Daily Papers

We present Darwin Family, a framework for training-free evolutionary merging of large language models via gradient-free weight-space recombination. We ask whether frontier-level reasoning performance can be improved without additional training, by reorganizing latent capabilities already encoded in existing checkpoints. Darwin introduces three key ideas: (i) a 14-dimensional adaptive merge genome enabling fine-grained component- and block-level recombination; (ii) MRI-Trust Fusion, which adaptively balances diagnostic layer-importance signals with evolutionary search through a learnable trust parameter; and (iii) an Architecture Mapper that enables cross-architecture breeding between heterogeneous model families. Empirically, the flagship Darwin-27B-Opus achieves 86.9% on GPQA Diamond, ranking #6 among 1,252 evaluated models, and outperforming its fully trained foundation model without any gradient-based training. Across scales from 4B to 35B parameters, Darwin models consistently improve over their parents, support recursive multi-generation evolution, and enable a training-free evolutionary merge that combines Transformer- and Mamba-based components. Together, the Darwin Family demonstrates that diagnostic-guided evolutionary merging is a practical and reproducible alternative to costly post-training pipelines for reasoning-centric language models.

Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that na\"ive linear flow matching on the simplex is insufficient toward this goal since it suffers from discontinuities in the training target and further pathologies. To overcome this, we develop Dirichlet flow matching on the simplex based on mixtures of Dirichlet distributions as probability paths. In this framework, we derive a connection between the mixtures' scores and the flow's vector field that allows for classifier and classifier-free guidance. Further, we provide distilled Dirichlet flow matching, which enables one-step sequence generation with minimal performance hits, resulting in O(L) speedups compared to autoregressive models. On complex DNA sequence generation tasks, we demonstrate superior performance compared to all baselines in distributional metrics and in achieving desired design targets for generated sequences. Finally, we show that our classifier-free guidance approach improves unconditional generation and is effective for generating DNA that satisfies design targets. Code is available at https://github.com/HannesStark/dirichlet-flow-matching.

Iterative improvement of model architectures is fundamental to deep learning: Transformers first enabled scaling, and recent advances in model hybridization have pushed the quality-efficiency frontier. However, optimizing architectures remains challenging and expensive. Current automated or manual approaches fall short, largely due to limited progress in the design of search spaces and due to the simplicity of resulting patterns and heuristics. In this work, we propose a new approach for the synthesis of tailored architectures (STAR). Our approach combines a novel search space based on the theory of linear input-varying systems, supporting a hierarchical numerical encoding into architecture genomes. STAR genomes are automatically refined and recombined with gradient-free, evolutionary algorithms to optimize for multiple model quality and efficiency metrics. Using STAR, we optimize large populations of new architectures, leveraging diverse computational units and interconnection patterns, improving over highly-optimized Transformers and striped hybrid models on the frontier of quality, parameter size, and inference cache for autoregressive language modeling.

Weight sharing is a fundamental concept in neural architecture search (NAS), enabling gradient-based methods to explore cell-based architecture spaces significantly faster than traditional blackbox approaches. In parallel, weight entanglement has emerged as a technique for intricate parameter sharing among architectures within macro-level search spaces. %However, the macro structure of such spaces poses compatibility challenges for gradient-based NAS methods. %As a result, blackbox optimization methods have been commonly employed, particularly in conjunction with supernet training, to maintain search efficiency. %Due to the inherent differences in the structure of these search spaces, these Since weight-entanglement poses compatibility challenges for gradient-based NAS methods, these two paradigms have largely developed independently in parallel sub-communities. This paper aims to bridge the gap between these sub-communities by proposing a novel scheme to adapt gradient-based methods for weight-entangled spaces. This enables us to conduct an in-depth comparative assessment and analysis of the performance of gradient-based NAS in weight-entangled search spaces. Our findings reveal that this integration of weight-entanglement and gradient-based NAS brings forth the various benefits of gradient-based methods (enhanced performance, improved supernet training properties and superior any-time performance), while preserving the memory efficiency of weight-entangled spaces. The code for our work is openly accessible https://anonymous.4open.science/r/TangleNAS-527C{here}

Conditional neural text generation models generate high-quality outputs, but often concentrate around a mode when what we really want is a diverse set of options. We present a search algorithm to construct lattices encoding a massive number of generation options. First, we restructure decoding as a best-first search, which explores the space differently than beam search and improves efficiency by avoiding pruning paths. Second, we revisit the idea of hypothesis recombination: we can identify pairs of similar generation candidates during search and merge them as an approximation. On both summarization and machine translation, we show that our algorithm encodes thousands of diverse options that remain grammatical and high-quality into one lattice. This algorithm provides a foundation for building downstream generation applications on top of massive-scale diverse outputs.

A challenging problem in many modern machine learning tasks is to process weight-space features, i.e., to transform or extract information from the weights and gradients of a neural network. Recent works have developed promising weight-space models that are equivariant to the permutation symmetries of simple feedforward networks. However, they are not applicable to general architectures, since the permutation symmetries of a weight space can be complicated by recurrence or residual connections. This work proposes an algorithm that automatically constructs permutation equivariant models, which we refer to as universal neural functionals (UNFs), for any weight space. Among other applications, we demonstrate how UNFs can be substituted into existing learned optimizer designs, and find promising improvements over prior methods when optimizing small image classifiers and language models. Our results suggest that learned optimizers can benefit from considering the (symmetry) structure of the weight space they optimize. We open-source our library for constructing UNFs at https://github.com/AllanYangZhou/universal_neural_functional.

Flow matching in the continuous simplex has emerged as a promising strategy for DNA sequence design, but struggles to scale to higher simplex dimensions required for peptide and protein generation. We introduce Gumbel-Softmax Flow and Score Matching, a generative framework on the simplex based on a novel Gumbel-Softmax interpolant with a time-dependent temperature. Using this interpolant, we introduce Gumbel-Softmax Flow Matching by deriving a parameterized velocity field that transports from smooth categorical distributions to distributions concentrated at a single vertex of the simplex. We alternatively present Gumbel-Softmax Score Matching which learns to regress the gradient of the probability density. Our framework enables high-quality, diverse generation and scales efficiently to higher-dimensional simplices. To enable training-free guidance, we propose Straight-Through Guided Flows (STGFlow), a classifier-based guidance method that leverages straight-through estimators to steer the unconditional velocity field toward optimal vertices of the simplex. STGFlow enables efficient inference-time guidance using classifiers pre-trained on clean sequences, and can be used with any discrete flow method. Together, these components form a robust framework for controllable de novo sequence generation. We demonstrate state-of-the-art performance in conditional DNA promoter design, sequence-only protein generation, and target-binding peptide design for rare disease treatment.

Designing biological sequences is an important challenge that requires satisfying complex constraints and thus is a natural problem to address with deep generative modeling. Diffusion generative models have achieved considerable success in many applications. Score-based generative stochastic differential equations (SDE) model is a continuous-time diffusion model framework that enjoys many benefits, but the originally proposed SDEs are not naturally designed for modeling discrete data. To develop generative SDE models for discrete data such as biological sequences, here we introduce a diffusion process defined in the probability simplex space with stationary distribution being the Dirichlet distribution. This makes diffusion in continuous space natural for modeling discrete data. We refer to this approach as Dirchlet diffusion score model. We demonstrate that this technique can generate samples that satisfy hard constraints using a Sudoku generation task. This generative model can also solve Sudoku, including hard puzzles, without additional training. Finally, we applied this approach to develop the first human promoter DNA sequence design model and showed that designed sequences share similar properties with natural promoter sequences.

We introduce a new family of physics-inspired generative models termed PFGM++ that unifies diffusion models and Poisson Flow Generative Models (PFGM). These models realize generative trajectories for N dimensional data by embedding paths in N{+}D dimensional space while still controlling the progression with a simple scalar norm of the D additional variables. The new models reduce to PFGM when D{=}1 and to diffusion models when D{to}infty. The flexibility of choosing D allows us to trade off robustness against rigidity as increasing D results in more concentrated coupling between the data and the additional variable norms. We dispense with the biased large batch field targets used in PFGM and instead provide an unbiased perturbation-based objective similar to diffusion models. To explore different choices of D, we provide a direct alignment method for transferring well-tuned hyperparameters from diffusion models (D{to} infty) to any finite D values. Our experiments show that models with finite D can be superior to previous state-of-the-art diffusion models on CIFAR-10/FFHQ 64{times}64 datasets, with FID scores of 1.91/2.43 when D{=}2048/128. In class-conditional setting, D{=}2048 yields current state-of-the-art FID of 1.74 on CIFAR-10. In addition, we demonstrate that models with smaller D exhibit improved robustness against modeling errors. Code is available at https://github.com/Newbeeer/pfgmpp

Protein design, a grand challenge of the day, involves optimization on a fitness landscape, and leading methods adopt a model-based approach where a model is trained on a training set (protein sequences and fitness) and proposes candidates to explore next. These methods are challenged by sparsity of high-fitness samples in the training set, a problem that has been in the literature. A less recognized but equally important problem stems from the distribution of training samples in the design space: leading methods are not designed for scenarios where the desired optimum is in a region that is not only poorly represented in training data, but also relatively far from the highly represented low-fitness regions. We show that this problem of "separation" in the design space is a significant bottleneck in existing model-based optimization tools and propose a new approach that uses a novel VAE as its search model to overcome the problem. We demonstrate its advantage over prior methods in robustly finding improved samples, regardless of the imbalance and separation between low- and high-fitness training samples. Our comprehensive benchmark on real and semi-synthetic protein datasets as well as solution design for physics-informed neural networks, showcases the generality of our approach in discrete and continuous design spaces. Our implementation is available at https://github.com/sabagh1994/PGVAE.

Connecting optimal transport and variational inference, we present a principled and systematic framework for sampling and generative modelling centred around divergences on path space. Our work culminates in the development of the Controlled Monte Carlo Diffusion sampler (CMCD) for Bayesian computation, a score-based annealing technique that crucially adapts both forward and backward dynamics in a diffusion model. On the way, we clarify the relationship between the EM-algorithm and iterative proportional fitting (IPF) for Schr{\"o}dinger bridges, deriving as well a regularised objective that bypasses the iterative bottleneck of standard IPF-updates. Finally, we show that CMCD has a strong foundation in the Jarzinsky and Crooks identities from statistical physics, and that it convincingly outperforms competing approaches across a wide array of experiments.

Flow-based generative models have been employed for sampling the Boltzmann distribution, but their application to high-dimensional systems is hindered by the significant computational cost of obtaining the Jacobian of the flow. To overcome this challenge, we introduce the flow perturbation method, which incorporates optimized stochastic perturbations into the flow. By reweighting trajectories generated by the perturbed flow, our method achieves unbiased sampling of the Boltzmann distribution with orders of magnitude speedup compared to both brute force Jacobian calculations and the Hutchinson estimator. Notably, it accurately sampled the Chignolin protein with all atomic Cartesian coordinates explicitly represented, which, to our best knowledge, is the largest molecule ever Boltzmann sampled in such detail using generative models.

In a convergence of machine learning and biology, we reveal that diffusion models are evolutionary algorithms. By considering evolution as a denoising process and reversed evolution as diffusion, we mathematically demonstrate that diffusion models inherently perform evolutionary algorithms, naturally encompassing selection, mutation, and reproductive isolation. Building on this equivalence, we propose the Diffusion Evolution method: an evolutionary algorithm utilizing iterative denoising -- as originally introduced in the context of diffusion models -- to heuristically refine solutions in parameter spaces. Unlike traditional approaches, Diffusion Evolution efficiently identifies multiple optimal solutions and outperforms prominent mainstream evolutionary algorithms. Furthermore, leveraging advanced concepts from diffusion models, namely latent space diffusion and accelerated sampling, we introduce Latent Space Diffusion Evolution, which finds solutions for evolutionary tasks in high-dimensional complex parameter space while significantly reducing computational steps. This parallel between diffusion and evolution not only bridges two different fields but also opens new avenues for mutual enhancement, raising questions about open-ended evolution and potentially utilizing non-Gaussian or discrete diffusion models in the context of Diffusion Evolution.

We propose an evolution strategies-based algorithm for estimating gradients in unrolled computation graphs, called ES-Single. Similarly to the recently-proposed Persistent Evolution Strategies (PES), ES-Single is unbiased, and overcomes chaos arising from recursive function applications by smoothing the meta-loss landscape. ES-Single samples a single perturbation per particle, that is kept fixed over the course of an inner problem (e.g., perturbations are not re-sampled for each partial unroll). Compared to PES, ES-Single is simpler to implement and has lower variance: the variance of ES-Single is constant with respect to the number of truncated unrolls, removing a key barrier in applying ES to long inner problems using short truncations. We show that ES-Single is unbiased for quadratic inner problems, and demonstrate empirically that its variance can be substantially lower than that of PES. ES-Single consistently outperforms PES on a variety of tasks, including a synthetic benchmark task, hyperparameter optimization, training recurrent neural networks, and training learned optimizers.

Simulation-free methods for training continuous-time generative models construct probability paths that go between noise distributions and individual data samples. Recent works, such as Flow Matching, derived paths that are optimal for each data sample. However, these algorithms rely on independent data and noise samples, and do not exploit underlying structure in the data distribution for constructing probability paths. We propose Multisample Flow Matching, a more general framework that uses non-trivial couplings between data and noise samples while satisfying the correct marginal constraints. At very small overhead costs, this generalization allows us to (i) reduce gradient variance during training, (ii) obtain straighter flows for the learned vector field, which allows us to generate high-quality samples using fewer function evaluations, and (iii) obtain transport maps with lower cost in high dimensions, which has applications beyond generative modeling. Importantly, we do so in a completely simulation-free manner with a simple minimization objective. We show that our proposed methods improve sample consistency on downsampled ImageNet data sets, and lead to better low-cost sample generation.

