arXiv subjects

Michael M. Bronstein

Publications and source records attributed to Michael M. Bronstein.

At least 19 recordsLinked to original sources

arXiv2026

Why Are DMD Students Lazy? Understanding the Copying Behavior in Few-Step Distillation

Distribution Matching Distillation (DMD) compresses pretrained diffusion models into efficient few-step generators by aligning their noised distributions across all scales. In principle, such distribution-level supervision remains agnostic to specific noise-data pairings of the teacher; this provides the student the freedom to remap latent noise, a behavior consistently observed in low-dimensional settings. Surprisingly, we find that in high-dimensional settings, distilled students spontaneously reproduce the original noise-data pairings of the teacher, a phenomenon we term copying. We demonstrate that copying is neither a byproduct of adversarial objectives nor a result of teacher memorization. Instead, our evidence suggests that copying is an emergent property arising from the limited geometric freedom of the student model during high-dimensional distillation.

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arXiv2026

Entropy Across the Bridge: Conditional-Marginal Discretization for Flow and Schr\"odinger Samplers

For a fixed flow-based generative model under a small inference budget, sample quality can depend strongly on where the sampler spends its few function evaluations. Flow matching and Schr\"odinger bridges define probability paths, yet their inference grids are usually heuristic or inherited from one-endpoint diffusion. We derive a conditional-marginal entropy-rate objective for bridge-aware discretization, separating endpoint-conditioned bridge geometry from marginal flow evolution, and use it to build a training-free entropic inference-time scheduler from first principles. For Gaussian Brownian bridges this rate is closed-form and U-shaped, motivating boundary-heavy nonuniform grids. On trained two-dimensional bridge/flow models, the estimated profile recovers the predicted shape and improves 10-step ODE-Heun MMD over linear by 18.1%, with a paired 22.7% SDE-Heun improvement in the same low-NFE sweep. On EDM/CIFAR-10, the entropic time-discretization gives the best tested five-step FID (186.3 \pm 4.0 versus 200.5 \pm 2.9 for linear and 238.0 \pm 5.3 for cosine). On AlphaFlow protein generation, entropic conditional-marginal (cond-marg) scheduling shows advantage in low-NFE regimes on both CAMEO22 and ATLAS benchmarks. These results support entropy-rate scheduling as a practical low-budget allocation signal for high-dimensional bridge and flow samplers.

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arXiv2026

A Mechanistic Analysis of Looped Reasoning Language Models

Reasoning has become a central capability in large language models. Recent research has shown that reasoning performance can be improved by looping an LLM's layers in the latent dimension, resulting in looped reasoning language models. Despite promising results, few works have investigated how their internal dynamics differ from those of standard feedforward models. In this paper, we conduct a mechanistic analysis of the latent states in looped language models, focusing in particular on how the stages of inference observed in feedforward models compare to those observed in looped ones. To this end, we analyze cyclic recurrence and show that for many of the studied models each layer in the cycle converges to a distinct fixed point; consequently, the recurrent block follows a consistent cyclic trajectory in the latent space. We provide evidence that as these fixed points are reached, attention-head behavior stabilizes, leading to constant behavior across recurrences. Empirically, we discover that recurrent blocks learn stages of inference that closely mirror those of feedforward models, repeating these stages in depth with each iteration. We study how recurrent block size, input injection, and normalization influence the emergence and stability of these cyclic fixed points. We believe these findings help translate mechanistic insights into practical guidance for architectural design.

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arXiv2026

Scaling Atomistic Protein Binder Design with Generative Pretraining and Test-Time Compute

Protein interaction modeling is central to protein design, which has been transformed by machine learning with applications in drug discovery and beyond. In this landscape, structure-based de novo binder design is cast as either conditional generative modeling or sequence optimization via structure predictors ("hallucination"). We argue that this is a false dichotomy and propose Proteina-Complexa, a novel fully atomistic binder generation method unifying both paradigms. We extend recent flow-based latent protein generation architectures and leverage the domain-domain interactions of monomeric computationally predicted protein structures to construct Teddymer, a new large-scale dataset of synthetic binder-target pairs for pretraining. Combined with high-quality experimental multimers, this enables training a strong base model. We then perform inference-time optimization with this generative prior, unifying the strengths of previously distinct generative and hallucination methods. Proteina-Complexa sets a new state of the art in computational binder design benchmarks: it delivers markedly higher in-silico success rates than existing generative approaches, and our novel test-time optimization strategies greatly outperform previous hallucination methods under normalized compute budgets. We also demonstrate interface hydrogen bond optimization, fold class-guided binder generation, and extensions to small molecule targets and enzyme design tasks, again surpassing prior methods. Code, models and new data will be publicly released.

