model parameters to the research community.

Training-free guided generation is a widely used and powerful technique that allows the end user to exert further control over the generative process of flow/diffusion models. Generally speaking, two families of techniques have emerged for solving this problem for gradient-based guidance: namely, posterior guidance (i.e., guidance via projecting the current sample to the target distribution via the target prediction model) and end-to-end guidance (i.e., guidance by performing backpropagation throughout the entire ODE solve). In this work, we show that these two seemingly separate families can actually be unified by looking at posterior guidance as a greedy strategy of end-to-end guidance. We explore the theoretical connections between these two families and provide an in-depth theoretical of these two techniques relative to the continuous ideal gradients. Motivated by this analysis we then show a method for interpolating between these two families enabling a trade-off between compute and accuracy of the guidance gradients. We then validate this work on several inverse image problems and property-guided molecular generation.

The data used to pretrain large language models has a decisive impact on a model's downstream performance, which has led to a large body of work on data selection methods that aim to automatically determine the most suitable data to use for pretraining. Existing data selection methods suffer from slow and computationally expensive processes, a problem amplified by the increasing size of models and of pretraining datasets. Data mixing, on the other hand, reduces the complexity of data selection by grouping data points together and determining sampling probabilities across entire groups. However, data mixing proportions are typically fixed before training and therefore cannot adapt to changing training dynamics. To address these limitations, we develop an efficient algorithm for Online Data Mixing (ODM) that combines elements from both data selection and data mixing. Based on multi-armed bandit algorithms, our online approach optimizes the data mixing proportions during training. Remarkably, our method trains a model that reaches the final perplexity of the next best method with 19\% fewer training iterations, and improves performance on the 5-shot MMLU benchmark by 1.9% relative accuracy, while adding negligible wall-clock time during pretraining.

Guidance in conditional diffusion generation is of great importance for sample quality and controllability. However, existing guidance schemes are to be desired. On one hand, mainstream methods such as classifier guidance and classifier-free guidance both require extra training with labeled data, which is time-consuming and unable to adapt to new conditions. On the other hand, training-free methods such as universal guidance, though more flexible, have yet to demonstrate comparable performance. In this work, through a comprehensive investigation into the design space, we show that it is possible to achieve significant performance improvements over existing guidance schemes by leveraging off-the-shelf classifiers in a training-free fashion, enjoying the best of both worlds. Employing calibration as a general guideline, we propose several pre-conditioning techniques to better exploit pretrained off-the-shelf classifiers for guiding diffusion generation. Extensive experiments on ImageNet validate our proposed method, showing that state-of-the-art diffusion models (DDPM, EDM, DiT) can be further improved (up to 20%) using off-the-shelf classifiers with barely any extra computational cost. With the proliferation of publicly available pretrained classifiers, our proposed approach has great potential and can be readily scaled up to text-to-image generation tasks. The code is available at https://github.com/AlexMaOLS/EluCD/tree/main.

Controllable image synthesis models allow creation of diverse images based on text instructions or guidance from a reference image. Recently, denoising diffusion probabilistic models have been shown to generate more realistic imagery than prior methods, and have been successfully demonstrated in unconditional and class-conditional settings. We investigate fine-grained, continuous control of this model class, and introduce a novel unified framework for semantic diffusion guidance, which allows either language or image guidance, or both. Guidance is injected into a pretrained unconditional diffusion model using the gradient of image-text or image matching scores, without re-training the diffusion model. We explore CLIP-based language guidance as well as both content and style-based image guidance in a unified framework. Our text-guided synthesis approach can be applied to datasets without associated text annotations. We conduct experiments on FFHQ and LSUN datasets, and show results on fine-grained text-guided image synthesis, synthesis of images related to a style or content reference image, and examples with both textual and image guidance.

Retrosynthetic planning aims to devise a complete multi-step synthetic route from starting materials to a target molecule. Current strategies use a decoupled approach of single-step retrosynthesis models and search algorithms, taking only the product as the input to predict the reactants for each planning step and ignoring valuable context information along the synthetic route. In this work, we propose a novel framework that utilizes context information for improved retrosynthetic planning. We view synthetic routes as reaction graphs and propose to incorporate context through three principled steps: encode molecules into embeddings, aggregate information over routes, and readout to predict reactants. Our approach is the first attempt to utilize in-context learning for retrosynthesis prediction in retrosynthetic planning. The entire framework can be efficiently optimized in an end-to-end fashion and produce more practical and accurate predictions. Comprehensive experiments demonstrate that by fusing in the context information over routes, our model significantly improves the performance of retrosynthetic planning over baselines that are not context-aware, especially for long synthetic routes. Code is available at https://github.com/SongtaoLiu0823/FusionRetro.

Researchers and scientists increasingly rely on specialized information retrieval (IR) or recommendation systems (RS) to support them in their daily research tasks. Paper recommender systems are one such tool scientists use to stay on top of the ever-increasing number of academic publications in their field. Improving research paper recommender systems is an active research field. However, less research has focused on how the interfaces of research paper recommender systems can be tailored to suit the needs of different research domains. For example, in the field of biomedicine and chemistry, researchers are not only interested in textual relevance but may also want to discover or compare the contained chemical entity information found in a paper's full text. Existing recommender systems for academic literature do not support the discovery of this non-textual, but semantically valuable, chemical entity data. We present the first implementation of a specialized chemistry paper recommender system capable of visualizing the contained chemical structures, chemical formulae, and synonyms for chemical compounds within the document's full text. We review existing tools and related research in this field before describing the implementation of our ChemVis system. With the help of chemists, we are expanding the functionality of ChemVis, and will perform an evaluation of recommendation performance and usability in future work.

The pursuit of diverse, complex, and large-scale instruction data is crucial for automatically aligning large language models (LLMs). While there are methods capable of generating synthetic instructions at scale, they either suffer from limited grounding sources, leading to a narrow distribution, or rely on trivial extensions that fail to produce meaningful trajectories in terms of complexity. In contrast, instructions that benefit efficient alignment are typically crafted with cognitive insights and grounded in real-world use cases. In this paper, we synthesize such instructions using attributed grounding, which involves 1) a top-down attribution process that grounds a selective set of real instructions to situated users, and 2) a bottom-up synthesis process that leverages web documents to first generate a situation, then a meaningful instruction. This framework allows us to harvest diverse and complex instructions at scale, utilizing the vast range of web documents. Specifically, we construct a dataset of 1 million instructions, called SynthQuestions, and demonstrate that models trained on it achieve leading performance on several common benchmarks, with improvements that continually scale with more web corpora. Data, models and codes will be available at https://github.com/Ignoramus0817/SynthQuestions.

Chemical reasoning usually involves complex, multi-step processes that demand precise calculations, where even minor errors can lead to cascading failures. Furthermore, large language models (LLMs) encounter difficulties handling domain-specific formulas, executing reasoning steps accurately, and integrating code effectively when tackling chemical reasoning tasks. To address these challenges, we present ChemAgent, a novel framework designed to improve the performance of LLMs through a dynamic, self-updating library. This library is developed by decomposing chemical tasks into sub-tasks and compiling these sub-tasks into a structured collection that can be referenced for future queries. Then, when presented with a new problem, ChemAgent retrieves and refines pertinent information from the library, which we call memory, facilitating effective task decomposition and the generation of solutions. Our method designs three types of memory and a library-enhanced reasoning component, enabling LLMs to improve over time through experience. Experimental results on four chemical reasoning datasets from SciBench demonstrate that ChemAgent achieves performance gains of up to 46% (GPT-4), significantly outperforming existing methods. Our findings suggest substantial potential for future applications, including tasks such as drug discovery and materials science. Our code can be found at https://github.com/gersteinlab/chemagent

The exploration of thermoelectric materials is challenging considering the large materials space, combined with added exponential degrees of freedom coming from doping and the diversity of synthetic pathways. Here we seek to incorporate historical data and update and refine it using experimental feedback by employing error-correction learning (ECL). We thus learn from prior datasets and then adapt the model to differences in synthesis and characterization that are otherwise difficult to parameterize. We then apply this strategy to discovering thermoelectric materials where we prioritize synthesis at temperatures < 300{\deg}C. We document a previously unreported chemical family of thermoelectric materials, PbSe:SnSb, finding that the best candidate in this chemical family, 2 wt% SnSb doped PbSe, exhibits a power factor more than 2x that of PbSe. Our investigations show that our closed-loop experimentation strategy reduces the required number of experiments to find an optimized material by as much as 3x compared to high-throughput searches powered by state-of-the-art machine learning models. We also observe that this improvement is dependent on the accuracy of prior in a manner that exhibits diminishing returns, and after a certain accuracy is reached, it is factors associated with experimental pathways that dictate the trends.