We introduce a gradient-free framework for Bayesian Optimal Experimental Design (BOED) in sequential settings, aimed at complex systems where gradient information is unavailable. Our method combines Ensemble Kalman Inversion (EKI) for design optimization with the Affine-Invariant Langevin Dynamics (ALDI) sampler for efficient posterior sampling-both of which are derivative-free and ensemble-based. To address the computational challenges posed by nested expectations in BOED, we propose variational Gaussian and parametrized Laplace approximations that provide tractable upper and lower bounds on the Expected Information Gain (EIG). These approximations enable scalable utility estimation in high-dimensional spaces and PDE-constrained inverse problems. We demonstrate the performance of our framework through numerical experiments ranging from linear Gaussian models to PDE-based inference tasks, highlighting the method's robustness, accuracy, and efficiency in information-driven experimental design.

Common deep learning approaches for antibody engineering focus on modeling the marginal distribution of sequences. By treating sequences as independent samples, however, these methods overlook affinity maturation as a rich and largely untapped source of information about the evolutionary process by which antibodies explore the underlying fitness landscape. In contrast, classical phylogenetic models explicitly represent evolutionary dynamics but lack the expressivity to capture complex epistatic interactions. We bridge this gap with CoSiNE, a continuous-time Markov chain parameterized by a deep neural network. Mathematically, we prove that CoSiNE provides a first-order approximation to the intractable sequential point mutation process, capturing epistatic effects with an error bound that is quadratic in branch length. Empirically, CoSiNE outperforms state-of-the-art language models in zero-shot variant effect prediction by explicitly disentangling selection from context-dependent somatic hypermutation. Finally, we introduce Guided Gillespie, a classifier-guided sampling scheme that steers CoSiNE at inference time, enabling efficient optimization of antibody binding affinity toward specific antigens.

The ability to engineer novel proteins with higher fitness for a desired property would be revolutionary for biotechnology and medicine. Modeling the combinatorially large space of sequences is infeasible; prior methods often constrain optimization to a small mutational radius, but this drastically limits the design space. Instead of heuristics, we propose smoothing the fitness landscape to facilitate protein optimization. First, we formulate protein fitness as a graph signal then use Tikunov regularization to smooth the fitness landscape. We find optimizing in this smoothed landscape leads to improved performance across multiple methods in the GFP and AAV benchmarks. Second, we achieve state-of-the-art results utilizing discrete energy-based models and MCMC in the smoothed landscape. Our method, called Gibbs sampling with Graph-based Smoothing (GGS), demonstrates a unique ability to achieve 2.5 fold fitness improvement (with in-silico evaluation) over its training set. GGS demonstrates potential to optimize proteins in the limited data regime. Code: https://github.com/kirjner/GGS

Diffusion models have shown promising generative capabilities across diverse domains, yet aligning their outputs with desired reward functions remains a challenge, particularly in cases where reward functions are non-differentiable. Some gradient-free guidance methods have been developed, but they often struggle to achieve optimal inference-time alignment. In this work, we newly frame inference-time alignment in diffusion as a search problem and propose Dynamic Search for Diffusion (DSearch), which subsamples from denoising processes and approximates intermediate node rewards. It also dynamically adjusts beam width and tree expansion to efficiently explore high-reward generations. To refine intermediate decisions, DSearch incorporates adaptive scheduling based on noise levels and a lookahead heuristic function. We validate DSearch across multiple domains, including biological sequence design, molecular optimization, and image generation, demonstrating superior reward optimization compared to existing approaches.

Score-based Generative Models (SGMs) have achieved state-of-the-art synthesis results on diverse tasks. However, the current design space of the forward diffusion process is largely unexplored and often relies on physical intuition or simplifying assumptions. Leveraging results from the design of scalable Bayesian posterior samplers, we present a complete recipe for constructing forward processes in SGMs, all of which are guaranteed to converge to the target distribution of interest. We show that several existing SGMs can be cast as specific instantiations of this parameterization. Furthermore, building on this recipe, we construct a novel SGM: Phase Space Langevin Diffusion (PSLD), which performs score-based modeling in a space augmented with auxiliary variables akin to a physical phase space. We show that PSLD outperforms competing baselines in terms of sample quality and the speed-vs-quality tradeoff across different samplers on various standard image synthesis benchmarks. Moreover, we show that PSLD achieves sample quality comparable to state-of-the-art SGMs (FID: 2.10 on unconditional CIFAR-10 generation), providing an attractive alternative as an SGM backbone for further development. We will publish our code and model checkpoints for reproducibility at https://github.com/mandt-lab/PSLD.

Large Transformer models are capable of implementing a plethora of so-called in-context learning algorithms. These include gradient descent, classification, sequence completion, transformation, and improvement. In this work, we investigate whether large language models (LLMs), which never explicitly encountered the task of black-box optimization, are in principle capable of implementing evolutionary optimization algorithms. While previous works have solely focused on language-based task specification, we move forward and focus on the zero-shot application of LLMs to black-box optimization. We introduce a novel prompting strategy, consisting of least-to-most sorting of discretized population members and querying the LLM to propose an improvement to the mean statistic, i.e. perform a type of black-box recombination operation. Empirically, we find that our setup allows the user to obtain an LLM-based evolution strategy, which we call `EvoLLM', that robustly outperforms baseline algorithms such as random search and Gaussian Hill Climbing on synthetic BBOB functions as well as small neuroevolution tasks. Hence, LLMs can act as `plug-in' in-context recombination operators. We provide several comparative studies of the LLM's model size, prompt strategy, and context construction. Finally, we show that one can flexibly improve EvoLLM's performance by providing teacher algorithm information via instruction fine-tuning on previously collected teacher optimization trajectories.

Despite the recent advances in the field of computational Schr\"odinger Bridges (SB), most existing SB solvers are still heavy-weighted and require complex optimization of several neural networks. It turns out that there is no principal solver which plays the role of simple-yet-effective baseline for SB just like, e.g., k-means method in clustering, logistic regression in classification or Sinkhorn algorithm in discrete optimal transport. We address this issue and propose a novel fast and simple SB solver. Our development is a smart combination of two ideas which recently appeared in the field: (a) parameterization of the Schr\"odinger potentials with sum-exp quadratic functions and (b) viewing the log-Schr\"odinger potentials as the energy functions. We show that combined together these ideas yield a lightweight, simulation-free and theoretically justified SB solver with a simple straightforward optimization objective. As a result, it allows solving SB in moderate dimensions in a matter of minutes on CPU without a painful hyperparameter selection. Our light solver resembles the Gaussian mixture model which is widely used for density estimation. Inspired by this similarity, we also prove an important theoretical result showing that our light solver is a universal approximator of SBs. Furthemore, we conduct the analysis of the generalization error of our light solver. The code for our solver can be found at https://github.com/ngushchin/LightSB

Training neural networks requires significant computational resources and energy. Methods like mixed-precision and quantization-aware training reduce bit usage, yet they still depend heavily on computationally expensive gradient-based optimization. In this work, we propose a paradigm shift: eliminate gradients altogether. One might hope that, in a finite quantized space, finding optimal weights with out gradients would be easier but we theoretically prove that this problem is NP-hard even in simple settings where the continuous case is efficiently solvable. To address this, we introduce a novel heuristic optimization framework that avoids full weight updates and significantly improves efficiency. Empirically, our method achieves performance comparable to that of full-precision gradient-based training on standard datasets and architectures, while using up to 3x less energy and requiring up to 5x fewer parameter updates.

Many recent reasoning gains in large language models can be explained as distribution sharpening: biasing generation toward high-likelihood trajectories already supported by the pretrained model, rather than modifying its weights. A natural formalization is the sequence-level power distribution π_α(ymid x)propto p_θ(ymid x)^α (α>1), which concentrates mass on whole sequences instead of adjusting token-level temperature. Prior work shows that Metropolis--Hastings (MH) sampling from this distribution recovers strong reasoning performance, but at order-of-magnitude inference slowdowns. We introduce Power-SMC, a training-free Sequential Monte Carlo scheme that targets the same objective while remaining close to standard decoding latency. Power-SMC advances a small particle set in parallel, corrects importance weights token-by-token, and resamples when necessary, all within a single GPU-friendly batched decode. We prove that temperature τ=1/α is the unique prefix-only proposal minimizing incremental weight variance, interpret residual instability via prefix-conditioned Rényi entropies, and introduce an exponent-bridging schedule that improves particle stability without altering the target. On MATH500, Power-SMC matches or exceeds MH power sampling while reducing latency from 16--28times to 1.4--3.3times over baseline decoding. The code is available at https://github.com/ArminAzizi98/Power-SMC.

We introduce a principled probabilistic framework for reward-guided decoding in large language models, addressing the limitations of standard decoding methods that optimize token-level likelihood rather than sequence-level quality. Our method defines a reward-augmented target distribution over complete sequences by combining model transition probabilities with prefix-dependent reward potentials. Importantly, the approach is training-free: it leaves model weights unchanged and instead modifies the inference distribution via reward potentials, with all gains arising purely from inference-time sampling. To sample from this distribution, we develop Sequential Monte Carlo algorithms, including a computationally efficient prefix-only variant and a lookahead variant whose intermediate targets match the exact marginals of the full sequence distribution. The framework also integrates resample-move updates with Metropolis-Hastings rejuvenation and supports block-wise generation, subsuming common decoding strategies such as temperature sampling and power-tempered objectives. Empirical results across three 7B models show significant gains. On code generation (HumanEval), our method improves base performance by up to 54.9% and surpasses the strongest sampling baselines by 9.1%-15.3%. On mathematical reasoning (MATH500), it achieves gains of up to 8.8%. Notably, it reaches 87.8% on HumanEval and 78.4% on MATH500 with Qwen2.5-7B, consistently outperforming the reinforcement learning method GRPO.

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.

To fully leverage the capabilities of diffusion models, we are often interested in optimizing downstream reward functions during inference. While numerous algorithms for reward-guided generation have been recently proposed due to their significance, current approaches predominantly focus on single-shot generation, transitioning from fully noised to denoised states. We propose a novel framework for inference-time reward optimization with diffusion models inspired by evolutionary algorithms. Our approach employs an iterative refinement process consisting of two steps in each iteration: noising and reward-guided denoising. This sequential refinement allows for the gradual correction of errors introduced during reward optimization. Besides, we provide a theoretical guarantee for our framework. Finally, we demonstrate its superior empirical performance in protein and cell-type-specific regulatory DNA design. The code is available at https://github.com/masa-ue/ProDifEvo-Refinement{https://github.com/masa-ue/ProDifEvo-Refinement}.

Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences. However, rather than merely generating designs that are natural, we often aim to optimize downstream reward functions while preserving the naturalness of these design spaces. Existing methods for achieving this goal often require ``differentiable'' proxy models (e.g., classifier guidance or DPS) or involve computationally expensive fine-tuning of diffusion models (e.g., classifier-free guidance, RL-based fine-tuning). In our work, we propose a new method to address these challenges. Our algorithm is an iterative sampling method that integrates soft value functions, which looks ahead to how intermediate noisy states lead to high rewards in the future, into the standard inference procedure of pre-trained diffusion models. Notably, our approach avoids fine-tuning generative models and eliminates the need to construct differentiable models. This enables us to (1) directly utilize non-differentiable features/reward feedback, commonly used in many scientific domains, and (2) apply our method to recent discrete diffusion models in a principled way. Finally, we demonstrate the effectiveness of our algorithm across several domains, including image generation, molecule generation, and DNA/RNA sequence generation. The code is available at https://github.com/masa-ue/SVDD{https://github.com/masa-ue/SVDD}.

We introduce a new family of particle evolution samplers suitable for constrained domains and non-Euclidean geometries. Stein Variational Mirror Descent and Mirrored Stein Variational Gradient Descent minimize the Kullback-Leibler (KL) divergence to constrained target distributions by evolving particles in a dual space defined by a mirror map. Stein Variational Natural Gradient exploits non-Euclidean geometry to more efficiently minimize the KL divergence to unconstrained targets. We derive these samplers from a new class of mirrored Stein operators and adaptive kernels developed in this work. We demonstrate that these new samplers yield accurate approximations to distributions on the simplex, deliver valid confidence intervals in post-selection inference, and converge more rapidly than prior methods in large-scale unconstrained posterior inference. Finally, we establish the convergence of our new procedures under verifiable conditions on the target distribution.

We resolve difficulties in training and sampling from a discrete generative model by learning a smoothed energy function, sampling from the smoothed data manifold with Langevin Markov chain Monte Carlo (MCMC), and projecting back to the true data manifold with one-step denoising. Our Discrete Walk-Jump Sampling formalism combines the contrastive divergence training of an energy-based model and improved sample quality of a score-based model, while simplifying training and sampling by requiring only a single noise level. We evaluate the robustness of our approach on generative modeling of antibody proteins and introduce the distributional conformity score to benchmark protein generative models. By optimizing and sampling from our models for the proposed distributional conformity score, 97-100% of generated samples are successfully expressed and purified and 70% of functional designs show equal or improved binding affinity compared to known functional antibodies on the first attempt in a single round of laboratory experiments. We also report the first demonstration of long-run fast-mixing MCMC chains where diverse antibody protein classes are visited in a single MCMC chain.

We propose a gradient flow procedure for generative modeling by transporting particles from an initial source distribution to a target distribution, where the gradient field on the particles is given by a noise-adaptive Wasserstein Gradient of the Maximum Mean Discrepancy (MMD). The noise-adaptive MMD is trained on data distributions corrupted by increasing levels of noise, obtained via a forward diffusion process, as commonly used in denoising diffusion probabilistic models. The result is a generalization of MMD Gradient Flow, which we call Diffusion-MMD-Gradient Flow or DMMD. The divergence training procedure is related to discriminator training in Generative Adversarial Networks (GAN), but does not require adversarial training. We obtain competitive empirical performance in unconditional image generation on CIFAR10, MNIST, CELEB-A (64 x64) and LSUN Church (64 x 64). Furthermore, we demonstrate the validity of the approach when MMD is replaced by a lower bound on the KL divergence.