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arXiv2025

Progressive Inference-Time Annealing of Diffusion Models for Sampling from Boltzmann Densities

Sampling efficiently from a target unnormalized probability density remains a core challenge, with relevance across countless high-impact scientific applications. A promising approach towards this challenge is the design of amortized samplers that borrow key ideas, such as probability path design, from state-of-the-art generative diffusion models. However, all existing diffusion-based samplers remain unable to draw samples from distributions at the scale of even simple molecular systems. In this paper, we propose Progressive Inference-Time Annealing (PITA), a novel framework to learn diffusion-based samplers that combines two complementary interpolation techniques: I.) Annealing of the Boltzmann distribution and II.) Diffusion smoothing. PITA trains a sequence of diffusion models from high to low temperatures by sequentially training each model at progressively higher temperatures, leveraging engineered easy access to samples of the temperature-annealed target density. In the subsequent step, PITA enables simulating the trained diffusion model to procure training samples at a lower temperature for the next diffusion model through inference-time annealing using a novel Feynman-Kac PDE combined with Sequential Monte Carlo. Empirically, PITA enables, for the first time, equilibrium sampling of N-body particle systems, Alanine Dipeptide, and tripeptides in Cartesian coordinates with dramatically lower energy function evaluations. Code available at: https://github.com/taraak/pita

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arXiv2025

Over-squashing in Spatiotemporal Graph Neural Networks

Graph Neural Networks (GNNs) have achieved remarkable success across various domains. However, recent theoretical advances have identified fundamental limitations in their information propagation capabilities, such as over-squashing, where distant nodes fail to effectively exchange information. While extensively studied in static contexts, this issue remains unexplored in Spatiotemporal GNNs (STGNNs), which process sequences associated with graph nodes. Nonetheless, the temporal dimension amplifies this challenge by increasing the information that must be propagated. In this work, we formalize the spatiotemporal over-squashing problem and demonstrate its distinct characteristics compared to the static case. Our analysis reveals that, counterintuitively, convolutional STGNNs favor information propagation from points temporally distant rather than close in time. Moreover, we prove that architectures that follow either time-and-space or time-then-space processing paradigms are equally affected by this phenomenon, providing theoretical justification for computationally efficient implementations. We validate our findings on synthetic and real-world datasets, providing deeper insights into their operational dynamics and principled guidance for more effective designs.

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arXiv2025

Functional correspondence by matrix completion

In this paper, we consider the problem of finding dense intrinsic correspondence between manifolds using the recently introduced functional framework. We pose the functional correspondence problem as matrix completion with manifold geometric structure and inducing functional localization with the $L_1$ norm. We discuss efficient numerical procedures for the solution of our problem. Our method compares favorably to the accuracy of state-of-the-art correspondence algorithms on non-rigid shape matching benchmarks, and is especially advantageous in settings when only scarce data is available.

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arXiv2025

Generalised Flow Maps for Few-Step Generative Modelling on Riemannian Manifolds

Geometric data and purpose-built generative models on them have become ubiquitous in high-impact deep learning application domains, ranging from protein backbone generation and computational chemistry to geospatial data. Current geometric generative models remain computationally expensive at inference -- requiring many steps of complex numerical simulation -- as they are derived from dynamical measure transport frameworks such as diffusion and flow-matching on Riemannian manifolds. In this paper, we propose Generalised Flow Maps (GFM), a new class of few-step generative models that generalises the Flow Map framework in Euclidean spaces to arbitrary Riemannian manifolds. We instantiate GFMs with three self-distillation-based training methods: Generalised Lagrangian Flow Maps, Generalised Eulerian Flow Maps, and Generalised Progressive Flow Maps. We theoretically show that GFMs, under specific design decisions, unify and elevate existing Euclidean few-step generative models, such as consistency models, shortcut models, and meanflows, to the Riemannian setting. We benchmark GFMs against other geometric generative models on a suite of geometric datasets, including geospatial data, RNA torsion angles, and hyperbolic manifolds, and achieve state-of-the-art sample quality for single- and few-step evaluations, and superior or competitive log-likelihoods using the implicit probability flow.

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arXiv2025

gLSTM: Mitigating Over-Squashing by Increasing Storage Capacity

Graph Neural Networks (GNNs) leverage the graph structure to transmit information between nodes, typically through the message-passing mechanism. While these models have found a wide variety of applications, they are known to suffer from over-squashing, where information from a large receptive field of node representations is collapsed into a single fixed sized vector, resulting in an information bottleneck. In this paper, we re-examine the over-squashing phenomenon through the lens of model storage and retrieval capacity, which we define as the amount of information that can be stored in a node's representation for later use. We study some of the limitations of existing tasks used to measure over-squashing and introduce a new synthetic task to demonstrate that an information bottleneck can saturate this capacity. Furthermore, we adapt ideas from the sequence modeling literature on associative memories, fast weight programmers, and the xLSTM model to develop a novel GNN architecture with improved capacity. We demonstrate strong performance of this architecture both on our capacity synthetic task, as well as a range of real-world graph benchmarks.