In many real-world applications, users rely on natural language instructions to guide large language models (LLMs) across a wide range of tasks. These instructions are often complex, diverse, and subject to frequent change. However, LLMs do not always attend to these instructions reliably, and users lack simple mechanisms to emphasize their importance beyond modifying prompt wording or structure. To address this, we present an inference-time method that enables users to emphasize specific parts of their prompt by steering the model's attention toward them, aligning the model's perceived importance of different prompt tokens with user intent. Unlike prior approaches that are limited to static instructions, require significant offline profiling, or rely on fixed biases, we dynamically update the proportion of model attention given to the user-specified parts--ensuring improved instruction following without performance degradation. We demonstrate that our approach improves instruction following across a variety of tasks involving multiple instructions and generalizes across models of varying scales.

In this paper, a mathematical model is developed to describe the evolution of the concentration of compounds through a gas chromatography column. The model couples mass balances and kinetic equations for all components. Both single and multiple-component cases are considered with constant or variable velocity. Non-dimensionalisation indicates the small effect of diffusion. The system where diffusion is neglected is analysed using Laplace transforms. In the multiple-component case, it is demonstrated that the competition between the compounds is negligible and the equations may be decoupled. This reduces the problem to solving a single integral equation to determine the concentration profile for all components (since they are scaled versions of each other). For a given analyte, we then only two parameters need to be fitted to the data. To verify this approach, the full governing equations are also solved numerically using the finite difference method and a global adaptive quadrature method to integrate the Laplace transformation. Comparison with the Laplace solution verifies the high degree of accuracy of the simpler Laplace form. The Laplace solution is then verified against experimental data from BTEX chromatography. This novel method, which involves solving a single equation and fitting parameters in pairs for individual components, is highly efficient. It is significantly faster and simpler than the full numerical solution and avoids the computationally expensive methods that would normally be used to fit all curves at the same time.

Chemical language models, combined with reinforcement learning (RL), have shown significant promise to efficiently traverse large chemical spaces for drug discovery. However, the performance of various RL algorithms and their best practices for practical drug discovery are still unclear. Here, starting from the principles of the REINFORCE algorithm, we investigate the effect of different components from RL theory including experience replay, hill-climbing, baselines to reduce variance, and alternative reward shaping. We propose a new regularization method more aligned to REINFORCE than current standard practices, and demonstrate how RL hyperparameters can be fine-tuned for effectiveness and efficiency. Lastly, we apply our learnings to practical drug discovery by demonstrating enhanced learning efficiency on frontier binding affinity models by using Boltz2 as a reward model. We share our RL models used in the ACEGEN repository, and hope the experiments here act as a guide to researchers applying RL to chemical language models for drug discovery.

Protein fitness optimization involves finding a protein sequence that maximizes desired quantitative properties in a combinatorially large design space of possible sequences. Recent developments in steering protein generative models (e.g diffusion models, language models) offer a promising approach. However, by and large, past studies have optimized surrogate rewards and/or utilized large amounts of labeled data for steering, making it unclear how well existing methods perform and compare to each other in real-world optimization campaigns where fitness is measured by low-throughput wet-lab assays. In this study, we explore fitness optimization using small amounts (hundreds) of labeled sequence-fitness pairs and comprehensively evaluate strategies such as classifier guidance and posterior sampling for guiding generation from different discrete diffusion models of protein sequences. We also demonstrate how guidance can be integrated into adaptive sequence selection akin to Thompson sampling in Bayesian optimization, showing that plug-and-play guidance strategies offer advantages compared to alternatives such as reinforcement learning with protein language models.

Personalizing text-to-image diffusion models is crucial for adapting the pre-trained models to specific target concepts, enabling diverse image generation. However, fine-tuning with few images introduces an inherent trade-off between aligning with the target distribution (e.g., subject fidelity) and preserving the broad knowledge of the original model (e.g., text editability). Existing sampling guidance methods, such as classifier-free guidance (CFG) and autoguidance (AG), fail to effectively guide the output toward well-balanced space: CFG restricts the adaptation to the target distribution, while AG compromises text alignment. To address these limitations, we propose personalization guidance, a simple yet effective method leveraging an unlearned weak model conditioned on a null text prompt. Moreover, our method dynamically controls the extent of unlearning in a weak model through weight interpolation between pre-trained and fine-tuned models during inference. Unlike existing guidance methods, which depend solely on guidance scales, our method explicitly steers the outputs toward a balanced latent space without additional computational overhead. Experimental results demonstrate that our proposed guidance can improve text alignment and target distribution fidelity, integrating seamlessly with various fine-tuning strategies.

This paper studies the impact of artificial intelligence on innovation, exploiting the randomized introduction of a new materials discovery technology to 1,018 scientists in the R&D lab of a large U.S. firm. AI-assisted researchers discover 44% more materials, resulting in a 39% increase in patent filings and a 17% rise in downstream product innovation. These compounds possess more novel chemical structures and lead to more radical inventions. However, the technology has strikingly disparate effects across the productivity distribution: while the bottom third of scientists see little benefit, the output of top researchers nearly doubles. Investigating the mechanisms behind these results, I show that AI automates 57% of "idea-generation" tasks, reallocating researchers to the new task of evaluating model-produced candidate materials. Top scientists leverage their domain knowledge to prioritize promising AI suggestions, while others waste significant resources testing false positives. Together, these findings demonstrate the potential of AI-augmented research and highlight the complementarity between algorithms and expertise in the innovative process. Survey evidence reveals that these gains come at a cost, however, as 82% of scientists report reduced satisfaction with their work due to decreased creativity and skill underutilization.

CONSPECTUS: Two-dimensional (2D) compound materials are promising materials for use in electronics, optoelectronics, flexible devices, etc. because they are ultrathin and cover a wide range of properties. Among all methods to prepare 2D materials, chemical vapor deposition (CVD) is promising because it produces materials with a high quality and reasonable cost. So far, much efforts have been made to produce 2D compound materials with large domain size, controllable number of layers, fast-growth rate, and high quality features, etc. However, due to the complicated growth mechanism like sublimation and diffusion processes of multiple precursors, maintaining the controllability, repeatability, and high quality of CVD grown 2D binary and ternary materials is still a big challenge, which prevents their widespread use. Here, taking 2D transition metal dichalcogenides (TMDCs) as examples, we review current progress and highlight some promising growth strategies for the growth of 2D compound materials. The key technology issues which affect the CVD process, including non-metal precursor, metal precursor, substrate engineering, temperature, and gas flow, are discussed. Also, methods in improving the quality of CVD-grown 2D materials and current understanding on their growth mechanism are highlighted. Finally, challenges and opportunities in this field are proposed. We believe this review will guide the future design of controllable CVD systems for the growth of 2D compound materials with good controllability and high quality, laying the foundations for their potential applications.

Instruction-following is a fundamental capability of language models, requiring the model to recognize even the most subtle requirements in the instructions and accurately reflect them in its output. Such an ability is well-suited for and often optimized by preference learning. However, existing methods often directly sample multiple independent responses from the model when creating preference pairs. Such practice can introduce content variations irrelevant to whether the instruction is precisely followed (e.g., different expressions about the same semantic), interfering with the goal of teaching models to recognize the key differences that lead to improved instruction following. In light of this, we introduce SPaR, a self-play framework integrating tree-search self-refinement to yield valid and comparable preference pairs free from distractions. By playing against itself, an LLM employs a tree-search strategy to refine its previous responses with respect to the instruction while minimizing unnecessary variations. Our experiments show that a LLaMA3-8B model, trained over three iterations guided by SPaR, surpasses GPT-4-Turbo on the IFEval benchmark without losing general capabilities. Furthermore, SPaR demonstrates promising scalability and transferability, greatly enhancing models like GLM-4-9B and LLaMA3-70B. We also identify how inference scaling in tree search would impact model performance. Our code and data are publicly available at https://github.com/thu-coai/SPaR.

Recent advances in diffusion models have shown remarkable potential in the conditional generation of novel molecules. These models can be guided in two ways: (i) explicitly, through additional features representing the condition, or (ii) implicitly, using a property predictor. However, training property predictors or conditional diffusion models requires an abundance of labeled data and is inherently challenging in real-world applications. We propose a novel approach that attenuates the limitations of acquiring large labeled datasets by leveraging domain knowledge from quantum chemistry as a non-differentiable oracle to guide an unconditional diffusion model. Instead of relying on neural networks, the oracle provides accurate guidance in the form of estimated gradients, allowing the diffusion process to sample from a conditional distribution specified by quantum chemistry. We show that this results in more precise conditional generation of novel and stable molecular structures. Our experiments demonstrate that our method: (1) significantly reduces atomic forces, enhancing the validity of generated molecules when used for stability optimization; (2) is compatible with both explicit and implicit guidance in diffusion models, enabling joint optimization of molecular properties and stability; and (3) generalizes effectively to molecular optimization tasks beyond stability optimization.