To build effective therapeutics, biologists iteratively mutate antibody sequences to improve binding and stability. Proposed mutations can be informed by previous measurements or by learning from large antibody databases to predict only typical antibodies. Unfortunately, the space of typical antibodies is enormous to search, and experiments often fail to find suitable antibodies on a budget. We introduce Clone-informed Bayesian Optimization (CloneBO), a Bayesian optimization procedure that efficiently optimizes antibodies in the lab by teaching a generative model how our immune system optimizes antibodies. Our immune system makes antibodies by iteratively evolving specific portions of their sequences to bind their target strongly and stably, resulting in a set of related, evolving sequences known as a clonal family. We train a large language model, CloneLM, on hundreds of thousands of clonal families and use it to design sequences with mutations that are most likely to optimize an antibody within the human immune system. We propose to guide our designs to fit previous measurements with a twisted sequential Monte Carlo procedure. We show that CloneBO optimizes antibodies substantially more efficiently than previous methods in realistic in silico experiments and designs stronger and more stable binders in in vitro wet lab experiments.

The development of powerful natural language models have increased the ability to learn meaningful representations of protein sequences. In addition, advances in high-throughput mutagenesis, directed evolution, and next-generation sequencing have allowed for the accumulation of large amounts of labeled fitness data. Leveraging these two trends, we introduce Regularized Latent Space Optimization (ReLSO), a deep transformer-based autoencoder which features a highly structured latent space that is trained to jointly generate sequences as well as predict fitness. Through regularized prediction heads, ReLSO introduces a powerful protein sequence encoder and novel approach for efficient fitness landscape traversal. Using ReLSO, we explicitly model the sequence-function landscape of large labeled datasets and generate new molecules by optimizing within the latent space using gradient-based methods. We evaluate this approach on several publicly-available protein datasets, including variant sets of anti-ranibizumab and GFP. We observe a greater sequence optimization efficiency (increase in fitness per optimization step) by ReLSO compared to other approaches, where ReLSO more robustly generates high-fitness sequences. Furthermore, the attention-based relationships learned by the jointly-trained ReLSO models provides a potential avenue towards sequence-level fitness attribution information.

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.

The controllable generation of diffusion models aims to steer the model to generate samples that optimize some given objective functions. It is desirable for a variety of applications including image generation, molecule generation, and DNA/sequence generation. Reinforcement Learning (RL) based fine-tuning of the base model is a popular approach but it can overfit the reward function while requiring significant resources. We frame controllable generation as a problem of finding a distribution that optimizes a KL-regularized objective function. We present SLCD -- Supervised Learning based Controllable Diffusion, which iteratively generates online data and trains a small classifier to guide the generation of the diffusion model. Similar to the standard classifier-guided diffusion, SLCD's key computation primitive is classification and does not involve any complex concepts from RL or control. Via a reduction to no-regret online learning analysis, we show that under KL divergence, the output from SLCD provably converges to the optimal solution of the KL-regularized objective. Further, we empirically demonstrate that SLCD can generate high quality samples with nearly the same inference time as the base model in both image generation with continuous diffusion and biological sequence generation with discrete diffusion. Our code is available at https://github.com/Owen-Oertell/slcd

Inspired by the success of unsupervised pre-training paradigms, researchers have applied these approaches to DNA pre-training. However, we argue that these approaches alone yield suboptimal results because pure DNA sequences lack sufficient information, since their functions are regulated by genomic profiles like chromatin accessibility. Here, we demonstrate that supervised training for genomic profile prediction serves as a more effective alternative to pure sequence pre-training. Furthermore, considering the multi-species and multi-profile nature of genomic profile prediction, we introduce our Species-Profile Adaptive Collaborative Experts (SPACE) that leverages Mixture of Experts (MoE) to better capture the relationships between DNA sequences across different species and genomic profiles, thereby learning more effective DNA representations. Through extensive experiments across various tasks, our model achieves state-of-the-art performance, establishing that DNA models trained with supervised genomic profiles serve as powerful DNA representation learners. The code is available at https://github.com/ZhuJiwei111/SPACE.

Diffusion-based manifold learning methods have proven useful in representation learning and dimensionality reduction of modern high dimensional, high throughput, noisy datasets. Such datasets are especially present in fields like biology and physics. While it is thought that these methods preserve underlying manifold structure of data by learning a proxy for geodesic distances, no specific theoretical links have been established. Here, we establish such a link via results in Riemannian geometry explicitly connecting heat diffusion to manifold distances. In this process, we also formulate a more general heat kernel based manifold embedding method that we call heat geodesic embeddings. This novel perspective makes clearer the choices available in manifold learning and denoising. Results show that our method outperforms existing state of the art in preserving ground truth manifold distances, and preserving cluster structure in toy datasets. We also showcase our method on single cell RNA-sequencing datasets with both continuum and cluster structure, where our method enables interpolation of withheld timepoints of data. Finally, we show that parameters of our more general method can be configured to give results similar to PHATE (a state-of-the-art diffusion based manifold learning method) as well as SNE (an attraction/repulsion neighborhood based method that forms the basis of t-SNE).

Diffusion models have gained prominence in generating high-quality sequences of text. Nevertheless, current approaches predominantly represent discrete text within a continuous diffusion space, which incurs substantial computational overhead during training and results in slower sampling speeds. In this paper, we introduce a soft absorbing state that facilitates the diffusion model in learning to reconstruct discrete mutations based on the underlying Gaussian space, thereby enhancing its capacity to recover conditional signals. During the sampling phase, we employ state-of-the-art ODE solvers within the continuous space to expedite the sampling process. Comprehensive experimental evaluations reveal that our proposed method effectively accelerates the training convergence by 4x and generates samples of similar quality 800x faster, rendering it significantly closer to practical application. The code is released at \url{https://github.com/Shark-NLP/DiffuSeq

Gradient descent has proven to be a powerful and effective technique for optimization in numerous machine learning applications. Recent advances in computational neuroscience have shown that learning in standard gradient descent optimization formulation is not consistent with learning in biological systems. This has opened up interesting avenues for building biologically inspired learning techniques. One such approach is inspired by Dale's law, which states that inhibitory and excitatory synapses do not swap roles during the course of learning. The resulting exponential gradient descent optimization scheme leads to log-normally distributed synaptic weights. Interestingly, the density that satisfies the Fokker-Planck equation corresponding to the stochastic differential equation (SDE) with geometric Brownian motion (GBM) is the log-normal density. Leveraging this connection, we start with the SDE governing geometric Brownian motion, and show that discretizing the corresponding reverse-time SDE yields a multiplicative update rule, which surprisingly, coincides with the sampling equivalent of the exponential gradient descent update founded on Dale's law. Furthermore, we propose a new formalism for multiplicative denoising score-matching, subsuming the loss function proposed by Hyvaerinen for non-negative data. Indeed, log-normally distributed data is positive and the proposed score-matching formalism turns out to be a natural fit. This allows for training of score-based models for image data and results in a novel multiplicative update scheme for sample generation starting from a log-normal density. Experimental results on MNIST, Fashion MNIST, and Kuzushiji datasets demonstrate generative capability of the new scheme. To the best of our knowledge, this is the first instance of a biologically inspired generative model employing multiplicative updates, founded on geometric Brownian motion.

Inverse protein folding -- the task of predicting a protein sequence from its backbone atom coordinates -- has surfaced as an important problem in the "top down", de novo design of proteins. Contemporary approaches have cast this problem as a conditional generative modelling problem, where a large generative model over protein sequences is conditioned on the backbone. While these generative models very rapidly produce promising sequences, independent draws from generative models may fail to produce sequences that reliably fold to the correct backbone. Furthermore, it is challenging to adapt pure generative approaches to other settings, e.g., when constraints exist. In this paper, we cast the problem of improving generated inverse folds as an optimization problem that we solve using recent advances in "deep" or "latent space" Bayesian optimization. Our approach consistently produces protein sequences with greatly reduced structural error to the target backbone structure as measured by TM score and RMSD while using fewer computational resources. Additionally, we demonstrate other advantages of an optimization-based approach to the problem, such as the ability to handle constraints.

Discrete diffusion models are promising alternatives to autoregressive approaches for text generation, yet their decoding methods remain under-studied. Standard decoding methods for autoregressive models, such as beam search, do not directly apply to iterative denoising, and existing diffusion decoding techniques provide limited control over in-batch diversity. To bridge this gap, we introduce a generalized beam-search framework for discrete diffusion that generates candidates in parallel and supports modular beam-selection objectives. As a diversity-focused instantiation, we propose D5P4, which formulates the selection step as MAP inference over a Determinantal Point Process. Leveraging a scalable greedy solver, D5P4 maintains multi-GPU compatibility and enables an explicit trade-off between model probability and target diversity with near-zero compute overhead. Experiments on free-form generation and question answering demonstrate that D5P4 improves diversity over strong baselines while maintaining competitive generation quality.

This paper introduces a novel framework for DNA sequence generation, comprising two key components: DiscDiff, a Latent Diffusion Model (LDM) tailored for generating discrete DNA sequences, and Absorb-Escape, a post-training algorithm designed to refine these sequences. Absorb-Escape enhances the realism of the generated sequences by correcting `round errors' inherent in the conversion process between latent and input spaces. Our approach not only sets new standards in DNA sequence generation but also demonstrates superior performance over existing diffusion models, in generating both short and long DNA sequences. Additionally, we introduce EPD-GenDNA, the first comprehensive, multi-species dataset for DNA generation, encompassing 160,000 unique sequences from 15 species. We hope this study will advance the generative modelling of DNA, with potential implications for gene therapy and protein production.

Significant recent work has studied the ability of gradient descent to recover a hidden planted direction θ^star in S^{d-1} in different high-dimensional settings, including tensor PCA and single-index models. The key quantity that governs the ability of gradient descent to traverse these landscapes is the information exponent k^star (Ben Arous et al., (2021)), which corresponds to the order of the saddle at initialization in the population landscape. Ben Arous et al., (2021) showed that n gtrsim d^{max(1, k^star-1)} samples were necessary and sufficient for online SGD to recover θ^star, and Ben Arous et al., (2020) proved a similar lower bound for Langevin dynamics. More recently, Damian et al., (2023) showed it was possible to circumvent these lower bounds by running gradient descent on a smoothed landscape, and that this algorithm succeeds with n gtrsim d^{max(1, k^star/2)} samples, which is optimal in the worst case. This raises the question of whether it is possible to achieve the same rate without explicit smoothing. In this paper, we show that Langevin dynamics can succeed with n gtrsim d^{ k^star/2 } samples if one considers the average iterate, rather than the last iterate. The key idea is that the combination of noise-injection and iterate averaging is able to emulate the effect of landscape smoothing. We apply this result to both the tensor PCA and single-index model settings. Finally, we conjecture that minibatch SGD can also achieve the same rate without adding any additional noise.

Equilibrium propagation (EP) is a compelling alternative to the backpropagation of error algorithm (BP) for computing gradients of neural networks on biological or analog neuromorphic substrates. Still, the algorithm requires weight symmetry and infinitesimal equilibrium perturbations, i.e., nudges, to estimate unbiased gradients efficiently. Both requirements are challenging to implement in physical systems. Yet, whether and how weight asymmetry affects its applicability is unknown because, in practice, it may be masked by biases introduced through the finite nudge. To address this question, we study generalized EP, which can be formulated without weight symmetry, and analytically isolate the two sources of bias. For complex-differentiable non-symmetric networks, we show that the finite nudge does not pose a problem, as exact derivatives can still be estimated via a Cauchy integral. In contrast, weight asymmetry introduces bias resulting in low task performance due to poor alignment of EP's neuronal error vectors compared to BP. To mitigate this issue, we present a new homeostatic objective that directly penalizes functional asymmetries of the Jacobian at the network's fixed point. This homeostatic objective dramatically improves the network's ability to solve complex tasks such as ImageNet 32x32. Our results lay the theoretical groundwork for studying and mitigating the adverse effects of imperfections of physical networks on learning algorithms that rely on the substrate's relaxation dynamics.

Diffusion models for continuous data gained widespread adoption owing to their high quality generation and control mechanisms. However, controllable diffusion on discrete data faces challenges given that continuous guidance methods do not directly apply to discrete diffusion. Here, we provide a straightforward derivation of classifier-free and classifier-based guidance for discrete diffusion, as well as a new class of diffusion models that leverage uniform noise and that are more guidable because they can continuously edit their outputs. We improve the quality of these models with a novel continuous-time variational lower bound that yields state-of-the-art performance, especially in settings involving guidance or fast generation. Empirically, we demonstrate that our guidance mechanisms combined with uniform noise diffusion improve controllable generation relative to autoregressive and diffusion baselines on several discrete data domains, including genomic sequences, small molecule design, and discretized image generation.

Generative modeling of discrete variables is challenging yet crucial for applications in natural language processing and biological sequence design. We introduce the Shortlisting Model (SLM), a novel simplex-based diffusion model inspired by progressive candidate pruning. SLM operates on simplex centroids, reducing generation complexity and enhancing scalability. Additionally, SLM incorporates a flexible implementation of classifier-free guidance, enhancing unconditional generation performance. Extensive experiments on DNA promoter and enhancer design, protein design, character-level and large-vocabulary language modeling demonstrate the competitive performance and strong potential of SLM. Our code can be found at https://github.com/GenSI-THUAIR/SLM

A central challenge to many fields of science and engineering involves minimizing non-convex error functions over continuous, high dimensional spaces. Gradient descent or quasi-Newton methods are almost ubiquitously used to perform such minimizations, and it is often thought that a main source of difficulty for the ability of these local methods to find the global minimum is the proliferation of local minima with much higher error than the global minimum. Here we argue, based on results from statistical physics, random matrix theory, and neural network theory, that a deeper and more profound difficulty originates from the proliferation of saddle points, not local minima, especially in high dimensional problems of practical interest. Such saddle points are surrounded by high error plateaus that can dramatically slow down learning, and give the illusory impression of the existence of a local minimum. Motivated by these arguments, we propose a new algorithm, the saddle-free Newton method, that can rapidly escape high dimensional saddle points, unlike gradient descent and quasi-Newton methods. We apply this algorithm to deep neural network training, and provide preliminary numerical evidence for its superior performance.