In line with recent advances in neural drug design and sensitivity prediction, we propose a novel architecture for interpretable prediction of anticancer compound sensitivity using a multimodal attention-based convolutional encoder. Our model is based on the three key pillars of drug sensitivity: compounds' structure in the form of a SMILES sequence, gene expression profiles of tumors and prior knowledge on intracellular interactions from protein-protein interaction networks. We demonstrate that our multiscale convolutional attention-based (MCA) encoder significantly outperforms a baseline model trained on Morgan fingerprints, a selection of encoders based on SMILES as well as previously reported state of the art for multimodal drug sensitivity prediction (R2 = 0.86 and RMSE = 0.89). Moreover, the explainability of our approach is demonstrated by a thorough analysis of the attention weights. We show that the attended genes significantly enrich apoptotic processes and that the drug attention is strongly correlated with a standard chemical structure similarity index. Finally, we report a case study of two receptor tyrosine kinase (RTK) inhibitors acting on a leukemia cell line, showcasing the ability of the model to focus on informative genes and submolecular regions of the two compounds. The demonstrated generalizability and the interpretability of our model testify its potential for in-silico prediction of anticancer compound efficacy on unseen cancer cells, positioning it as a valid solution for the development of personalized therapies as well as for the evaluation of candidate compounds in de novo drug design.

In this work, we introduce ChemBFN, a language model that handles chemistry tasks based on Bayesian flow networks working on discrete data. A new accuracy schedule is proposed to improve the sampling quality by significantly reducing the reconstruction loss. We show evidence that our method is appropriate for generating molecules with satisfied diversity even when a smaller number of sampling steps is used. A classifier-free guidance method is adapted for conditional generation. It is also worthwhile to point out that after generative training, our model can be fine-tuned on regression and classification tasks with the state-of-the-art performance, which opens the gate of building all-in-one models in a single module style. Our model has been open sourced at https://github.com/Augus1999/bayesian-flow-network-for-chemistry.

Large Language Models(LLMs) have demonstrated remarkable performance across various domains, yet their capabilities in molecular reasoning remain insufficiently explored. Current approaches tend to rely heavily on general-purpose prompting, which lacks domain-specific molecular semantics, while those that use fine-tuning strategies often face challenges with interpretability and reasoning depth. To address these issues, we introduce MolReasoner, a two-stage framework designed to transition LLMs from memorization towards chemical reasoning. First, we propose Mol-SFT, which initializes the model's reasoning abilities via synthetic Chain-of-Thought(CoT) samples generated by GPT-4o and verified for chemical accuracy. Subsequently, Mol-RL applies reinforcement learning with specialized reward functions designed explicitly to align chemical structures with linguistic descriptions, thereby enhancing molecular reasoning capabilities. Our approach notably enhances interpretability, improving the model 's molecular understanding and enabling better generalization. Extensive experiments demonstrate that MolReasoner outperforms existing methods, and marking a significant shift from memorization-based outputs to robust chemical reasoning.

Language model performance depends on identifying the optimal mixture of data groups to train on (e.g., law, code, math). Prior work has proposed a diverse set of methods to efficiently learn mixture proportions, ranging from fitting regression models over training runs to dynamically updating proportions throughout training. Surprisingly, we find that no existing method consistently outperforms a simple stratified sampling baseline in terms of average test perplexity. To understand this inconsistency, we unify existing methods into a standard framework, showing they are equivalent to solving a common optimization problem: minimize average loss subject to a method-specific mixing law -- an implicit assumption on the relationship between loss and mixture proportions. This framework suggests that measuring the fidelity of a method's mixing law can offer insights into its performance. Empirically, we find that existing methods set their mixing law parameters inaccurately, resulting in the inconsistent mixing performance we observe. Using this insight, we derive a new online method named Aioli, which directly estimates the mixing law parameters throughout training and uses them to dynamically adjust proportions. Aioli outperforms stratified sampling on 6 out of 6 datasets by an average of 0.27 test perplexity points, whereas existing methods fail to consistently beat stratified sampling, doing up to 6.9 points worse. Moreover, in a practical setting where proportions are learned on shorter runs due to computational constraints, Aioli can dynamically adjust these proportions over the full training run, consistently improving performance over existing methods by up to 12.012 test perplexity points.

The meaning of complex phrases in natural language is composed of their individual components. The task of compositional generalization evaluates a model's ability to understand new combinations of components. Previous studies trained smaller, task-specific models, which exhibited poor generalization. While large language models (LLMs) exhibit impressive generalization abilities on many tasks through in-context learning (ICL), their potential for compositional generalization remains unexplored. In this paper, we first empirically investigate prevailing ICL methods in compositional generalization. We find that they struggle with complex compositional questions due to cumulative errors in long reasoning steps and intricate logic required for tool-making. Consequently, we propose a human-guided tool manipulation framework (HTM) that generates tools for sub-questions and integrates multiple tools. Our method enhances the effectiveness of tool creation and usage with minimal human effort. Experiments show that our method achieves state-of-the-art performance on two compositional generalization benchmarks and outperforms existing methods on the most challenging test split by 70%.

We introduce TESS 2, a general instruction-following diffusion language model that outperforms contemporary instruction-tuned diffusion models, as well as matches and sometimes exceeds strong autoregressive (AR) models. We train TESS 2 by first adapting a strong AR model via continued pretraining with the usual cross-entropy as diffusion loss, and then performing further instruction tuning. We find that adaptation training as well as the choice of the base model is crucial for training good instruction-following diffusion models. We further propose reward guidance, a novel and modular inference-time guidance procedure to align model outputs without needing to train the underlying model. Finally, we show that TESS 2 further improves with increased inference-time compute, highlighting the utility of diffusion LMs in having fine-grained controllability over the amount of compute used at inference time. Code and models are available at https://github.com/hamishivi/tess-2.

We present Readout Guidance, a method for controlling text-to-image diffusion models with learned signals. Readout Guidance uses readout heads, lightweight networks trained to extract signals from the features of a pre-trained, frozen diffusion model at every timestep. These readouts can encode single-image properties, such as pose, depth, and edges; or higher-order properties that relate multiple images, such as correspondence and appearance similarity. Furthermore, by comparing the readout estimates to a user-defined target, and back-propagating the gradient through the readout head, these estimates can be used to guide the sampling process. Compared to prior methods for conditional generation, Readout Guidance requires significantly fewer added parameters and training samples, and offers a convenient and simple recipe for reproducing different forms of conditional control under a single framework, with a single architecture and sampling procedure. We showcase these benefits in the applications of drag-based manipulation, identity-consistent generation, and spatially aligned control. Project page: https://readout-guidance.github.io.

Computer-aided synthesis planning (CASP) has long been envisioned as a complementary tool for synthetic chemists. However, existing frameworks often lack mechanisms to allow interaction with human experts, limiting their ability to integrate chemists' insights. In this work, we introduce Synthelite, a synthesis planning framework that uses large language models (LLMs) to directly propose retrosynthetic transformations. Synthelite can generate end-to-end synthesis routes by harnessing the intrinsic chemical knowledge and reasoning capabilities of LLMs, while allowing expert intervention through natural language prompts. Our experiments demonstrate that Synthelite can flexibly adapt its planning trajectory to diverse user-specified constraints, achieving up to 95\% success rates in both strategy-constrained and starting-material-constrained synthesis tasks. Additionally, Synthelite exhibits the ability to account for chemical feasibility during route design. We envision Synthelite to be both a useful tool and a step toward a paradigm where LLMs are the central orchestrators of synthesis planning.

Knowledge of mixtures' phase equilibria is crucial in nature and technical chemistry. Phase equilibria calculations of mixtures require activity coefficients. However, experimental data on activity coefficients is often limited due to high cost of experiments. For an accurate and efficient prediction of activity coefficients, machine learning approaches have been recently developed. However, current machine learning approaches still extrapolate poorly for activity coefficients of unknown molecules. In this work, we introduce the SMILES-to-Properties-Transformer (SPT), a natural language processing network to predict binary limiting activity coefficients from SMILES codes. To overcome the limitations of available experimental data, we initially train our network on a large dataset of synthetic data sampled from COSMO-RS (10 Million data points) and then fine-tune the model on experimental data (20 870 data points). This training strategy enables SPT to accurately predict limiting activity coefficients even for unknown molecules, cutting the mean prediction error in half compared to state-of-the-art models for activity coefficient predictions such as COSMO-RS, UNIFAC, and improving on recent machine learning approaches.

The rapid evolution of artificial intelligence in drug discovery encounters challenges with generalization and extensive training, yet Large Language Models (LLMs) offer promise in reshaping interactions with complex molecular data. Our novel contribution, InstructMol, a multi-modal LLM, effectively aligns molecular structures with natural language via an instruction-tuning approach, utilizing a two-stage training strategy that adeptly combines limited domain-specific data with molecular and textual information. InstructMol showcases substantial performance improvements in drug discovery-related molecular tasks, surpassing leading LLMs and significantly reducing the gap with specialized models, thereby establishing a robust foundation for a versatile and dependable drug discovery assistant.

Pretraining data of large language models composes multiple domains (e.g., web texts, academic papers, codes), whose mixture proportions crucially impact the competence of outcome models. While existing endeavors rely on heuristics or qualitative strategies to tune the proportions, we discover the quantitative predictability of model performance regarding the mixture proportions in function forms, which we refer to as the data mixing laws. Fitting such functions on sample mixtures unveils model performance on unseen mixtures before actual runs, thus guiding the selection of an ideal data mixture. Furthermore, we propose nested use of the scaling laws of training steps, model sizes, and our data mixing law to enable predicting the performance of large models trained on massive data under various mixtures with only small-scale training. Moreover, experimental results verify that our method effectively optimizes the training mixture of a 1B model trained for 100B tokens in RedPajama, reaching a performance comparable to the one trained for 48% more steps on the default mixture. Extending the application of data mixing laws to continual training accurately predicts the critical mixture proportion that avoids catastrophic forgetting and outlooks the potential for dynamic data schedules

Fine-tuning large language models (LLMs) with a collection of large and diverse instructions has improved the model's generalization to different tasks, even for unseen tasks. However, most existing instruction datasets include only single instructions, and they struggle to follow complex instructions composed of multiple subtasks (Wang et al., 2023a). In this work, we propose a novel concept of compositional instructions called chain-of-instructions (CoI), where the output of one instruction becomes an input for the next like a chain. Unlike the conventional practice of solving single instruction tasks, our proposed method encourages a model to solve each subtask step by step until the final answer is reached. CoI-tuning (i.e., fine-tuning with CoI instructions) improves the model's ability to handle instructions composed of multiple subtasks. CoI-tuned models also outperformed baseline models on multilingual summarization, demonstrating the generalizability of CoI models on unseen composite downstream tasks.

Large Language Models (LLMs) and agent-based systems often struggle with compositional generalization due to a data bottleneck in which complex skill combinations follow a long-tailed, power-law distribution, limiting both instruction-following performance and generalization in agent-centric tasks. To address this challenge, we propose STEPS, a Skill Taxonomy guided Entropy-based Post-training data Synthesis framework for generating compositionally challenging data. STEPS explicitly targets compositional generalization by uncovering latent relationships among skills and organizing them into an interpretable, hierarchical skill taxonomy using structural information theory. Building on this taxonomy, we formulate data synthesis as a constrained information maximization problem, selecting skill combinations that maximize marginal structural information within the hierarchy while preserving semantic coherence. Experiments on challenging instruction-following benchmarks show that STEPS outperforms existing data synthesis baselines, while also yielding improved compositional generalization in downstream agent-based evaluations.

We present a novel approach for the prediction of anticancer compound sensitivity by means of multi-modal attention-based neural networks (PaccMann). In our approach, we integrate three key pillars of drug sensitivity, namely, the molecular structure of compounds, transcriptomic profiles of cancer cells as well as prior knowledge about interactions among proteins within cells. Our models ingest a drug-cell pair consisting of SMILES encoding of a compound and the gene expression profile of a cancer cell and predicts an IC50 sensitivity value. Gene expression profiles are encoded using an attention-based encoding mechanism that assigns high weights to the most informative genes. We present and study three encoders for SMILES string of compounds: 1) bidirectional recurrent 2) convolutional 3) attention-based encoders. We compare our devised models against a baseline model that ingests engineered fingerprints to represent the molecular structure. We demonstrate that using our attention-based encoders, we can surpass the baseline model. The use of attention-based encoders enhance interpretability and enable us to identify genes, bonds and atoms that were used by the network to make a prediction.

Classifier-free guidance (CFG) has become an essential component of modern diffusion models to enhance both generation quality and alignment with input conditions. However, CFG requires specific training procedures and is limited to conditional generation. To address these limitations, we propose Token Perturbation Guidance (TPG), a novel method that applies perturbation matrices directly to intermediate token representations within the diffusion network. TPG employs a norm-preserving shuffling operation to provide effective and stable guidance signals that improve generation quality without architectural changes. As a result, TPG is training-free and agnostic to input conditions, making it readily applicable to both conditional and unconditional generation. We further analyze the guidance term provided by TPG and show that its effect on sampling more closely resembles CFG compared to existing training-free guidance techniques. Extensive experiments on SDXL and Stable Diffusion 2.1 show that TPG achieves nearly a 2times improvement in FID for unconditional generation over the SDXL baseline, while closely matching CFG in prompt alignment. These results establish TPG as a general, condition-agnostic guidance method that brings CFG-like benefits to a broader class of diffusion models. The code is available at https://github.com/TaatiTeam/Token-Perturbation-Guidance

Diffusion models have shown impressive results in generating high-quality conditional samples using guidance techniques such as Classifier-Free Guidance (CFG). However, existing methods often require additional training or neural function evaluations (NFEs), making them incompatible with guidance-distilled models. Also, they rely on heuristic approaches that need identifying target layers. In this work, we propose a novel and efficient method, termed PLADIS, which boosts pre-trained models (U-Net/Transformer) by leveraging sparse attention. Specifically, we extrapolate query-key correlations using softmax and its sparse counterpart in the cross-attention layer during inference, without requiring extra training or NFEs. By leveraging the noise robustness of sparse attention, our PLADIS unleashes the latent potential of text-to-image diffusion models, enabling them to excel in areas where they once struggled with newfound effectiveness. It integrates seamlessly with guidance techniques, including guidance-distilled models. Extensive experiments show notable improvements in text alignment and human preference, offering a highly efficient and universally applicable solution.

Diffusion models have demonstrated superior performance across various generative tasks including images, videos, and audio. However, they encounter difficulties in directly generating high-resolution samples. Previously proposed solutions to this issue involve modifying the architecture, further training, or partitioning the sampling process into multiple stages. These methods have the limitation of not being able to directly utilize pre-trained models as-is, requiring additional work. In this paper, we introduce upsample guidance, a technique that adapts pretrained diffusion model (e.g., 512^2) to generate higher-resolution images (e.g., 1536^2) by adding only a single term in the sampling process. Remarkably, this technique does not necessitate any additional training or relying on external models. We demonstrate that upsample guidance can be applied to various models, such as pixel-space, latent space, and video diffusion models. We also observed that the proper selection of guidance scale can improve image quality, fidelity, and prompt alignment.

Recent diffusion models achieve the state-of-the-art performance in image generation, but often suffer from semantic inconsistencies or hallucinations. While various inference-time guidance methods can enhance generation, they often operate indirectly by relying on external signals or architectural modifications, which introduces additional computational overhead. In this paper, we propose Tangential Amplifying Guidance (TAG), a more efficient and direct guidance method that operates solely on trajectory signals without modifying the underlying diffusion model. TAG leverages an intermediate sample as a projection basis and amplifies the tangential components of the estimated scores with respect to this basis to correct the sampling trajectory. We formalize this guidance process by leveraging a first-order Taylor expansion, which demonstrates that amplifying the tangential component steers the state toward higher-probability regions, thereby reducing inconsistencies and enhancing sample quality. TAG is a plug-and-play, architecture-agnostic module that improves diffusion sampling fidelity with minimal computational addition, offering a new perspective on diffusion guidance.

Generative models have demonstrated substantial promise in Natural Language Processing (NLP) and have found application in designing molecules, as seen in General Pretrained Transformer (GPT) models. In our efforts to develop such a tool for exploring the organic chemical space in search of potentially electro-active compounds, we present "LLamol", a single novel generative transformer model based on the LLama 2 architecture, which was trained on a 13M superset of organic compounds drawn from diverse public sources. To allow for a maximum flexibility in usage and robustness in view of potentially incomplete data, we introduce "Stochastic Context Learning" as a new training procedure. We demonstrate that the resulting model adeptly handles single- and multi-conditional organic molecule generation with up to four conditions, yet more are possible. The model generates valid molecular structures in SMILES notation while flexibly incorporating three numerical and/or one token sequence into the generative process, just as requested. The generated compounds are very satisfactory in all scenarios tested. In detail, we showcase the model's capability to utilize token sequences for conditioning, either individually or in combination with numerical properties, making LLamol a potent tool for de novo molecule design, easily expandable with new properties.