We present a genetic algorithm framework for automatically discovering deep learning optimization algorithms. Our approach encodes optimizers as genomes that specify combinations of primitive update terms (gradient, momentum, RMS normalization, Adam-style adaptive terms, and sign-based updates) along with hyperparameters and scheduling options. Through evolutionary search over 50 generations with a population of 50 individuals, evaluated across multiple vision tasks, we discover an evolved optimizer that outperforms Adam by 2.6% in aggregate fitness and achieves a 7.7% relative improvement on CIFAR-10. The evolved optimizer combines sign-based gradient terms with adaptive moment estimation, uses lower momentum coefficients than Adam (β_1=0.86, β_2=0.94), and notably disables bias correction while enabling learning rate warmup and cosine decay. Our results demonstrate that evolutionary search can discover competitive optimization algorithms and reveal design principles that differ from hand-crafted optimizers. Code is available at https://github.com/mmarfinetz/evo-optimizer.

We study the behavior of an algorithm derived from the cavity method for the Prize-Collecting Steiner Tree (PCST) problem on graphs. The algorithm is based on the zero temperature limit of the cavity equations and as such is formally simple (a fixed point equation resolved by iteration) and distributed (parallelizable). We provide a detailed comparison with state-of-the-art algorithms on a wide range of existing benchmarks networks and random graphs. Specifically, we consider an enhanced derivative of the Goemans-Williamson heuristics and the DHEA solver, a Branch and Cut Linear/Integer Programming based approach. The comparison shows that the cavity algorithm outperforms the two algorithms in most large instances both in running time and quality of the solution. Finally we prove a few optimality properties of the solutions provided by our algorithm, including optimality under the two post-processing procedures defined in the Goemans-Williamson derivative and global optimality in some limit cases.

Recently, Stitchable Neural Networks (SN-Net) is proposed to stitch some pre-trained networks for quickly building numerous networks with different complexity and performance trade-offs. In this way, the burdens of designing or training the variable-sized networks, which can be used in application scenarios with diverse resource constraints, are alleviated. However, SN-Net still faces a few challenges. 1) Stitching from multiple independently pre-trained anchors introduces high storage resource consumption. 2) SN-Net faces challenges to build smaller models for low resource constraints. 3). SN-Net uses an unlearned initialization method for stitch layers, limiting the final performance. To overcome these challenges, motivated by the recently proposed Learngene framework, we propose a novel method called Learngene Pool. Briefly, Learngene distills the critical knowledge from a large pre-trained model into a small part (termed as learngene) and then expands this small part into a few variable-sized models. In our proposed method, we distill one pretrained large model into multiple small models whose network blocks are used as learngene instances to construct the learngene pool. Since only one large model is used, we do not need to store more large models as SN-Net and after distilling, smaller learngene instances can be created to build small models to satisfy low resource constraints. We also insert learnable transformation matrices between the instances to stitch them into variable-sized models to improve the performance of these models. Exhaustive experiments have been implemented and the results validate the effectiveness of the proposed Learngene Pool compared with SN-Net.

The curse-of-dimensionality taxes computational resources heavily with exponentially increasing computational cost as the dimension increases. This poses great challenges in solving high-dimensional PDEs, as Richard E. Bellman first pointed out over 60 years ago. While there has been some recent success in solving numerically partial differential equations (PDEs) in high dimensions, such computations are prohibitively expensive, and true scaling of general nonlinear PDEs to high dimensions has never been achieved. We develop a new method of scaling up physics-informed neural networks (PINNs) to solve arbitrary high-dimensional PDEs. The new method, called Stochastic Dimension Gradient Descent (SDGD), decomposes a gradient of PDEs into pieces corresponding to different dimensions and randomly samples a subset of these dimensional pieces in each iteration of training PINNs. We prove theoretically the convergence and other desired properties of the proposed method. We demonstrate in various diverse tests that the proposed method can solve many notoriously hard high-dimensional PDEs, including the Hamilton-Jacobi-Bellman (HJB) and the Schrödinger equations in tens of thousands of dimensions very fast on a single GPU using the PINNs mesh-free approach. Notably, we solve nonlinear PDEs with nontrivial, anisotropic, and inseparable solutions in 100,000 effective dimensions in 12 hours on a single GPU using SDGD with PINNs. Since SDGD is a general training methodology of PINNs, it can be applied to any current and future variants of PINNs to scale them up for arbitrary high-dimensional PDEs.

Solving partial differential equations (PDEs) with machine learning typically requires training a new neural network for every new equation. This optimization is slow. We introduce MetaColloc. It is an optimization-free and data-free framework that removes this bottleneck completely. We decouple basis discovery from the solving process. We meta-train a dual-branch neural network on diverse Gaussian Random Fields. This offline process creates a universal dictionary of neural basis functions. At test time, we freeze the network. We solve the PDE by assembling a collocation matrix. We find the solution through a single linear least squares step. For non-linear PDEs, we apply the Newton-Raphson method to achieve fast quadratic convergence. Our experiments across six 2D and 3D PDEs show massive improvements. MetaColloc reaches state-of-the-art accuracy on smooth and non-linear problems. It also reduces test-time computation by several orders of magnitude. Finally, we provide a detailed frequency sweep analysis. This analysis reveals a critical mismatch between function approximation and operator stability at extremely high frequencies. This profound finding opens a clear path toward future operator-aware meta-learning.

Practitioners frequently aim to infer an unobserved population trajectory using sample snapshots at multiple time points. For instance, in single-cell sequencing, scientists would like to learn how gene expression evolves over time. But sequencing any cell destroys that cell. So we cannot access any cell's full trajectory, but we can access snapshot samples from many cells. Stochastic differential equations are commonly used to analyze systems with full individual-trajectory access; since here we have only sample snapshots, these methods are inapplicable. The deep learning community has recently explored using Schr\"odinger bridges (SBs) and their extensions to estimate these dynamics. However, these methods either (1) interpolate between just two time points or (2) require a single fixed reference dynamic within the SB, which is often just set to be Brownian motion. But learning piecewise from adjacent time points can fail to capture long-term dependencies. And practitioners are typically able to specify a model class for the reference dynamic but not the exact values of the parameters within it. So we propose a new method that (1) learns the unobserved trajectories from sample snapshots across multiple time points and (2) requires specification only of a class of reference dynamics, not a single fixed one. In particular, we suggest an iterative projection method inspired by Schr\"odinger bridges; we alternate between learning a piecewise SB on the unobserved trajectories and using the learned SB to refine our best guess for the dynamics within the reference class. We demonstrate the advantages of our method via a well-known simulated parametric model from ecology, simulated and real data from systems biology, and real motion-capture data.

Diffusion models are emerging expressive generative models, in which a large number of time steps (inference steps) are required for a single image generation. To accelerate such tedious process, reducing steps uniformly is considered as an undisputed principle of diffusion models. We consider that such a uniform assumption is not the optimal solution in practice; i.e., we can find different optimal time steps for different models. Therefore, we propose to search the optimal time steps sequence and compressed model architecture in a unified framework to achieve effective image generation for diffusion models without any further training. Specifically, we first design a unified search space that consists of all possible time steps and various architectures. Then, a two stage evolutionary algorithm is introduced to find the optimal solution in the designed search space. To further accelerate the search process, we employ FID score between generated and real samples to estimate the performance of the sampled examples. As a result, the proposed method is (i).training-free, obtaining the optimal time steps and model architecture without any training process; (ii). orthogonal to most advanced diffusion samplers and can be integrated to gain better sample quality. (iii). generalized, where the searched time steps and architectures can be directly applied on different diffusion models with the same guidance scale. Experimental results show that our method achieves excellent performance by using only a few time steps, e.g. 17.86 FID score on ImageNet 64 times 64 with only four steps, compared to 138.66 with DDIM. The code is available at https://github.com/lilijiangg/AutoDiffusion.

Aligning diffusion model outputs with downstream objectives is essential for improving task-specific performance. Broadly, inference-time training-free approaches for aligning diffusion models can be categorized into two main strategies: sampling-based methods, which explore multiple candidate outputs and select those with higher reward signals, and gradient-guided methods, which use differentiable reward approximations to directly steer the generation process. In this work, we propose a universal algorithm, UniCoDe, which brings together the strengths of sampling and gradient-based guidance into a unified framework. UniCoDe integrates local gradient signals during sampling, thereby addressing the sampling inefficiency inherent in complex reward-based sampling approaches. By cohesively combining these two paradigms, UniCoDe enables more efficient sampling while offering better trade-offs between reward alignment and divergence from the diffusion unconditional prior. Empirical results demonstrate that UniCoDe remains competitive with state-of-the-art baselines across a range of tasks. The code is available at https://github.com/maurya-goyal10/UniCoDe

Fast, scalable decoding architectures that operate in a block-wise parallel fashion across space and time are essential for real-time fault-tolerant quantum computing. We introduce a scalable AI-based pre-decoder for the surface code that performs local, parallel error correction with low decoding runtimes, removing the majority of physical errors before passing residual syndromes to a downstream global decoder. This modular architecture is backend-agnostic and composes with arbitrary global decoding algorithms designed for surface codes, and our implementation is completely open source. Integrated with uncorrelated PyMatching, the pipeline achieves end-to-end decoding runtimes of order O(1 μs) per round at large code distances on NVIDIA GB300 GPUs while reducing logical error rates (LERs) relative to global decoding alone. In a block-wise parallel decoding scheme with access to multiple GPUs, the decoding runtime can be reduced to well below O(1 μs) per round. We observe further LER improvements by training a larger model, outperforming correlated PyMatching up to distance-13. We additionally introduce a noise-learning architecture that infers decoding weights directly from experimentally accessible syndrome statistics without requiring an explicit circuit-level noise model. We show that purely data-driven graph weight estimation can nearly match uncorrelated PyMatching and exceed correlated PyMatching in certain regimes, enabling highly-optimized decoding when hardware noise models are unknown or time-varying, as well as training pre-decoders with realistic noise models. Together, these results establish a practical, modular, and high-throughput decoding framework suitable for large-distance surface-code implementations.

Training-free metrics (a.k.a. zero-cost proxies) are widely used to avoid resource-intensive neural network training, especially in Neural Architecture Search (NAS). Recent studies show that existing training-free metrics have several limitations, such as limited correlation and poor generalisation across different search spaces and tasks. Hence, we propose Sample-Wise Activation Patterns and its derivative, SWAP-Score, a novel high-performance training-free metric. It measures the expressivity of networks over a batch of input samples. The SWAP-Score is strongly correlated with ground-truth performance across various search spaces and tasks, outperforming 15 existing training-free metrics on NAS-Bench-101/201/301 and TransNAS-Bench-101. The SWAP-Score can be further enhanced by regularisation, which leads to even higher correlations in cell-based search space and enables model size control during the search. For example, Spearman's rank correlation coefficient between regularised SWAP-Score and CIFAR-100 validation accuracies on NAS-Bench-201 networks is 0.90, significantly higher than 0.80 from the second-best metric, NWOT. When integrated with an evolutionary algorithm for NAS, our SWAP-NAS achieves competitive performance on CIFAR-10 and ImageNet in approximately 6 minutes and 9 minutes of GPU time respectively.

This work proposes a simple yet effective sampling framework for combinatorial optimization (CO). Our method builds on discrete Langevin dynamics (LD), an efficient gradient-guided generative paradigm. However, we observe that directly applying LD often leads to limited exploration. To overcome this limitation, we propose the Regularized Langevin Dynamics (RLD), which enforces an expected distance between the sampled and current solutions, effectively avoiding local minima. We develop two CO solvers on top of RLD, one based on simulated annealing (SA), and the other one based on neural network (NN). Empirical results on three classic CO problems demonstrate that both of our methods can achieve comparable or better performance against the previous state-of-the-art (SOTA) SA- and NN-based solvers. In particular, our SA algorithm reduces the runtime of the previous SOTA SA method by up to 80\%, while achieving equal or superior performance. In summary, RLD offers a promising framework for enhancing both traditional heuristics and NN models to solve CO problems. Our code is available at https://github.com/Shengyu-Feng/RLD4CO.

Training deep neural networks--and more recently, large models--demands efficient and scalable optimizers. Adaptive gradient algorithms like Adam, AdamW, and their variants have been central to this task. Despite the development of numerous variance reduction algorithms in the past decade aimed at accelerating stochastic optimization in both convex and nonconvex settings, variance reduction has not found widespread success in training deep neural networks or large language models. Consequently, it has remained a less favored approach in modern AI. In this paper, to unleash the power of variance reduction for efficient training of large models, we propose a unified optimization framework, MARS (Make vAriance Reduction Shine), which reconciles preconditioned gradient methods with variance reduction via a scaled stochastic recursive momentum technique. Within our framework, we introduce three instances of MARS that leverage preconditioned gradient updates based on AdamW, Lion, and Shampoo, respectively. We also draw a connection between our algorithms and existing optimizers. Experimental results on training GPT-2 models indicate that MARS consistently outperforms AdamW by a large margin.

Weighted graphs are ubiquitous throughout biology, chemistry, and the social sciences, motivating the development of generative models for abstract weighted graph data using deep neural networks. However, most current deep generative models are either designed for unweighted graphs and are not easily extended to weighted topologies or incorporate edge weights without consideration of a joint distribution with topology. Furthermore, learning a distribution over weighted graphs must account for complex nonlocal dependencies between both the edges of the graph and corresponding weights of each edge. We develop an autoregressive model BiGG-E, a nontrivial extension of the BiGG model, that learns a joint distribution over weighted graphs while still exploiting sparsity to generate a weighted graph with n nodes and m edges in O((n + m)log n) time. Simulation studies and experiments on a variety of benchmark datasets demonstrate that BiGG-E best captures distributions over weighted graphs while remaining scalable and computationally efficient.

Weight-space merging aims to combine multiple fine-tuned LLMs into a single model without retraining, yet most existing approaches remain fundamentally parameter-space heuristics. This creates three practical limitations. First, linear averaging, task vectors, and related rules operate on Euclidean coordinates, even though the desired goal is to merge functionality, i.e., predictive behaviors across tasks. Second, when the source checkpoints are farther apart or more heterogeneous, Euclidean blends often trigger representation collapse, manifested as activation variance shrinkage and effective-rank degradation, which sharply degrades accuracy. Third, many geometry-inspired methods are most natural for two-model interpolation and do not extend cleanly to merging N>2 experts with a principled objective. We address these issues by formulating model merging as computing a weighted Karcher mean on the Fisher--Rao manifold, which is locally equivalent to minimizing a KL-based function distance between predictive distributions. We derive a practical fixed-point algorithm using a lightweight spherical proxy that preserves norms and generalizes directly to multi-expert merging. Across various benchmarks and collapse diagnostics, our method remains stable as the number and heterogeneity of merged models increase, consistently outperforming prior baselines.

In recent years, particle-based variational inference (ParVI) methods such as Stein variational gradient descent (SVGD) have grown in popularity as scalable methods for Bayesian inference. Unfortunately, the properties of such methods invariably depend on hyperparameters such as the learning rate, which must be carefully tuned by the practitioner in order to ensure convergence to the target measure at a suitable rate. In this paper, we introduce a suite of new particle-based methods for scalable Bayesian inference based on coin betting, which are entirely learning-rate free. We illustrate the performance of our approach on a range of numerical examples, including several high-dimensional models and datasets, demonstrating comparable performance to other ParVI algorithms with no need to tune a learning rate.

Classifier-free guidance (CFG) is a widely used technique for controllable generation in diffusion and flow-based models. Despite its empirical success, CFG relies on a heuristic linear extrapolation that is often sensitive to the guidance scale. In this work, we provide a principled interpretation of CFG through the lens of optimization. We demonstrate that the velocity field in flow matching corresponds to the gradient of a sequence of smoothed distance functions, which guides latent variables toward the scaled target image set. This perspective reveals that the standard CFG formulation is an approximation of this gradient, where the prediction gap, the discrepancy between conditional and unconditional outputs, governs guidance sensitivity. Leveraging this insight, we reformulate the CFG sampling as a homotopy optimization with a manifold constraint. This formulation necessitates a manifold projection step, which we implement via an incremental gradient descent scheme during sampling. To improve computational efficiency and stability, we further enhance this iterative process with Anderson Acceleration without requiring additional model evaluations. Our proposed methods are training-free and consistently refine generation fidelity, prompt alignment, and robustness to the guidance scale. We validate their effectiveness across diverse benchmarks, demonstrating significant improvements on large-scale models such as DiT-XL-2-256, Flux, and Stable Diffusion 3.5.

Recently, Ainsworth et al. showed that using weight matching (WM) to minimize the L_2 distance in a permutation search of model parameters effectively identifies permutations that satisfy linear mode connectivity (LMC), in which the loss along a linear path between two independently trained models with different seeds remains nearly constant. This paper provides a theoretical analysis of LMC using WM, which is crucial for understanding stochastic gradient descent's effectiveness and its application in areas like model merging. We first experimentally and theoretically show that permutations found by WM do not significantly reduce the L_2 distance between two models and the occurrence of LMC is not merely due to distance reduction by WM in itself. We then provide theoretical insights showing that permutations can change the directions of the singular vectors, but not the singular values, of the weight matrices in each layer. This finding shows that permutations found by WM mainly align the directions of singular vectors associated with large singular values across models. This alignment brings the singular vectors with large singular values, which determine the model functionality, closer between pre-merged and post-merged models, so that the post-merged model retains functionality similar to the pre-merged models, making it easy to satisfy LMC. Finally, we analyze the difference between WM and straight-through estimator (STE), a dataset-dependent permutation search method, and show that WM outperforms STE, especially when merging three or more models.

Learning a transport model that maps a source distribution to a target distribution is a canonical problem in machine learning, but scientific applications increasingly require models that can generalize to source and target distributions unseen during training. We introduce distribution-conditioned transport (DCT), a framework that conditions transport maps on learned embeddings of source and target distributions, enabling generalization to unseen distribution pairs. DCT also allows semi-supervised learning for distributional forecasting problems: because it learns from arbitrary distribution pairs, it can leverage distributions observed at only one condition to improve transport prediction. DCT is agnostic to the underlying transport mechanism, supporting models ranging from flow matching to distributional divergence-based models (e.g. Wasserstein, MMD). We demonstrate the practical performance benefits of DCT on synthetic benchmarks and four applications in biology: batch effect transfer in single-cell genomics, perturbation prediction from mass cytometry data, learning clonal transcriptional dynamics in hematopoiesis, and modeling T-cell receptor sequence evolution.

Building efficient and effective generative models for neural network weights has been a research focus of significant interest that faces challenges posed by the high-dimensional weight spaces of modern neural networks and their symmetries. Several prior generative models are limited to generating partial neural network weights, particularly for larger models, such as ResNet and ViT. Those that do generate complete weights struggle with generation speed or require finetuning of the generated models. In this work, we present DeepWeightFlow, a Flow Matching model that operates directly in weight space to generate diverse and high-accuracy neural network weights for a variety of architectures, neural network sizes, and data modalities. The neural networks generated by DeepWeightFlow do not require fine-tuning to perform well and can scale to large networks. We apply Git Re-Basin and TransFusion for neural network canonicalization in the context of generative weight models to account for the impact of neural network permutation symmetries and to improve generation efficiency for larger model sizes. The generated networks excel at transfer learning, and ensembles of hundreds of neural networks can be generated in minutes, far exceeding the efficiency of diffusion-based methods. DeepWeightFlow models pave the way for more efficient and scalable generation of diverse sets of neural networks.

Many natural dynamic processes -- such as in vivo cellular differentiation or disease progression -- can only be observed through the lens of static sample snapshots. While challenging, reconstructing their temporal evolution to decipher underlying dynamic properties is of major interest to scientific research. Existing approaches enable data transport along a temporal axis but are poorly scalable in high dimension and require restrictive assumptions to be met. To address these issues, we propose \textbf{Multi-Marginal temporal Schr\"odinger Bridge Matching} (MMtSBM) for video generation from unpaired data, extending the theoretical guarantees and empirical efficiency of Diffusion Schr\"odinger Bridge Matching (arXiv:archive/2303.16852) by deriving the Iterative Markovian Fitting algorithm to multiple marginals in a novel factorized fashion. Experiments show that MMtSBM retains theoretical properties on toy examples, achieves state-of-the-art performance on real world datasets such as transcriptomic trajectory inference in 100 dimensions, and for the first time recovers couplings and dynamics in very high dimensional image settings. Our work establishes multi-marginal Schr\"odinger bridges as a practical and principled approach for recovering hidden dynamics from static data.

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.

Generating graph-structured data requires learning the underlying distribution of graphs. Yet, this is a challenging problem, and the previous graph generative methods either fail to capture the permutation-invariance property of graphs or cannot sufficiently model the complex dependency between nodes and edges, which is crucial for generating real-world graphs such as molecules. To overcome such limitations, we propose a novel score-based generative model for graphs with a continuous-time framework. Specifically, we propose a new graph diffusion process that models the joint distribution of the nodes and edges through a system of stochastic differential equations (SDEs). Then, we derive novel score matching objectives tailored for the proposed diffusion process to estimate the gradient of the joint log-density with respect to each component, and introduce a new solver for the system of SDEs to efficiently sample from the reverse diffusion process. We validate our graph generation method on diverse datasets, on which it either achieves significantly superior or competitive performance to the baselines. Further analysis shows that our method is able to generate molecules that lie close to the training distribution yet do not violate the chemical valency rule, demonstrating the effectiveness of the system of SDEs in modeling the node-edge relationships. Our code is available at https://github.com/harryjo97/GDSS.

Diffusion models based on permutation-equivariant networks can learn permutation-invariant distributions for graph data. However, in comparison to their non-invariant counterparts, we have found that these invariant models encounter greater learning challenges since 1) their effective target distributions exhibit more modes; 2) their optimal one-step denoising scores are the score functions of Gaussian mixtures with more components. Motivated by this analysis, we propose a non-invariant diffusion model, called SwinGNN, which employs an efficient edge-to-edge 2-WL message passing network and utilizes shifted window based self-attention inspired by SwinTransformers. Further, through systematic ablations, we identify several critical training and sampling techniques that significantly improve the sample quality of graph generation. At last, we introduce a simple post-processing trick, i.e., randomly permuting the generated graphs, which provably converts any graph generative model to a permutation-invariant one. Extensive experiments on synthetic and real-world protein and molecule datasets show that our SwinGNN achieves state-of-the-art performances. Our code is released at https://github.com/qiyan98/SwinGNN.

Recent studies have demonstrated the strong empirical performance of diffusion models on discrete sequences across domains from natural language to biological sequence generation. For example, in the protein inverse folding task, conditional diffusion models have achieved impressive results in generating natural-like sequences that fold back into the original structure. However, practical design tasks often require not only modeling a conditional distribution but also optimizing specific task objectives. For instance, we may prefer protein sequences with high stability. To address this, we consider the scenario where we have pre-trained discrete diffusion models that can generate natural-like sequences, as well as reward models that map sequences to task objectives. We then formulate the reward maximization problem within discrete diffusion models, analogous to reinforcement learning (RL), while minimizing the KL divergence against pretrained diffusion models to preserve naturalness. To solve this RL problem, we propose a novel algorithm, DRAKES, that enables direct backpropagation of rewards through entire trajectories generated by diffusion models, by making the originally non-differentiable trajectories differentiable using the Gumbel-Softmax trick. Our theoretical analysis indicates that our approach can generate sequences that are both natural-like and yield high rewards. While similar tasks have been recently explored in diffusion models for continuous domains, our work addresses unique algorithmic and theoretical challenges specific to discrete diffusion models, which arise from their foundation in continuous-time Markov chains rather than Brownian motion. Finally, we demonstrate the effectiveness of DRAKES in generating DNA and protein sequences that optimize enhancer activity and protein stability, respectively, important tasks for gene therapies and protein-based therapeutics.

Diffusion models excel at joint pixel sampling for image generation but lack efficient training-free methods for partial conditional sampling (e.g., inpainting with known pixels). Prior work typically formulates this as an intractable inverse problem, relying on coarse variational approximations, heuristic losses requiring expensive backpropagation, or slow stochastic sampling. These limitations preclude: (1) accurate distributional matching in inpainting results, (2) efficient inference modes without gradient, (3) compatibility with fast ODE-based samplers. To address these limitations, we propose LanPaint: a training-free, asymptotically exact partial conditional sampling methods for ODE-based and rectified flow diffusion models. By leveraging carefully designed Langevin dynamics, LanPaint enables fast, backpropagation-free Monte Carlo sampling. Experiments demonstrate that our approach achieves superior performance with precise partial conditioning and visually coherent inpainting across diverse tasks.

Realistic hair strand generation is crucial for applications like computer graphics and virtual reality. While diffusion models can generate hairstyles from text or images, these inputs lack precision and user-friendliness. Instead, we propose the first sketch-based strand generation model, which offers finer control while remaining user-friendly. Our framework tackles key challenges, such as modeling complex strand interactions and diverse sketch patterns, through two main innovations: a learnable strand upsampling strategy that encodes 3D strands into multi-scale latent spaces, and a multi-scale adaptive conditioning mechanism using a transformer with diffusion heads to ensure consistency across granularity levels. Experiments on several benchmark datasets show our method outperforms existing approaches in realism and precision. Qualitative results further confirm its effectiveness. Code will be released at [GitHub](https://github.com/fighting-Zhang/StrandDesigner).

Given an unconditional diffusion model and a predictor for a target property of interest (e.g., a classifier), the goal of training-free guidance is to generate samples with desirable target properties without additional training. Existing methods, though effective in various individual applications, often lack theoretical grounding and rigorous testing on extensive benchmarks. As a result, they could even fail on simple tasks, and applying them to a new problem becomes unavoidably difficult. This paper introduces a novel algorithmic framework encompassing existing methods as special cases, unifying the study of training-free guidance into the analysis of an algorithm-agnostic design space. Via theoretical and empirical investigation, we propose an efficient and effective hyper-parameter searching strategy that can be readily applied to any downstream task. We systematically benchmark across 7 diffusion models on 16 tasks with 40 targets, and improve performance by 8.5% on average. Our framework and benchmark offer a solid foundation for conditional generation in a training-free manner.

We present a novel approach to accelerate stochastic gradient descent (SGD) by utilizing curvature information obtained from Hessian-vector products or finite differences of parameters and gradients, similar to the BFGS algorithm. Our approach involves two preconditioners: a matrix-free preconditioner and a low-rank approximation preconditioner. We update both preconditioners online using a criterion that is robust to stochastic gradient noise and does not require line search or damping. To preserve the corresponding symmetry or invariance, our preconditioners are constrained to certain connected Lie groups. The Lie group's equivariance property simplifies the preconditioner fitting process, while its invariance property eliminates the need for damping, which is commonly required in second-order optimizers. As a result, the learning rate for parameter updating and the step size for preconditioner fitting are naturally normalized, and their default values work well in most scenarios. Our proposed approach offers a promising direction for improving the convergence of SGD with low computational overhead. We demonstrate that Preconditioned SGD (PSGD) outperforms SoTA on Vision, NLP, and RL tasks across multiple modern deep-learning architectures. We have provided code for reproducing toy and large scale experiments in this paper.

Designing sequences that satisfy multiple, often conflicting, objectives is a central challenge in therapeutic and biomolecular engineering. Existing generative frameworks largely operate in continuous spaces with single-objective guidance, while discrete approaches lack guarantees for multi-objective Pareto optimality. We introduce AReUReDi (Annealed Rectified Updates for Refining Discrete Flows), a discrete optimization algorithm with theoretical guarantees of convergence to the Pareto front. Building on Rectified Discrete Flows (ReDi), AReUReDi combines Tchebycheff scalarization, locally balanced proposals, and annealed Metropolis-Hastings updates to bias sampling toward Pareto-optimal states while preserving distributional invariance. Applied to peptide and SMILES sequence design, AReUReDi simultaneously optimizes up to five therapeutic properties (including affinity, solubility, hemolysis, half-life, and non-fouling) and outperforms both evolutionary and diffusion-based baselines. These results establish AReUReDi as a powerful, sequence-based framework for multi-property biomolecule generation.