Large-scale pre-training methodologies for chemical language models represent a breakthrough in cheminformatics. These methods excel in tasks such as property prediction and molecule generation by learning contextualized representations of input tokens through self-supervised learning on large unlabeled corpora. Typically, this involves pre-training on unlabeled data followed by fine-tuning on specific tasks, reducing dependence on annotated datasets and broadening chemical language representation understanding. This paper introduces a large encoder-decoder chemical foundation models pre-trained on a curated dataset of 91 million SMILES samples sourced from PubChem, which is equivalent to 4 billion of molecular tokens. The proposed foundation model supports different complex tasks, including quantum property prediction, and offer flexibility with two main variants (289M and 8times289M). Our experiments across multiple benchmark datasets validate the capacity of the proposed model in providing state-of-the-art results for different tasks. We also provide a preliminary assessment of the compositionality of the embedding space as a prerequisite for the reasoning tasks. We demonstrate that the produced latent space is separable compared to the state-of-the-art with few-shot learning capabilities.

Instruction-following is essential for aligning large language models (LLMs) with user intent. While recent reasoning-oriented models exhibit impressive performance on complex mathematical problems, their ability to adhere to natural language instructions remains underexplored. In this work, we introduce MathIF, a dedicated benchmark for evaluating instruction-following in mathematical reasoning tasks. Our empirical analysis reveals a consistent tension between scaling up reasoning capacity and maintaining controllability, as models that reason more effectively often struggle to comply with user directives. We find that models tuned on distilled long chains-of-thought or trained with reasoning-oriented reinforcement learning often degrade in instruction adherence, especially when generation length increases. Furthermore, we show that even simple interventions can partially recover obedience, though at the cost of reasoning performance. These findings highlight a fundamental tension in current LLM training paradigms and motivate the need for more instruction-aware reasoning models. We release the code and data at https://github.com/TingchenFu/MathIF.

We consider the problem of eliciting compositional generalization capabilities in large language models (LLMs) with a novel type of prompting strategy. Compositional generalization empowers the LLMs to solve problems that are harder than the ones they have seen (i.e., easy-to-hard generalization), which is a critical reasoning capability of human-like intelligence. However, even the current state-of-the-art LLMs still struggle with this form of reasoning. To bridge this gap, we propose skills-in-context (SKiC) prompting, which instructs LLMs how to compose basic skills to resolve more complex problems. We find that it is crucial to demonstrate both the skills and the compositional examples within the same prompting context. With as few as two examplars, our SKiC prompting initiates strong synergies between skills and their composition capabilities. Notably, it empowers LLMs to solve unseen problems that require innovative skill compositions, achieving near-perfect generalization on a broad range of challenging compositionality tasks. Intriguingly, SKiC prompting unlocks the latent potential of LLMs, enabling them to leverage pre-existing internal skills acquired during earlier pre-training stages, even when these skills are not explicitly presented in the prompting context. This results in the capability of LLMs to solve unseen complex problems by activating and composing internal competencies. With such prominent features, SKiC prompting is able to achieve state-of-the-art performance on challenging mathematical reasoning benchmarks (e.g., MATH).

Finding new drugs is getting harder and harder. One of the hopes of drug discovery is to use machine learning models to predict molecular properties. That is why models for molecular property prediction are being developed and tested on benchmarks such as MoleculeNet. However, existing benchmarks are unrealistic and are too different from applying the models in practice. We have created a new practical Lo-Hi benchmark consisting of two tasks: Lead Optimization (Lo) and Hit Identification (Hi), corresponding to the real drug discovery process. For the Hi task, we designed a novel molecular splitting algorithm that solves the Balanced Vertex Minimum k-Cut problem. We tested state-of-the-art and classic ML models, revealing which works better under practical settings. We analyzed modern benchmarks and showed that they are unrealistic and overoptimistic. Review: https://openreview.net/forum?id=H2Yb28qGLV Lo-Hi benchmark: https://github.com/SteshinSS/lohi_neurips2023 Lo-Hi splitter library: https://github.com/SteshinSS/lohi_splitter

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.

Chemistry plays a crucial role in many domains, such as drug discovery and material science. While large language models (LLMs) such as GPT-4 exhibit remarkable capabilities on natural language processing tasks, existing work shows their performance on chemistry tasks is discouragingly low. In this paper, however, we demonstrate that our developed LLMs can achieve very strong results on a comprehensive set of chemistry tasks, outperforming the most advanced GPT-4 across all the tasks by a substantial margin and approaching the SoTA task-specific models. The key to our success is a large-scale, comprehensive, high-quality dataset for instruction tuning named SMolInstruct. It contains 14 meticulously selected chemistry tasks and over three million high-quality samples, laying a solid foundation for training and evaluating LLMs for chemistry. Based on SMolInstruct, we fine-tune a set of open-source LLMs, among which, we find that Mistral serves as the best base model for chemistry tasks. We further conduct analysis on the impact of trainable parameters, providing insights for future research.

In recent years, Large Language Models (LLMs) have achieved significant success in natural language processing (NLP) and various interdisciplinary areas. However, applying LLMs to chemistry is a complex task that requires specialized domain knowledge. This paper provides a thorough exploration of the nuanced methodologies employed in integrating LLMs into the field of chemistry, delving into the complexities and innovations at this interdisciplinary juncture. Specifically, our analysis begins with examining how molecular information is fed into LLMs through various representation and tokenization methods. We then categorize chemical LLMs into three distinct groups based on the domain and modality of their input data, and discuss approaches for integrating these inputs for LLMs. Furthermore, this paper delves into the pretraining objectives with adaptations to chemical LLMs. After that, we explore the diverse applications of LLMs in chemistry, including novel paradigms for their application in chemistry tasks. Finally, we identify promising research directions, including further integration with chemical knowledge, advancements in continual learning, and improvements in model interpretability, paving the way for groundbreaking developments in the field.

The diffusion model presents a powerful ability to capture the entire (conditional) data distribution. However, due to the lack of sufficient training and data to learn to cover low-probability areas, the model will be penalized for failing to generate high-quality images corresponding to these areas. To achieve better generation quality, guidance strategies such as classifier free guidance (CFG) can guide the samples to the high-probability areas during the sampling stage. However, the standard CFG often leads to over-simplified or distorted samples. On the other hand, the alternative line of guiding diffusion model with its bad version is limited by carefully designed degradation strategies, extra training and additional sampling steps. In this paper, we proposed a simple yet effective strategy Internal Guidance (IG), which introduces an auxiliary supervision on the intermediate layer during training process and extrapolates the intermediate and deep layer's outputs to obtain generative results during sampling process. This simple strategy yields significant improvements in both training efficiency and generation quality on various baselines. On ImageNet 256x256, SiT-XL/2+IG achieves FID=5.31 and FID=1.75 at 80 and 800 epochs. More impressively, LightningDiT-XL/1+IG achieves FID=1.34 which achieves a large margin between all of these methods. Combined with CFG, LightningDiT-XL/1+IG achieves the current state-of-the-art FID of 1.19.

Tunnelling reactions of molecules embedded on cryogenic noble-gas matrices are being used in fundamental studies of how reactivity varies with the nature of the supposedly inert matrix as well as pointers to the chemistry occurring in the interstellar medium on ice-grains. To these ends we present chemical kinetic rate constants for the cis to trans isomerisation of seleno-, thio- and monomeric formic acids and that of their three dimeric species, based on multidimensional calculations in the gas-phase, from 10~K to 300~K as a guide to the matrix reactions.

Retrosynthesis planning, essential in organic synthesis and drug discovery, has greatly benefited from recent AI-driven advancements. Nevertheless, existing methods frequently face limitations in both applicability and explainability. Traditional graph-based and sequence-to-sequence models often lack generalized chemical knowledge, leading to predictions that are neither consistently accurate nor easily explainable. To address these challenges, we introduce RetroDFM-R, a reasoning-based large language model (LLM) designed specifically for chemical retrosynthesis. Leveraging large-scale reinforcement learning guided by chemically verifiable rewards, RetroDFM-R significantly enhances prediction accuracy and explainability. Comprehensive evaluations demonstrate that RetroDFM-R significantly outperforms state-of-the-art methods, achieving a top-1 accuracy of 65.0% on the USPTO-50K benchmark. Double-blind human assessments further validate the chemical plausibility and practical utility of RetroDFM-R's predictions. RetroDFM-R also accurately predicts multistep retrosynthetic routes reported in the literature for both real-world drug molecules and perovskite materials. Crucially, the model's explicit reasoning process provides human-interpretable insights, thereby enhancing trust and practical value in real-world retrosynthesis applications.