Diffusion and flow models have become the dominant paradigm for generative modeling on Riemannian manifolds, with successful applications in protein backbone generation and DNA sequence design. However, these methods require tens to hundreds of neural network evaluations at inference time, which can become a computational bottleneck in large-scale scientific sampling workflows. We introduce Riemannian MeanFlow~(RMF), a framework for learning flow maps directly on manifolds, enabling high-quality generations with as few as one forward pass. We derive three equivalent characterizations of the manifold average velocity (Eulerian, Lagrangian, and semigroup identities), and analyze parameterizations and stabilization techniques to improve training on high-dimensional manifolds. In promoter DNA design and protein backbone generation settings, RMF achieves comparable sample quality to prior methods while requiring up to 10times fewer function evaluations. Finally, we show that few-step flow maps enable efficient reward-guided design through reward look-ahead, where terminal states can be predicted from intermediate steps at minimal additional cost.

The Entropic Optimal Transport (EOT) problem and its dynamic counterpart, the Schrödinger bridge (SB) problem, play an important role in modern machine learning, linking generative modeling with optimal transport theory. While recent advances in discrete diffusion and flow models have sparked growing interest in applying SB methods to discrete domains, there is still no reliable way to evaluate how well these methods actually solve the underlying problem. We address this challenge by introducing a benchmark for SB on discrete spaces. Our construction yields pairs of probability distributions with analytically known SB solutions, enabling rigorous evaluation. As a byproduct of building this benchmark, we obtain two new SB algorithms, DLightSB and DLightSB-M, and additionally extend prior related work to construct the α-CSBM algorithm. We demonstrate the utility of our benchmark by evaluating both existing and new solvers in high-dimensional discrete settings. This work provides the first step toward proper evaluation of SB methods on discrete spaces, paving the way for more reproducible future studies.

Non-linear state-space models, also known as general hidden Markov models, are ubiquitous in statistical machine learning, being the most classical generative models for serial data and sequences in general. The particle-based, rapid incremental smoother PaRIS is a sequential Monte Carlo (SMC) technique allowing for efficient online approximation of expectations of additive functionals under the smoothing distribution in these models. Such expectations appear naturally in several learning contexts, such as likelihood estimation (MLE) and Markov score climbing (MSC). PARIS has linear computational complexity, limited memory requirements and comes with non-asymptotic bounds, convergence results and stability guarantees. Still, being based on self-normalised importance sampling, the PaRIS estimator is biased. Our first contribution is to design a novel additive smoothing algorithm, the Parisian particle Gibbs PPG sampler, which can be viewed as a PaRIS algorithm driven by conditional SMC moves, resulting in bias-reduced estimates of the targeted quantities. We substantiate the PPG algorithm with theoretical results, including new bounds on bias and variance as well as deviation inequalities. Our second contribution is to apply PPG in a learning framework, covering MLE and MSC as special examples. In this context, we establish, under standard assumptions, non-asymptotic bounds highlighting the value of bias reduction and the implicit Rao--Blackwellization of PPG. These are the first non-asymptotic results of this kind in this setting. We illustrate our theoretical results with numerical experiments supporting our claims.

Inference-time scaling offers a versatile paradigm for aligning visual generative models with downstream objectives without parameter updates. However, existing approaches that optimize the high-dimensional initial noise suffer from severe inefficiency, as many search directions exert negligible influence on the final generation. We show that this inefficiency is closely related to a spectral bias in generative dynamics: model sensitivity to initial perturbations diminishes rapidly as frequency increases. Building on this insight, we propose Spectral Evolution Search (SES), a plug-and-play framework for initial noise optimization that executes gradient-free evolutionary search within a low-frequency subspace. Theoretically, we derive the Spectral Scaling Prediction from perturbation propagation dynamics, which explains the systematic differences in the impact of perturbations across frequencies. Extensive experiments demonstrate that SES significantly advances the Pareto frontier of generation quality versus computational cost, consistently outperforming strong baselines under equivalent budgets.

Modeling stochastic dynamics from discrete observations is a key interdisciplinary challenge. Existing methods often fail to estimate the continuous evolution of probability densities from trajectories or face the curse of dimensionality. To address these limitations, we presents a novel paradigm: modeling dynamics directly in the weight space of a neural network by projecting the evolving probability distribution. We first theoretically establish the connection between dynamic optimal transport in measure space and an equivalent energy functional in weight space. Subsequently, we design WeightFlow, which constructs the neural network weights into a graph and learns its evolution via a graph controlled differential equation. Experiments on interdisciplinary datasets demonstrate that WeightFlow improves performance by an average of 43.02\% over state-of-the-art methods, providing an effective and scalable solution for modeling high-dimensional stochastic dynamics.

Designing antibody sequences to better resemble those observed in natural human repertoires is a key challenge in biologics development. We introduce IgCraft: a multi-purpose model for paired human antibody sequence generation, built on Bayesian Flow Networks. IgCraft presents one of the first unified generative modeling frameworks capable of addressing multiple antibody sequence design tasks with a single model, including unconditional sampling, sequence inpainting, inverse folding, and CDR motif scaffolding. Our approach achieves competitive results across the full spectrum of these tasks while constraining generation to the space of human antibody sequences, exhibiting particular strengths in CDR motif scaffolding (grafting) where we achieve state-of-the-art performance in terms of humanness and preservation of structural properties. By integrating previously separate tasks into a single scalable generative model, IgCraft provides a versatile platform for sampling human antibody sequences under a variety of contexts relevant to antibody discovery and engineering. Model code and weights are publicly available at github.com/mgreenig/IgCraft.

We introduce Psi-Sampler, an SMC-based framework incorporating pCNL-based initial particle sampling for effective inference-time reward alignment with a score-based generative model. Inference-time reward alignment with score-based generative models has recently gained significant traction, following a broader paradigm shift from pre-training to post-training optimization. At the core of this trend is the application of Sequential Monte Carlo (SMC) to the denoising process. However, existing methods typically initialize particles from the Gaussian prior, which inadequately captures reward-relevant regions and results in reduced sampling efficiency. We demonstrate that initializing from the reward-aware posterior significantly improves alignment performance. To enable posterior sampling in high-dimensional latent spaces, we introduce the preconditioned Crank-Nicolson Langevin (pCNL) algorithm, which combines dimension-robust proposals with gradient-informed dynamics. This approach enables efficient and scalable posterior sampling and consistently improves performance across various reward alignment tasks, including layout-to-image generation, quantity-aware generation, and aesthetic-preference generation, as demonstrated in our experiments.

Neural networks increasingly embed non-differentiable components (spiking neurons, quantized layers, discrete routing, blackbox simulators, etc.) where backpropagation is inapplicable and surrogate gradients introduce bias. We present PolyStep, a gradient-free optimizer that updates parameters using only forward passes. Each step evaluates the loss at structured polytope vertices in a compressed subspace, computes softmax-weighted assignments over the resulting cost matrix, and displaces particles toward low-cost vertices via barycentric projection. This update corresponds to the one-sided limit of a regularized optimal-transport problem, inheriting its geometric structure without Sinkhorn iterations. PolyStep trains genuinely non-differentiable models where existing gradient-free methods collapse to near-random accuracy. On hard-LIF spiking networks we reach 93.4% test accuracy, outperforming all gradient-free baselines by over 60~pp and closing to within 4.4~pp of a surrogate-gradient Adam ceiling. Across four additional non-differentiable architectures (int8 quantization, argmax attention, staircase activations, hard MoE routing) we lead every gradient-free competitor. On MAX-SAT scaling from 100 to 1M variables, we sustain above 92% clause satisfaction while evolution strategies drop 8--12~pp. On RL policy search, we match OpenAI-ES on classical control and retain performance under integer and binary quantization that collapses gradient-based methods. We prove convergence to conservative-stationary points at rate O(log T/T) on piecewise-smooth losses, upgraded to Clarke-stationary on the headline architectures and extended to the piecewise-constant regime via a hitting-time bound. These rates match the known zeroth-order query-complexity lower bounds that all forward-only methods inherit. Code is available at https://github.com/anindex/polystep.

Many real-world problems require reasoning across multiple scales, demanding models which operate not on single data points, but on entire distributions. We introduce generative distribution embeddings (GDE), a framework that lifts autoencoders to the space of distributions. In GDEs, an encoder acts on sets of samples, and the decoder is replaced by a generator which aims to match the input distribution. This framework enables learning representations of distributions by coupling conditional generative models with encoder networks which satisfy a criterion we call distributional invariance. We show that GDEs learn predictive sufficient statistics embedded in the Wasserstein space, such that latent GDE distances approximately recover the W_2 distance, and latent interpolation approximately recovers optimal transport trajectories for Gaussian and Gaussian mixture distributions. We systematically benchmark GDEs against existing approaches on synthetic datasets, demonstrating consistently stronger performance. We then apply GDEs to six key problems in computational biology: learning representations of cell populations from lineage-tracing data (150K cells), predicting perturbation effects on single-cell transcriptomes (1M cells), predicting perturbation effects on cellular phenotypes (20M single-cell images), modeling tissue-specific DNA methylation patterns (253M sequences), designing synthetic yeast promoters (34M sequences), and spatiotemporal modeling of viral protein sequences (1M sequences).

Text-to-image diffusion models deliver high-quality images, yet aligning them with human preferences remains challenging. We revisit diffusion-based Direct Preference Optimization (DPO) for these models and identify a critical pathology: enlarging the preference margin does not necessarily improve generation quality. In particular, the standard Diffusion-DPO objective can increase the reconstruction error of both winner and loser branches. Consequently, degradation of the less-preferred outputs can become sufficiently severe that the preferred branch is also adversely affected even as the margin grows. To address this, we introduce Diffusion-SDPO, a safeguarded update rule that preserves the winner by adaptively scaling the loser gradient according to its alignment with the winner gradient. A first-order analysis yields a closed-form scaling coefficient that guarantees the error of the preferred output is non-increasing at each optimization step. Our method is simple, model-agnostic, broadly compatible with existing DPO-style alignment frameworks and adds only marginal computational overhead. Across standard text-to-image benchmarks, Diffusion-SDPO delivers consistent gains over preference-learning baselines on automated preference, aesthetic, and prompt alignment metrics. Code is publicly available at https://github.com/AIDC-AI/Diffusion-SDPO.

Using the weights of trained Neural Network (NN) models as data modality has recently gained traction as a research field - dubbed Weight Space Learning (WSL). Multiple recent works propose WSL methods to analyze models, evaluate methods, or synthesize weights. Weight space learning methods require populations of trained models as datasets for development and evaluation. However, existing collections of models - called `model zoos' - are unstructured or follow a rudimentary definition of diversity. In parallel, work rooted in statistical physics has identified phases and phase transitions in NN models. Models are homogeneous within the same phase but qualitatively differ from one phase to another. We combine the idea of `model zoos' with phase information to create a controlled notion of diversity in populations. We introduce 12 large-scale zoos that systematically cover known phases and vary over model architecture, size, and datasets. These datasets cover different modalities, such as computer vision, natural language processing, and scientific ML. For every model, we compute loss landscape metrics and validate full coverage of the phases. With this dataset, we provide the community with a resource with a wide range of potential applications for WSL and beyond. Evidence suggests the loss landscape phase plays a role in applications such as model training, analysis, or sparsification. We demonstrate this in an exploratory study of the downstream methods like transfer learning or model weights averaging.

We introduce Gradient Agreement Filtering (GAF) to improve on gradient averaging in distributed deep learning optimization. Traditional distributed data-parallel stochastic gradient descent involves averaging gradients of microbatches to calculate a macrobatch gradient that is then used to update model parameters. We find that gradients across microbatches are often orthogonal or negatively correlated, especially in late stages of training, which leads to memorization of the training set, reducing generalization. In this paper, we introduce a simple, computationally effective way to reduce gradient variance by computing the cosine distance between micro-gradients during training and filtering out conflicting updates prior to averaging. We improve validation accuracy with significantly smaller microbatch sizes. We also show this reduces memorizing noisy labels. We demonstrate the effectiveness of this technique on standard image classification benchmarks including CIFAR-100 and CIFAR-100N-Fine. We show this technique consistently outperforms validation accuracy, in some cases by up to 18.2\% compared to traditional training approaches while reducing the computation required nearly an order of magnitude because we can now rely on smaller microbatch sizes without destabilizing training.

Machine learning-based unfolding has enabled unbinned and high-dimensional differential cross section measurements. Two main approaches have emerged in this research area: one based on discriminative models and one based on generative models. The main advantage of discriminative models is that they learn a small correction to a starting simulation while generative models scale better to regions of phase space with little data. We propose to use Schroedinger Bridges and diffusion models to create SBUnfold, an unfolding approach that combines the strengths of both discriminative and generative models. The key feature of SBUnfold is that its generative model maps one set of events into another without having to go through a known probability density as is the case for normalizing flows and standard diffusion models. We show that SBUnfold achieves excellent performance compared to state of the art methods on a synthetic Z+jets dataset.

Classifying genome sequences based on metadata has been an active area of research in comparative genomics for decades with many important applications across the life sciences. Established methods for classifying genomes can be broadly grouped into sequence alignment-based and alignment-free models. Conventional alignment-based models rely on genome similarity measures calculated based on local sequence alignments or consistent ordering among sequences. However, such methods are computationally expensive when dealing with large ensembles of even moderately sized genomes. In contrast, alignment-free (AF) approaches measure genome similarity based on summary statistics in an unsupervised setting and are efficient enough to analyze large datasets. However, both alignment-based and AF methods typically assume fixed scoring rubrics that lack the flexibility to assign varying importance to different parts of the sequences based on prior knowledge. In this study, we integrate AI and network science approaches to develop a comparative genomic analysis framework that addresses these limitations. Our approach, termed the Genome Misclassification Network Analysis (GMNA), simultaneously leverages misclassified instances, a learned scoring rubric, and label information to classify genomes based on associated metadata and better understand potential drivers of misclassification. We evaluate the utility of the GMNA using Naive Bayes and convolutional neural network models, supplemented by additional experiments with transformer-based models, to construct SARS-CoV-2 sampling location classifiers using over 500,000 viral genome sequences and study the resulting network of misclassifications. We demonstrate the global health potential of the GMNA by leveraging the SARS-CoV-2 genome misclassification networks to investigate the role human mobility played in structuring geographic clustering of SARS-CoV-2.