While score-based generative models are the model of choice across diverse domains, there are limited tools available for controlling inference-time behavior in a principled manner, e.g. for composing multiple pretrained models. Existing classifier-free guidance methods use a simple heuristic to mix conditional and unconditional scores to approximately sample from conditional distributions. However, such methods do not approximate the intermediate distributions, necessitating additional 'corrector' steps. In this work, we provide an efficient and principled method for sampling from a sequence of annealed, geometric-averaged, or product distributions derived from pretrained score-based models. We derive a weighted simulation scheme which we call Feynman-Kac Correctors (FKCs) based on the celebrated Feynman-Kac formula by carefully accounting for terms in the appropriate partial differential equations (PDEs). To simulate these PDEs, we propose Sequential Monte Carlo (SMC) resampling algorithms that leverage inference-time scaling to improve sampling quality. We empirically demonstrate the utility of our methods by proposing amortized sampling via inference-time temperature annealing, improving multi-objective molecule generation using pretrained models, and improving classifier-free guidance for text-to-image generation. Our code is available at https://github.com/martaskrt/fkc-diffusion.

Large language models (LLMs) have gained widespread interest due to their ability to process human language and perform tasks on which they have not been explicitly trained. This is relevant for the chemical sciences, which face the problem of small and diverse datasets that are frequently in the form of text. LLMs have shown promise in addressing these issues and are increasingly being harnessed to predict chemical properties, optimize reactions, and even design and conduct experiments autonomously. However, we still have only a very limited systematic understanding of the chemical reasoning capabilities of LLMs, which would be required to improve models and mitigate potential harms. Here, we introduce "ChemBench," an automated framework designed to rigorously evaluate the chemical knowledge and reasoning abilities of state-of-the-art LLMs against the expertise of human chemists. We curated more than 7,000 question-answer pairs for a wide array of subfields of the chemical sciences, evaluated leading open and closed-source LLMs, and found that the best models outperformed the best human chemists in our study on average. The models, however, struggle with some chemical reasoning tasks that are easy for human experts and provide overconfident, misleading predictions, such as about chemicals' safety profiles. These findings underscore the dual reality that, although LLMs demonstrate remarkable proficiency in chemical tasks, further research is critical to enhancing their safety and utility in chemical sciences. Our findings also indicate a need for adaptations to chemistry curricula and highlight the importance of continuing to develop evaluation frameworks to improve safe and useful LLMs.

General-purpose large language models (LLMs) that rely on in-context learning do not reliably deliver the scientific understanding and performance required for drug discovery tasks. Simply increasing model size or introducing reasoning tokens does not yield significant performance gains. To address this gap, we introduce the MMAI Gym for Science, a one-stop shop molecular data formats and modalities as well as task-specific reasoning, training, and benchmarking recipes designed to teach foundation models the 'language of molecules' in order to solve practical drug discovery problems. We use MMAI Gym to train an efficient Liquid Foundation Model (LFM) for these applications, demonstrating that smaller, purpose-trained foundation models can outperform substantially larger general-purpose or specialist models on molecular benchmarks. Across essential drug discovery tasks - including molecular optimization, ADMET property prediction, retrosynthesis, drug-target activity prediction, and functional group reasoning - the resulting model achieves near specialist-level performance and, in the majority of settings, surpasses larger models, while remaining more efficient and broadly applicable in the domain.

Classifier guidance -- using the gradients of an image classifier to steer the generations of a diffusion model -- has the potential to dramatically expand the creative control over image generation and editing. However, currently classifier guidance requires either training new noise-aware models to obtain accurate gradients or using a one-step denoising approximation of the final generation, which leads to misaligned gradients and sub-optimal control. We highlight this approximation's shortcomings and propose a novel guidance method: Direct Optimization of Diffusion Latents (DOODL), which enables plug-and-play guidance by optimizing diffusion latents w.r.t. the gradients of a pre-trained classifier on the true generated pixels, using an invertible diffusion process to achieve memory-efficient backpropagation. Showcasing the potential of more precise guidance, DOODL outperforms one-step classifier guidance on computational and human evaluation metrics across different forms of guidance: using CLIP guidance to improve generations of complex prompts from DrawBench, using fine-grained visual classifiers to expand the vocabulary of Stable Diffusion, enabling image-conditioned generation with a CLIP visual encoder, and improving image aesthetics using an aesthetic scoring network. Code at https://github.com/salesforce/DOODL.

Retrosynthesis, which aims to find a route to synthesize a target molecule from commercially available starting materials, is a critical task in drug discovery and materials design. Recently, the combination of ML-based single-step reaction predictors with multi-step planners has led to promising results. However, the single-step predictors are mostly trained offline to optimize the single-step accuracy, without considering complete routes. Here, we leverage reinforcement learning (RL) to improve the single-step predictor, by using a tree-shaped MDP to optimize complete routes. Specifically, we propose a novel online training algorithm, called Planning with Dual Value Networks (PDVN), which alternates between the planning phase and updating phase. In PDVN, we construct two separate value networks to predict the synthesizability and cost of molecules, respectively. To maintain the single-step accuracy, we design a two-branch network structure for the single-step predictor. On the widely-used USPTO dataset, our PDVN algorithm improves the search success rate of existing multi-step planners (e.g., increasing the success rate from 85.79% to 98.95% for Retro*, and reducing the number of model calls by half while solving 99.47% molecules for RetroGraph). Additionally, PDVN helps find shorter synthesis routes (e.g., reducing the average route length from 5.76 to 4.83 for Retro*, and from 5.63 to 4.78 for RetroGraph).

Given an unconditional generative model and a predictor for a target property (e.g., a classifier), the goal of training-free guidance is to generate samples with desirable target properties without additional training. As a highly efficient technique for steering generative models toward flexible outcomes, training-free guidance has gained increasing attention in diffusion models. However, existing methods only handle data in continuous spaces, while many scientific applications involve both continuous and discrete data (referred to as multimodality). Another emerging trend is the growing use of the simple and general flow matching framework in building generative foundation models, where guided generation remains under-explored. To address this, we introduce TFG-Flow, a novel training-free guidance method for multimodal generative flow. TFG-Flow addresses the curse-of-dimensionality while maintaining the property of unbiased sampling in guiding discrete variables. We validate TFG-Flow on four molecular design tasks and show that TFG-Flow has great potential in drug design by generating molecules with desired properties.

Large Language Models (LLMs) have shown promise in assisting molecular property prediction tasks but often rely on human-crafted prompts and chain-of-thought templates. While recent advanced large reasoning models like DeepSeek-R1 employ reinforcement learning for an extended ``thinking'' process, their reasoning can be verbose and lack relevance. We introduce AttriLens-Mol, an attribute-guided reinforcement learning framework for molecular property prediction with LLMs. AttriLens-Mol steers the model's reasoning by using: (1) a format reward encouraging attribute-based structured output, (2) a count reward to avoid enumerating irrelevant attributes, and (3) a rationality reward using advanced LLMs and RDKit to verify the relatedness of the generated attributes. This approach implicitly elicits the model's inherent knowledge of relevant molecular attributes during reasoning, enables making predictions for the molecular property more effectively. Experiments on both in-distribution and out-of-distribution datasets show that, training both 7B-size R1-Distilled-Qwen2.5 and R1-Distilled-LLaMA3.1 models on 4,000 samples with our proposed AttriLens-Mol method significantly boosts the performance, getting comparable or better results than supervised fine-tuning models (Mol-Instructions, ChemDFM, etc.) and advanced models (GPT-3.5, GPT-4o, DeepSeek-V3, DeepSeek-R1, etc.). Further, our extracted attributes for the target property, when used as features for an interpretable decision tree model, yield superior performance compared to attributes generated by prompting LLMs. This shows that AttriLens-Mol effectively elicits more relevant and predictive molecular attributes, leading to enhanced interpretability and performance for property prediction. We release the code in https://github.com/szu-tera/AttriLens-Mol.

Finding relevant literature underpins the practice of evidence-based medicine. From 2014 to 2016, TREC conducted a clinical decision support track, wherein participants were tasked with finding articles relevant to clinical questions posed by physicians. In total, 87 teams have participated over the past three years, generating 395 runs. During this period, each team has trialled a variety of methods. While there was significant overlap in the methods employed by different teams, the results were varied. Due to the diversity of the platforms used, the results arising from the different techniques are not directly comparable, reducing the ability to build on previous work. By using a stable platform, we have been able to compare different document and query processing techniques, allowing us to experiment with different search parameters. We have used our system to reproduce leading teams runs, and compare the results obtained. By benchmarking our indexing and search techniques, we can statistically test a variety of hypotheses, paving the way for further research.