The Multi-Prize Lottery Ticket Hypothesis posits that randomly initialized neural networks contain several subnetworks that achieve comparable accuracy to fully trained models of the same architecture. However, current methods require that the network is sufficiently overparameterized. In this work, we propose a modification to two state-of-the-art algorithms (Edge-Popup and Biprop) that finds high-accuracy subnetworks with no additional storage cost or scaling. The algorithm, Iterative Weight Recycling, identifies subsets of important weights within a randomly initialized network for intra-layer reuse. Empirically we show improvements on smaller network architectures and higher prune rates, finding that model sparsity can be increased through the "recycling" of existing weights. In addition to Iterative Weight Recycling, we complement the Multi-Prize Lottery Ticket Hypothesis with a reciprocal finding: high-accuracy, randomly initialized subnetwork's produce diverse masks, despite being generated with the same hyperparameter's and pruning strategy. We explore the landscapes of these masks, which show high variability.

In this paper, we study a class of composite optimization problems whose objective function is given by the summation of a general smooth and nonsmooth component, together with a relatively simple nonsmooth term. While restart strategies are commonly employed in first-order methods to achieve optimal convergence under strong convexity, they introduce structural complexity and practical overhead, making algorithm design and nesting cumbersome. To address this, we propose a restart-free stochastic gradient sliding algorithm that eliminates the need for explicit restart phases when the simple nonsmooth component is strongly convex. Through a novel and carefully designed parameter selection strategy, we prove that the proposed algorithm achieves an ε-solution with only O(log(1ε)) gradient evaluations for the smooth component and O(1ε) stochastic subgradient evaluations for the nonsmooth component, matching the optimal complexity of existing multi-phase (restart-based) methods. Moreover, for the case where the nonsmooth component is structured, allowing the overall problem to be reformulated as a bilinear saddle-point problem, we develop a restart-free accelerated stochastic gradient sliding algorithm. We show that the resulting method requires only O(log(1ε)) gradient computations for the smooth component while preserving an overall iteration complexity of O(1{sqrtε}) for solving the corresponding saddle-point problems. Our work thus provides simpler, restart-f

Given a set of K probability densities, we consider the multimarginal generative modeling problem of learning a joint distribution that recovers these densities as marginals. The structure of this joint distribution should identify multi-way correspondences among the prescribed marginals. We formalize an approach to this task within a generalization of the stochastic interpolant framework, leading to efficient learning algorithms built upon dynamical transport of measure. Our generative models are defined by velocity and score fields that can be characterized as the minimizers of simple quadratic objectives, and they are defined on a simplex that generalizes the time variable in the usual dynamical transport framework. The resulting transport on the simplex is influenced by all marginals, and we show that multi-way correspondences can be extracted. The identification of such correspondences has applications to style transfer, algorithmic fairness, and data decorruption. In addition, the multimarginal perspective enables an efficient algorithm for reducing the dynamical transport cost in the ordinary two-marginal setting. We demonstrate these capacities with several numerical examples.

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.

Distribution Matching Distillation (DMD) is a powerful acceleration paradigm, yet its stability is often compromised in Forbidden Zone, regions where the real teacher provides unreliable guidance while the fake teacher exerts insufficient repulsive force. In this work, we propose a unified optimization framework that reinterprets prior art as implicit strategies to avoid these corrupted regions. Based on this insight, we introduce Adaptive Matching Distillation (AMD), a self-correcting mechanism that utilizes reward proxies to explicitly detect and escape Forbidden Zones. AMD dynamically prioritizes corrective gradients via structural signal decomposition and introduces Repulsive Landscape Sharpening to enforce steep energy barriers against failure mode collapse. Extensive experiments across image and video generation tasks (e.g., SDXL, Wan2.1) and rigorous benchmarks (e.g., VBench, GenEval) demonstrate that AMD significantly enhances sample fidelity and training robustness. For instance, AMD improves the HPSv2 score on SDXL from 30.64 to 31.25, outperforming state-of-the-art baselines. These findings validate that explicitly rectifying optimization trajectories within Forbidden Zones is essential for pushing the performance ceiling of few-step generative models.

The problem of visual metamerism is defined as finding a family of perceptually indistinguishable, yet physically different images. In this paper, we propose our NeuroFovea metamer model, a foveated generative model that is based on a mixture of peripheral representations and style transfer forward-pass algorithms. Our gradient-descent free model is parametrized by a foveated VGG19 encoder-decoder which allows us to encode images in high dimensional space and interpolate between the content and texture information with adaptive instance normalization anywhere in the visual field. Our contributions include: 1) A framework for computing metamers that resembles a noisy communication system via a foveated feed-forward encoder-decoder network -- We observe that metamerism arises as a byproduct of noisy perturbations that partially lie in the perceptual null space; 2) A perceptual optimization scheme as a solution to the hyperparametric nature of our metamer model that requires tuning of the image-texture tradeoff coefficients everywhere in the visual field which are a consequence of internal noise; 3) An ABX psychophysical evaluation of our metamers where we also find that the rate of growth of the receptive fields in our model match V1 for reference metamers and V2 between synthesized samples. Our model also renders metamers at roughly a second, presenting a times1000 speed-up compared to the previous work, which allows for tractable data-driven metamer experiments.

The ever-growing scale of deep learning models and training data underscores the critical importance of efficient optimization methods. While preconditioned gradient methods such as Adam and AdamW are the de facto optimizers for training neural networks and large language models, structure-aware preconditioned optimizers like Shampoo and Muon, which utilize the matrix structure of gradients, have demonstrated promising evidence of faster convergence. In this paper, we introduce a unifying framework for analyzing "matrix-aware" preconditioned methods, which not only sheds light on the effectiveness of Muon and related optimizers but also leads to a class of new structure-aware preconditioned methods. A key contribution of this framework is its precise distinction between preconditioning strategies that treat neural network weights as vectors (addressing curvature anisotropy) versus those that consider their matrix structure (addressing gradient anisotropy). This perspective provides new insights into several empirical phenomena in language model pre-training, including Adam's training instabilities, Muon's accelerated convergence, and the necessity of learning rate warmup for Adam. Building upon this framework, we introduce PolarGrad, a new class of preconditioned optimization methods based on the polar decomposition of matrix-valued gradients. As a special instance, PolarGrad includes Muon with updates scaled by the nuclear norm of the gradients. We provide numerical implementations of these methods, leveraging efficient numerical polar decomposition algorithms for enhanced convergence. Our extensive evaluations across diverse matrix optimization problems and language model pre-training tasks demonstrate that PolarGrad outperforms both Adam and Muon.

Based on the theory of homogeneous spaces we derive geometrically optimal edge attributes to be used within the flexible message-passing framework. We formalize the notion of weight sharing in convolutional networks as the sharing of message functions over point-pairs that should be treated equally. We define equivalence classes of point-pairs that are identical up to a transformation in the group and derive attributes that uniquely identify these classes. Weight sharing is then obtained by conditioning message functions on these attributes. As an application of the theory, we develop an efficient equivariant group convolutional network for processing 3D point clouds. The theory of homogeneous spaces tells us how to do group convolutions with feature maps over the homogeneous space of positions R^3, position and orientations R^3 {times} S^2, and the group SE(3) itself. Among these, R^3 {times} S^2 is an optimal choice due to the ability to represent directional information, which R^3 methods cannot, and it significantly enhances computational efficiency compared to indexing features on the full SE(3) group. We support this claim with state-of-the-art results -- in accuracy and speed -- on five different benchmarks in 2D and 3D, including interatomic potential energy prediction, trajectory forecasting in N-body systems, and generating molecules via equivariant diffusion models.

Training-free guided sampling in diffusion models leverages off-the-shelf pre-trained networks, such as an aesthetic evaluation model, to guide the generation process. Current training-free guided sampling algorithms obtain the guidance energy function based on a one-step estimate of the clean image. However, since the off-the-shelf pre-trained networks are trained on clean images, the one-step estimation procedure of the clean image may be inaccurate, especially in the early stages of the generation process in diffusion models. This causes the guidance in the early time steps to be inaccurate. To overcome this problem, we propose Symplectic Adjoint Guidance (SAG), which calculates the gradient guidance in two inner stages. Firstly, SAG estimates the clean image via n function calls, where n serves as a flexible hyperparameter that can be tailored to meet specific image quality requirements. Secondly, SAG uses the symplectic adjoint method to obtain the gradients accurately and efficiently in terms of the memory requirements. Extensive experiments demonstrate that SAG generates images with higher qualities compared to the baselines in both guided image and video generation tasks.

We propose a new uncertainty estimator for gradient-free optimisation of black-box simulators using deep generative surrogate models. Optimisation of these simulators is especially challenging for stochastic simulators and higher dimensions. To address these issues, we utilise a deep generative surrogate approach to model the black box response for the entire parameter space. We then leverage this knowledge to estimate the proposed uncertainty based on the Wasserstein distance - the Wasserstein uncertainty. This approach is employed in a posterior agnostic gradient-free optimisation algorithm that minimises regret over the entire parameter space. A series of tests were conducted to demonstrate that our method is more robust to the shape of both the black box function and the stochastic response of the black box than state-of-the-art methods, such as efficient global optimisation with a deep Gaussian process surrogate.

Classifier-Free Guidance (CFG) has been a default technique in various visual generative models, yet it requires inference from both conditional and unconditional models during sampling. We propose to build visual models that are free from guided sampling. The resulting algorithm, Guidance-Free Training (GFT), matches the performance of CFG while reducing sampling to a single model, halving the computational cost. Unlike previous distillation-based approaches that rely on pretrained CFG networks, GFT enables training directly from scratch. GFT is simple to implement. It retains the same maximum likelihood objective as CFG and differs mainly in the parameterization of conditional models. Implementing GFT requires only minimal modifications to existing codebases, as most design choices and hyperparameters are directly inherited from CFG. Our extensive experiments across five distinct visual models demonstrate the effectiveness and versatility of GFT. Across domains of diffusion, autoregressive, and masked-prediction modeling, GFT consistently achieves comparable or even lower FID scores, with similar diversity-fidelity trade-offs compared with CFG baselines, all while being guidance-free. Code will be available at https://github.com/thu-ml/GFT.

Given the generational gap in available hardware between lay practitioners and the most endowed institutions, LLMs are becoming increasingly inaccessible as they grow in size. Whilst many approaches have been proposed to compress LLMs to make their resource consumption manageable, these methods themselves tend to be resource intensive, putting them out of the reach of the very user groups they target. In this work, we explore the problem of structured pruning of LLMs using only forward passes. We seek to empower practitioners to prune models so large that their available hardware has just enough memory to run inference. We develop Bonsai, a gradient-free, perturbative pruning method capable of delivering small, fast, and accurate pruned models. We observe that Bonsai outputs pruned models that (i) outperform those generated by more expensive gradient-based structured pruning methods, and (ii) are twice as fast (with comparable accuracy) as those generated by semi-structured pruning methods requiring comparable resources as Bonsai. We also leverage Bonsai to produce a new sub-2B model using a single A6000 that yields state-of-the-art performance on 4/6 tasks on the Huggingface Open LLM leaderboard.

The widespread use of neural networks across different scientific domains often involves constraining them to satisfy certain symmetries, conservation laws, or other domain knowledge. Such constraints are often imposed as soft penalties during model training and effectively act as domain-specific regularizers of the empirical risk loss. Physics-informed neural networks is an example of this philosophy in which the outputs of deep neural networks are constrained to approximately satisfy a given set of partial differential equations. In this work we review recent advances in scientific machine learning with a specific focus on the effectiveness of physics-informed neural networks in predicting outcomes of physical systems and discovering hidden physics from noisy data. We will also identify and analyze a fundamental mode of failure of such approaches that is related to numerical stiffness leading to unbalanced back-propagated gradients during model training. To address this limitation we present a learning rate annealing algorithm that utilizes gradient statistics during model training to balance the interplay between different terms in composite loss functions. We also propose a novel neural network architecture that is more resilient to such gradient pathologies. Taken together, our developments provide new insights into the training of constrained neural networks and consistently improve the predictive accuracy of physics-informed neural networks by a factor of 50-100x across a range of problems in computational physics. All code and data accompanying this manuscript are publicly available at https://github.com/PredictiveIntelligenceLab/GradientPathologiesPINNs.

Typical generative diffusion models rely on a Gaussian diffusion process for training the backward transformations, which can then be used to generate samples from Gaussian noise. However, real world data often takes place in discrete-state spaces, including many scientific applications. Here, we develop a theoretical formulation for arbitrary discrete-state Markov processes in the forward diffusion process using exact (as opposed to variational) analysis. We relate the theory to the existing continuous-state Gaussian diffusion as well as other approaches to discrete diffusion, and identify the corresponding reverse-time stochastic process and score function in the continuous-time setting, and the reverse-time mapping in the discrete-time setting. As an example of this framework, we introduce ``Blackout Diffusion'', which learns to produce samples from an empty image instead of from noise. Numerical experiments on the CIFAR-10, Binarized MNIST, and CelebA datasets confirm the feasibility of our approach. Generalizing from specific (Gaussian) forward processes to discrete-state processes without a variational approximation sheds light on how to interpret diffusion models, which we discuss.

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution.

In this paper, we present gfnx, a fast and scalable package for training and evaluating Generative Flow Networks (GFlowNets) written in JAX. gfnx provides an extensive set of environments and metrics for benchmarking, accompanied with single-file implementations of core objectives for training GFlowNets. We include synthetic hypergrids, multiple sequence generation environments with various editing regimes and particular reward designs for molecular generation, phylogenetic tree construction, Bayesian structure learning, and sampling from the Ising model energy. Across different tasks, gfnx achieves significant wall-clock speedups compared to Pytorch-based benchmarks (such as torchgfn library) and author implementations. For example, gfnx achieves up to 55 times speedup on CPU-based sequence generation environments, and up to 80 times speedup with the GPU-based Bayesian network structure learning setup. Our package provides a diverse set of benchmarks and aims to standardize empirical evaluation and accelerate research and applications of GFlowNets. The library is available on GitHub (https://github.com/d-tiapkin/gfnx) and on pypi (https://pypi.org/project/gfnx/). Documentation is available on https://gfnx.readthedocs.io.