Recent advances in large language models (LLMs) have led to models that tackle diverse molecular tasks, such as chemical reaction prediction and molecular property prediction. Large-scale molecular instruction-tuning datasets have enabled sequence-only (e.g., SMILES or SELFIES) generalist molecular LLMs, and researchers are now exploring multimodal approaches that incorporate molecular structural information for further gains. However, a genuinely multimodal, generalist LLM that covers a broad spectrum of molecular tasks has yet to be fully investigated. We observe that naive next token prediction training ignores graph-structural information, limiting an LLM's ability to exploit molecular graphs. To address this, we propose (i) Molecular structure Preference Optimization (MolPO), which facilitates graph usage by optimizing preferences between pairs of correct and perturbed molecular structures, and (ii) an advanced graph encoder with a tailored pre-training strategy to improve the effect of graph utilization by MolPO. Building on these contributions, we introduce Mol-LLM, the first multimodal generalist model that (a) handles a broad spectrum of molecular tasks among molecular LLMs, (b) explicitly leverages molecular-structure information, and (c) takes advantage of extensive instruction tuning. Mol-LLM attains state-of-the-art or comparable results across the most comprehensive molecular-LLM benchmark-even on out-of-distribution datasets for reaction and property prediction, where it surpasses prior generalist molecular LLMs by a large margin.

Large language models (LLMs) have demonstrated remarkable performance in diverse tasks using zero-shot and few-shot prompting. Even though their capabilities of data synthesis have been studied well in recent years, the generated data suffers from a lack of diversity, less adherence to the prompt, and potential biases that creep into the data from the generator model. In this work, we tackle the challenge of generating datasets with high diversity, upon which a student model is trained for downstream tasks. Taking the route of decoding-time guidance-based approaches, we propose CorrSynth, which generates data that is more diverse and faithful to the input prompt using a correlated sampling strategy. Further, our method overcomes the complexity drawbacks of some other guidance-based techniques like classifier-based guidance. With extensive experiments, we show the effectiveness of our approach and substantiate our claims. In particular, we perform intrinsic evaluation to show the improvements in diversity. Our experiments show that CorrSynth improves both student metrics and intrinsic metrics upon competitive baselines across four datasets, showing the innate advantage of our method.

A well-known pitfall of molecular generative models is that they are not guaranteed to generate synthesizable molecules. There have been considerable attempts to address this problem, but given the exponentially large combinatorial space of synthesizable molecules, existing methods have shown limited coverage of the space and poor molecular optimization performance. To tackle these problems, we introduce ReaSyn, a generative framework for synthesizable projection where the model explores the neighborhood of given molecules in the synthesizable space by generating pathways that result in synthesizable analogs. To fully utilize the chemical knowledge contained in the synthetic pathways, we propose a novel perspective that views synthetic pathways akin to reasoning paths in large language models (LLMs). Specifically, inspired by chain-of-thought (CoT) reasoning in LLMs, we introduce the chain-of-reaction (CoR) notation that explicitly states reactants, reaction types, and intermediate products for each step in a pathway. With the CoR notation, ReaSyn can get dense supervision in every reaction step to explicitly learn chemical reaction rules during supervised training and perform step-by-step reasoning. In addition, to further enhance the reasoning capability of ReaSyn, we propose reinforcement learning (RL)-based finetuning and goal-directed test-time compute scaling tailored for synthesizable projection. ReaSyn achieves the highest reconstruction rate and pathway diversity in synthesizable molecule reconstruction and the highest optimization performance in synthesizable goal-directed molecular optimization, and significantly outperforms previous synthesizable projection methods in synthesizable hit expansion. These results highlight ReaSyn's superior ability to navigate combinatorially-large synthesizable chemical space.

Molecular property prediction is crucial for drug discovery and materials science, yet existing approaches suffer from limited interpretability, poor cross-task generalization, and lack of chemical reasoning capabilities. Traditional machine learning models struggle with task transferability, while specialized molecular language models provide little insight into their decision-making processes. To address these limitations, we propose MPPReasoner, a multimodal large language model that incorporates chemical reasoning for molecular property prediction. Our approach, built upon Qwen2.5-VL-7B-Instruct, integrates molecular images with SMILES strings to enable comprehensive molecular understanding. We develop a two-stage training strategy: supervised fine-tuning (SFT) using 16,000 high-quality reasoning trajectories generated through expert knowledge and multiple teacher models, followed by Reinforcement Learning from Principle-Guided Rewards (RLPGR). RLPGR employs verifiable, rule-based rewards that systematically evaluate chemical principle application, molecular structure analysis, and logical consistency through computational verification. Extensive experiments across 8 datasets demonstrate significant performance improvements, with MPPReasoner outperforming the best baselines by 7.91\% and 4.53\% on in-distribution and out-of-distribution tasks respectively. MPPReasoner exhibits exceptional cross-task generalization and generates chemically sound reasoning paths that provide valuable insights into molecular property analysis, substantially enhancing both interpretability and practical utility for chemists. Code is available at https://anonymous.4open.science/r/MPPReasoner-12687.

Negative guidance -- explicitly suppressing unwanted attributes -- remains a fundamental challenge in diffusion models, particularly in few-step sampling regimes. While Classifier-Free Guidance (CFG) works well in standard settings, it fails under aggressive sampling step compression due to divergent predictions between positive and negative branches. We present Normalized Attention Guidance (NAG), an efficient, training-free mechanism that applies extrapolation in attention space with L1-based normalization and refinement. NAG restores effective negative guidance where CFG collapses while maintaining fidelity. Unlike existing approaches, NAG generalizes across architectures (UNet, DiT), sampling regimes (few-step, multi-step), and modalities (image, video), functioning as a universal plug-in with minimal computational overhead. Through extensive experimentation, we demonstrate consistent improvements in text alignment (CLIP Score), fidelity (FID, PFID), and human-perceived quality (ImageReward). Our ablation studies validate each design component, while user studies confirm significant preference for NAG-guided outputs. As a model-agnostic inference-time approach requiring no retraining, NAG provides effortless negative guidance for all modern diffusion frameworks -- pseudocode in the Appendix!

Chemical similarity searches are widely used in-silico methods for identifying new drug-like molecules. These methods have historically relied on structure-based comparisons to compute molecular similarity. Here, we use a chemical language model to create a vector-based chemical search. We extend implementations by creating a prompt engineering strategy that utilizes two different chemical string representation algorithms: one for the query and the other for the database. We explore this method by reviewing the search results from five drug-like query molecules (penicillin G, nirmatrelvir, zidovudine, lysergic acid diethylamide, and fentanyl) and three dye-like query molecules (acid blue 25, avobenzone, and 2-diphenylaminocarbazole). We find that this novel method identifies molecules that are functionally similar to the query, indicated by the associated patent literature, and that many of these molecules are structurally distinct from the query, making them unlikely to be found with traditional chemical similarity search methods. This method may aid in the discovery of novel structural classes of molecules that achieve target functionality.

Large Language Models (LLMs) have shown strong performance in solving mathematical problems, with code-based solutions proving particularly effective. However, the best practice to leverage coding instruction data to enhance mathematical reasoning remains underexplored. This study investigates three key questions: (1) How do different coding styles of mathematical code-based rationales impact LLMs' learning performance? (2) Can general-domain coding instructions improve performance? (3) How does integrating textual rationales with code-based ones during training enhance mathematical reasoning abilities? Our findings reveal that code-based rationales with concise comments, descriptive naming, and hardcoded solutions are beneficial, while improvements from general-domain coding instructions and textual rationales are relatively minor. Based on these insights, we propose CoinMath, a learning strategy designed to enhance mathematical reasoning by diversifying the coding styles of code-based rationales. CoinMath generates a variety of code-based rationales incorporating concise comments, descriptive naming conventions, and hardcoded solutions. Experimental results demonstrate that CoinMath significantly outperforms its baseline model, MAmmoTH, one of the SOTA math LLMs.

Instruction Tuning involves finetuning a language model on a collection of instruction-formatted datasets in order to enhance the generalizability of the model to unseen tasks. Studies have shown the importance of balancing different task proportions during finetuning, but finding the right balance remains challenging. Unfortunately, there's currently no systematic method beyond manual tuning or relying on practitioners' intuition. In this paper, we introduce SMART (Submodular data Mixture strAtegy for instRuction Tuning) - a novel data mixture strategy which makes use of a submodular function to assign importance scores to tasks which are then used to determine the mixture weights. Given a fine-tuning budget, SMART redistributes the budget among tasks and selects non-redundant samples from each task. Experimental results demonstrate that SMART significantly outperforms traditional methods such as examples proportional mixing and equal mixing. Furthermore, SMART facilitates the creation of data mixtures based on a few representative subsets of tasks alone and through task pruning analysis, we reveal that in a limited budget setting, allocating budget among a subset of representative tasks yields superior performance compared to distributing the budget among all tasks. The code for reproducing our results is open-sourced at https://github.com/kowndinya-renduchintala/SMART.

Curriculum learning (CL), motivated by the intuition that learning in increasing order of difficulty should ease generalization, is commonly adopted both in pre-training and post-training of large language models (LLMs). The intuition of CL is particularly compelling for compositional reasoning, where complex problems are built from elementary inference rules; however, the actual impact of CL on such tasks remains largely underexplored. We present a systematic empirical study of CL for post-training of LLMs, using synthetic arithmetic and logical benchmarks where difficulty is characterized by reasoning complexity rather than surface-level proxies. Surprisingly, across multiple model families and curriculum schedules, we find no robust advantage in difficulty-based sequencing over standard random sampling in either accuracy or response length. These findings persist across both supervised fine-tuning (SFT) and reinforcement learning (RL) methods. Our study suggests that, in the context of deductive reasoning, the specific ordering of training examples plays a negligible role in achieving compositional generalization, challenging the practical utility of curriculum-based post-training.

Molecules play a crucial role in biomedical research and discovery, particularly in the field of small molecule drug development. Given the rapid advancements in large language models, especially the recent emergence of reasoning models, it is natural to explore how a general-purpose language model can be efficiently adapted for molecular science applications. In this work, we introduce BioMedGPT-Mol, a molecular language model designed to support molecular understanding and generation tasks. By curating and unifying existing public instruction datasets, we have assembled a large-scale, comprehensive, and high-quality training dataset. The model is then fine-tuned through a meticulously designed multi-task learning framework. On a consolidated benchmark derived from LlaSMol, TOMG-Bench, and MuMOInstruct, BioMedGPT-Mol achieves remarkable performance. Our experimental results demonstrate that a general-purpose reasoning model can be effectively and efficiently post-trained into a professional molecular language model through a well-structured multi-task curriculum. Leveraging these capabilities, we further apply the model to multi-step retrosynthetic planning, achieving state-of-the-art performance on RetroBench and demonstrating its superior efficacy as an end-to-end retrosynthetic planner. We anticipate that our approach can be extended to other biomedical scientific domains.

According to the principle of compositional generalization, the meaning of a complex expression can be understood as a function of the meaning of its parts and of how they are combined. This principle is crucial for human language processing and also, arguably, for NLP models in the face of out-of-distribution data. However, many neural network models, including Transformers, have been shown to struggle with compositional generalization. In this paper, we hypothesize that forcing models to in-context learn can provide an inductive bias to promote compositional generalization. To test this hypothesis, we train a causal Transformer in a setting that renders ordinary learning very difficult: we present it with different orderings of the training instance and shuffle instance labels. This corresponds to training the model on all possible few-shot learning problems attainable from the dataset. The model can solve the task, however, by utilizing earlier examples to generalize to later ones (i.e. in-context learning). In evaluations on the datasets, SCAN, COGS, and GeoQuery, models trained in this manner indeed show improved compositional generalization. This indicates the usefulness of in-context learning problems as an inductive bias for generalization.

Large Language Models (LLMs), with their remarkable task-handling capabilities and innovative outputs, have catalyzed significant advancements across a spectrum of fields. However, their proficiency within specialized domains such as biomolecular studies remains limited. To address this challenge, we introduce Mol-Instructions, a meticulously curated, comprehensive instruction dataset expressly designed for the biomolecular realm. Mol-Instructions is composed of three pivotal components: molecule-oriented instructions, protein-oriented instructions, and biomolecular text instructions, each curated to enhance the understanding and prediction capabilities of LLMs concerning biomolecular features and behaviors. Through extensive instruction tuning experiments on the representative LLM, we underscore the potency of Mol-Instructions to enhance the adaptability and cognitive acuity of large models within the complex sphere of biomolecular studies, thereby promoting advancements in the biomolecular research community. Mol-Instructions is made publicly accessible for future research endeavors and will be subjected to continual updates for enhanced applicability.

The gradual insertion method for direct calculation of the chemical potential by molecular simulation is applied in the NpT ensemble to different quadrupolar two-centre Lennard-Jones fluids at high density state points. The results agree well with Widom's test particle insertion but show at very high densities significantly smaller statistical uncertainties. The gradual insertion method, which is coupled here with preferential sampling, extends the density range where reliable information on the chemical potential can be obtained. Application details are reported.

Molecule discovery is a pivotal research field, impacting everything from the medicines we take to the materials we use. Recently, Large Language Models (LLMs) have been widely adopted in molecule understanding and generation, yet the alignments between molecules and their corresponding captions remain a significant challenge. Previous endeavours often treat the molecule as a general SMILES string or molecular graph, neglecting the fine-grained alignments between the molecular sub-structures and the descriptive textual phrases, which are crucial for accurate and explainable predictions. In this case, we introduce MolReFlect, a novel teacher-student framework designed to contextually perform the molecule-caption alignments in a fine-grained way. Our approach initially leverages a larger teacher LLM to label the detailed alignments by directly extracting critical phrases from molecule captions or SMILES strings and implying them to corresponding sub-structures or characteristics. To refine these alignments, we propose In-Context Selective Reflection, which retrieves previous extraction results as context examples for teacher LLM to reflect and lets a smaller student LLM select from in-context reflection and previous extraction results. Finally, we enhance the learning process of the student LLM through Chain-of-Thought In-Context Molecule Tuning, integrating the fine-grained alignments and the reasoning processes within the Chain-of-Thought format. Our experimental results demonstrate that MolReFlect enables LLMs like Mistral-7B to significantly outperform the previous baselines, achieving SOTA performance on the ChEBI-20 dataset. This advancement not only enhances the generative capabilities of LLMs in the molecule-caption translation task, but also contributes to a more explainable framework.

Text-to-image diffusion models can generate diverse, high-fidelity images based on user-provided text prompts. Recent research has extended these models to support text-guided image editing. While text guidance is an intuitive editing interface for users, it often fails to ensure the precise concept conveyed by users. To address this issue, we propose Custom-Edit, in which we (i) customize a diffusion model with a few reference images and then (ii) perform text-guided editing. Our key discovery is that customizing only language-relevant parameters with augmented prompts improves reference similarity significantly while maintaining source similarity. Moreover, we provide our recipe for each customization and editing process. We compare popular customization methods and validate our findings on two editing methods using various datasets.

Continual pre-training is widely used to adapt LLMs to target languages and domains, yet the mixture ratio of training data remains a sensitive hyperparameter that is expensive to tune: they must be fixed before training begins, and a suboptimal choice can waste weeks of compute. In this work, we propose OptiMer, which decouples ratio selection from training: we train one CPT model per dataset, extract each model's distribution vector, which represents the parameter shift induced by that dataset, and search for optimal composition weights post-hoc via Bayesian optimization. Experiments on Gemma 3 27B across languages (Japanese, Chinese) and domains (Math, Code) show that OptiMer consistently outperforms data mixture and model averaging baselines with 15-35 times lower search cost. Key findings reveal that 1) the optimized weights can be interpreted as data mixture ratios, and retraining with these ratios improves data mixture CPT, and 2) the same vector pool can be re-optimized for a given objective without any retraining, producing target-tailored models on demand. Our work establishes that data mixture ratio selection, traditionally a pre-training decision, can be reformulated as a post-hoc optimization over distribution vectors, offering a more flexible paradigm for continual pre-training.

Methods for designing organic materials with desired properties have high potential impact across fields such as medicine, renewable energy, petrochemical engineering, and agriculture. However, using generative modeling to design substances with desired properties is difficult because candidate compounds must satisfy multiple constraints, including synthetic accessibility and other metrics that are intuitive to domain experts but challenging to quantify. We propose C5T5, a novel self-supervised pretraining method that enables transformers to make zero-shot select-and-replace edits, altering organic substances towards desired property values. C5T5 operates on IUPAC names -- a standardized molecular representation that intuitively encodes rich structural information for organic chemists but that has been largely ignored by the ML community. Our technique requires no edited molecule pairs to train and only a rough estimate of molecular properties, and it has the potential to model long-range dependencies and symmetric molecular structures more easily than graph-based methods. C5T5 also provides a powerful interface to domain experts: it grants users fine-grained control over the generative process by selecting and replacing IUPAC name fragments, which enables experts to leverage their intuitions about structure-activity relationships. We demonstrate C5T5's effectiveness on four physical properties relevant for drug discovery, showing that it learns successful and chemically intuitive strategies for altering molecules towards desired property values.