The structure of topology underpins much of the research on performance and robustness, yet available topology data are typically scarce, necessitating the generation of synthetic graphs with desired properties for testing or release. Prior diffusion-based approaches either embed conditions into the diffusion model, requiring retraining for each attribute and hindering real-time applicability, or use classifier-based guidance post-training, which does not account for topology scale and practical constraints. In this paper, we show from a discrete perspective that gradients from a pre-trained graph-level classifier can be incorporated into the discrete reverse diffusion posterior to steer generation toward specified structural properties. Based on this insight, we propose Classifier-guided Conditional Topology Generation with Persistent Homology (CoPHo), which builds a persistent homology filtration over intermediate graphs and interprets features as guidance signals that steer generation toward the desired properties at each denoising step. Experiments on four generic/network datasets demonstrate that CoPHo outperforms existing methods at matching target metrics, and we further validate its transferability on the QM9 molecular dataset.

Diffusion models achieve strong performance in generative modeling, but their success often relies heavily on classifier-free guidance (CFG), an inference-time heuristic that modifies the sampling trajectory. In theory, diffusion models trained with standard denoising score matching (DSM) should recover the target data distribution, raising two fundamental questions: (i) why is inference-time guidance necessary in practice, and (ii) can its underlying effect be internalized into a principled training objective? In this work, we argue that a key limitation of standard DSM is insufficient inter-class separation. To address this issue, we propose MCLR, an alignment objective that explicitly maximizes inter-class likelihood-ratios during training. Fine-tuning diffusion models with MCLR induces CFG-like improvements under standard sampling, substantially improving guidance-free conditional generation and narrowing the gap to inference-time CFG. Beyond these empirical benefits, we show theoretically that the CFG-guided score is exactly the optimal solution to a sample-adaptive weighted MCLR objective. This result connects CFG to alignment-based objectives, providing a mechanistic interpretation of CFG as an implicit inference-time contrastive alignment procedure.

Bilevel optimization has shown its utility across various machine learning settings, yet most algorithms in practice require second-order information, making it challenging to scale them up. Only recently, a paradigm of first-order algorithms has emerged in the theoretical literature, capable of effectively addressing bilevel optimization problems. Nevertheless, the practical efficiency of this paradigm remains unverified, particularly in the context of large language models (LLMs). This paper introduces the first scalable instantiation of this paradigm called ScaleBiO, focusing on bilevel optimization for large-scale LLM data reweighting. By combining with a recently proposed memory-efficient training technique called LISA, our novel algorithm allows the paradigm to scale to sim30B-sized LLMs on 8timesH100 GPUs, marking the first successful application of bilevel optimization under practical scenarios for large-sized LLMs. Empirically, extensive experiments on data reweighting verify the effectiveness of ScaleBiO for different-scaled models, including Llama-3-8B, Gemma-2-9B, Qwen-2-7B, and Qwen-2.5-32B, where bilevel optimization succeeds in instruction-following and math reasoning tasks, outperforming several popular baselines, including uniform sampling, influence-aware data filtering, and reference-model-based sampling methods. Theoretically, ScaleBiO ensures the optimality of the learned data weights, along with a convergence guarantee matching the conventional first-order bilevel optimization paradigm on smooth and strongly convex objectives.

Iterative optimization is central to modern artificial intelligence (AI) and provides a crucial framework for understanding adaptive systems. This review provides a unified perspective on this subject, bridging classic theory with neural network training and biological learning. Although gradient-based methods, powered by the efficient but biologically implausible backpropagation (BP), dominate machine learning, their computational demands can hinder scalability in high-dimensional settings. In contrast, derivative-free or zeroth-order (ZO) optimization feature computationally lighter approaches that rely only on function evaluations and randomness. While generally less sample efficient, recent breakthroughs demonstrate that modern ZO methods can effectively approximate gradients and achieve performance competitive with BP in neural network models. This ZO paradigm is also particularly relevant for biology. Its core principles of random exploration (probing) and feedback-guided adaptation (reinforcing) parallel key mechanisms of biological learning, offering a mathematically principled perspective on how the brain learns. In this review, we begin by categorizing optimization approaches based on the order of derivative information they utilize, ranging from first-, second-, and higher-order gradient-based to ZO methods. We then explore how these methods are adapted to the unique challenges of neural network training and the resulting learning dynamics. Finally, we build upon these insights to view biological learning through an optimization lens, arguing that a ZO paradigm leverages the brain's intrinsic noise as a computational resource. This framework not only illuminates our understanding of natural intelligence but also holds vast implications for neuromorphic hardware, helping us design fast and energy-efficient AI systems that exploit intrinsic hardware noise.

Score-based diffusion models, while achieving remarkable empirical performance, often suffer from low sampling speed, due to extensive function evaluations needed during the sampling phase. Despite a flurry of recent activities towards speeding up diffusion generative modeling in practice, theoretical underpinnings for acceleration techniques remain severely limited. In this paper, we design novel training-free algorithms to accelerate popular deterministic (i.e., DDIM) and stochastic (i.e., DDPM) samplers. Our accelerated deterministic sampler converges at a rate O(1/{T}^2) with T the number of steps, improving upon the O(1/T) rate for the DDIM sampler; and our accelerated stochastic sampler converges at a rate O(1/T), outperforming the rate O(1/T) for the DDPM sampler. The design of our algorithms leverages insights from higher-order approximation, and shares similar intuitions as popular high-order ODE solvers like the DPM-Solver-2. Our theory accommodates ell_2-accurate score estimates, and does not require log-concavity or smoothness on the target distribution.

This paper introduces a novel theoretical simplification of the Diffusion Schr\"odinger Bridge (DSB) that facilitates its unification with Score-based Generative Models (SGMs), addressing the limitations of DSB in complex data generation and enabling faster convergence and enhanced performance. By employing SGMs as an initial solution for DSB, our approach capitalizes on the strengths of both frameworks, ensuring a more efficient training process and improving the performance of SGM. We also propose a reparameterization technique that, despite theoretical approximations, practically improves the network's fitting capabilities. Our extensive experimental evaluations confirm the effectiveness of the simplified DSB, demonstrating its significant improvements. We believe the contributions of this work pave the way for advanced generative modeling. The code is available at https://github.com/checkcrab/SDSB.

Riemannian diffusion models draw inspiration from standard Euclidean space diffusion models to learn distributions on general manifolds. Unfortunately, the additional geometric complexity renders the diffusion transition term inexpressible in closed form, so prior methods resort to imprecise approximations of the score matching training objective that degrade performance and preclude applications in high dimensions. In this work, we reexamine these approximations and propose several practical improvements. Our key observation is that most relevant manifolds are symmetric spaces, which are much more amenable to computation. By leveraging and combining various ans\"{a}tze, we can quickly compute relevant quantities to high precision. On low dimensional datasets, our correction produces a noticeable improvement, allowing diffusion to compete with other methods. Additionally, we show that our method enables us to scale to high dimensional tasks on nontrivial manifolds. In particular, we model QCD densities on SU(n) lattices and contrastively learned embeddings on high dimensional hyperspheres.

Deep neural networks can be exploited using natural adversarial samples, which do not impact human perception. Current approaches often rely on deep neural networks' white-box nature to generate these adversarial samples or synthetically alter the distribution of adversarial samples compared to the training distribution. In contrast, we propose EvoSeed, a novel evolutionary strategy-based algorithmic framework for generating photo-realistic natural adversarial samples. Our EvoSeed framework uses auxiliary Conditional Diffusion and Classifier models to operate in a black-box setting. We employ CMA-ES to optimize the search for an initial seed vector, which, when processed by the Conditional Diffusion Model, results in the natural adversarial sample misclassified by the Classifier Model. Experiments show that generated adversarial images are of high image quality, raising concerns about generating harmful content bypassing safety classifiers. Our research opens new avenues to understanding the limitations of current safety mechanisms and the risk of plausible attacks against classifier systems using image generation. Project Website can be accessed at: https://shashankkotyan.github.io/EvoSeed.

We propose Beam Tree Recursive Cell (BT-Cell) - a backpropagation-friendly framework to extend Recursive Neural Networks (RvNNs) with beam search for latent structure induction. We further extend this framework by proposing a relaxation of the hard top-k operators in beam search for better propagation of gradient signals. We evaluate our proposed models in different out-of-distribution splits in both synthetic and realistic data. Our experiments show that BTCell achieves near-perfect performance on several challenging structure-sensitive synthetic tasks like ListOps and logical inference while maintaining comparable performance in realistic data against other RvNN-based models. Additionally, we identify a previously unknown failure case for neural models in generalization to unseen number of arguments in ListOps. The code is available at: https://github.com/JRC1995/BeamTreeRecursiveCells.

We study inference-time scaling for diffusion models, where the goal is to adapt a pre-trained model to new target distributions without retraining. Existing guidance-based methods are simple but introduce bias, while particle-based corrections suffer from weight degeneracy and high computational cost. We introduce DriftLite, a lightweight, training-free particle-based approach that steers the inference dynamics on the fly with provably optimal stability control. DriftLite exploits a previously unexplored degree of freedom in the Fokker-Planck equation between the drift and particle potential, and yields two practical instantiations: Variance- and Energy-Controlling Guidance (VCG/ECG) for approximating the optimal drift with minimal overhead. Across Gaussian mixture models, particle systems, and large-scale protein-ligand co-folding problems, DriftLite consistently reduces variance and improves sample quality over pure guidance and sequential Monte Carlo baselines. These results highlight a principled, efficient route toward scalable inference-time adaptation of diffusion models.

Generative machine learning methods, such as diffusion models and flow matching, have shown great potential in modeling complex system behaviors and building efficient surrogate models. However, these methods typically learn the underlying physics implicitly from data. We propose Physics-Based Flow Matching (PBFM), a novel generative framework that explicitly embeds physical constraints, both PDE residuals and algebraic relations, into the flow matching objective. We also introduce temporal unrolling at training time that improves the accuracy of the final, noise-free sample prediction. Our method jointly minimizes the flow matching loss and the physics-based residual loss without requiring hyperparameter tuning of their relative weights. Additionally, we analyze the role of the minimum noise level, sigma_{min}, in the context of physical constraints and evaluate a stochastic sampling strategy that helps to reduce physical residuals. Through extensive benchmarks on three representative PDE problems, we show that our approach yields up to an 8times more accurate physical residuals compared to FM, while clearly outperforming existing algorithms in terms of distributional accuracy. PBFM thus provides a principled and efficient framework for surrogate modeling, uncertainty quantification, and accelerated simulation in physics and engineering applications.

Hyper-Connections (HC) generalizes residual connections by introducing dynamic residual matrices that mix information across multiple residual streams, accelerating convergence in deep neural networks. However, unconstrained residual matrices can compromise training stability. To address this, DeepSeek's Manifold-Constrained Hyper-Connections (mHC) approximately projects these matrices onto the Birkhoff polytope via iterative Sinkhorn--Knopp (SK) normalization. We identify two limitations of this approach: (i) finite SK iterations do not guarantee exact doubly stochasticity, leaving an approximation gap that can accumulate through network depth and undermine stability; (ii) efficient SK implementation requires highly specialized CUDA kernels, raising engineering barriers and reducing portability. Motivated by the Birkhoff--von Neumann theorem, we propose mHC-lite, a simple reparameterization that explicitly constructs doubly stochastic matrices as convex combinations of permutation matrices. This approach guarantees exact doubly stochasticity by construction and can be implemented using only native matrix operations. Extensive experiments demonstrate that mHC-lite matches or exceeds mHC in performance while achieving higher training throughput with a naive implementation and eliminating the residual instabilities observed in both HC and mHC. The code is publicly available at https://github.com/FFTYYY/mhc-lite.

Learning-based methods have gained attention as general-purpose solvers due to their ability to automatically learn problem-specific heuristics, reducing the need for manually crafted heuristics. However, these methods often face scalability challenges. To address these issues, the improved Sampling algorithm for Combinatorial Optimization (iSCO), using discrete Langevin dynamics, has been proposed, demonstrating better performance than several learning-based solvers. This study proposes a different approach that integrates gradient-based update through continuous relaxation, combined with Quasi-Quantum Annealing (QQA). QQA smoothly transitions the objective function, starting from a simple convex function, minimized at half-integral values, to the original objective function, where the relaxed variables are minimized only in the discrete space. Furthermore, we incorporate parallel run communication leveraging GPUs to enhance exploration capabilities and accelerate convergence. Numerical experiments demonstrate that our method is a competitive general-purpose solver, achieving performance comparable to iSCO and learning-based solvers across various benchmark problems. Notably, our method exhibits superior speed-quality trade-offs for large-scale instances compared to iSCO, learning-based solvers, commercial solvers, and specialized algorithms.

Is the lottery ticket phenomenon an idiosyncrasy of gradient-based training or does it generalize to evolutionary optimization? In this paper we establish the existence of highly sparse trainable initializations for evolution strategies (ES) and characterize qualitative differences compared to gradient descent (GD)-based sparse training. We introduce a novel signal-to-noise iterative pruning procedure, which incorporates loss curvature information into the network pruning step. This can enable the discovery of even sparser trainable network initializations when using black-box evolution as compared to GD-based optimization. Furthermore, we find that these initializations encode an inductive bias, which transfers across different ES, related tasks and even to GD-based training. Finally, we compare the local optima resulting from the different optimization paradigms and sparsity levels. In contrast to GD, ES explore diverse and flat local optima and do not preserve linear mode connectivity across sparsity levels and independent runs. The results highlight qualitative differences between evolution and gradient-based learning dynamics, which can be uncovered by the study of iterative pruning procedures.