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arXiv2025

Carr\'e du champ flow matching: better quality-generalisation tradeoff in generative models

Deep generative models often face a fundamental tradeoff: high sample quality can come at the cost of memorisation, where the model reproduces training data rather than generalising across the underlying data geometry. We introduce Carr\'e du champ flow matching (CDC-FM), a generalisation of flow matching (FM), that improves the quality-generalisation tradeoff by regularising the probability path with a geometry-aware noise. Our method replaces the homogeneous, isotropic noise in FM with a spatially varying, anisotropic Gaussian noise whose covariance captures the local geometry of the latent data manifold. We prove that this geometric noise can be optimally estimated from the data and is scalable to large data. Further, we provide an extensive experimental evaluation on diverse datasets (synthetic manifolds, point clouds, single-cell genomics, animal motion capture, and images) as well as various neural network architectures (MLPs, CNNs, and transformers). We demonstrate that CDC-FM consistently offers a better quality-generalisation tradeoff. We observe significant improvements over standard FM in data-scarce regimes and in highly non-uniformly sampled datasets, which are often encountered in AI for science applications. Our work provides a mathematical framework for studying the interplay between data geometry, generalisation and memorisation in generative models, as well as a robust and scalable algorithm that can be readily integrated into existing flow matching pipelines.

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arXiv2025

ResCP: Reservoir Conformal Prediction for Time Series Forecasting

Conformal prediction offers a powerful framework for building distribution-free prediction intervals for exchangeable data. Existing methods that extend conformal prediction to sequential data rely on fitting a relatively complex model to capture temporal dependencies. However, these methods can fail if the sample size is small and often require expensive retraining when the underlying data distribution changes. To overcome these limitations, we propose Reservoir Conformal Prediction (ResCP), a novel training-free conformal prediction method for time series. Our approach leverages the efficiency and representation learning capabilities of reservoir computing to dynamically reweight conformity scores. In particular, we compute similarity scores among reservoir states and use them to adaptively reweight the observed residuals at each step. With this approach, ResCP enables us to account for local temporal dynamics when modeling the error distribution without compromising computational scalability. We prove that, under reasonable assumptions, ResCP achieves asymptotic conditional coverage, and we empirically demonstrate its effectiveness across diverse forecasting tasks.

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arXiv2025

CrediBench: Building Web-Scale Network Datasets for Information Integrity

Automatically assessing the credibility of online sources presents an invaluable tool for navigating today's information ecosystem. However, existing approaches either depend on scarce and costly human annotations, or focus exclusively on assessments at the level of individual claims. Misinformation often spreads via interlinked web domains, whose connections evolve over time. Focusing on claims alone ignores these structural and temporal credibility signals evident in the changing web topology. Existing datasets fail to capture these central modalities in web domain credibility prediction: namely, internet topology, temporality and text (webpage) content. To address this gap, we present CrediBench, a dataset containing eights months of web graph data; of which we analyze the three months surrounding the 2024 U.S. federal elections, a time of heightened misinformation propagation online. Each monthly snapshot contains over 40 million nodes, their scraped webpage content, and over 1 billion hyperlink edges. CrediBench supports credibility prediction as both a regression (continuous credibility score) and a binary classification task (credible or not). For classification, we curate a novel binary label set containing 662,575 web domains labelled for boolean credibility, spanning four areas (misinformation, crowd-sourced, malware and phishing). Our empirical experiments support that all task modalities-graph, text and time-contribute significantly to achieving the best performance. In particular, our multi-modal regression model trained on CrediBench outperforms other configurations and existing baselines, decreasing Mean Average Error from 0.162 to 0.107 on the regression task, while the multi-modal classifier improves accuracy from 56% to 85% on the classification one. CrediBench, our proposed web-scale multi-modal dataset, is available on Huggingface for future research.

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arXiv2025

Learning Inter-Atomic Potentials without Explicit Equivariance

Accurate and scalable machine-learned inter-atomic potentials (MLIPs) are essential for molecular simulations ranging from drug discovery to new material design. Current state-of-the-art models enforce roto-translational symmetries through equivariant neural network architectures, a hard-wired inductive bias that can often lead to reduced flexibility, computational efficiency, and scalability. In this work, we introduce TransIP: Transformer-based Inter-Atomic Potentials, a novel training paradigm for interatomic potentials achieving symmetry compliance without explicit architectural constraints. Our approach guides a generic non-equivariant Transformer-based model to learn SO(3)-equivariance by optimizing its representations in the embedding space. Trained on the recent Open Molecules (OMol25) collection, a large and diverse molecular dataset built specifically for MLIPs and covering different types of molecules (including small organics, biomolecular fragments, and electrolyte-like species), TransIP attains comparable performance in machine-learning force fields versus state-of-the-art equivariant baselines. Further, compared to a data augmentation baseline, TransIP achieves 40% to 60% improvement in performance across varying OMol25 dataset sizes. More broadly, our work shows that learned equivariance can be a powerful and efficient alternative to equivariant or augmentation-based MLIP models. Our code is available at: https://github.com/Ahmed-A-A-Elhag/TransIP.

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arXiv2025

Amortized Sampling with Transferable Normalizing Flows

Efficient equilibrium sampling of molecular conformations remains a core challenge in computational chemistry and statistical inference. Classical approaches such as molecular dynamics or Markov chain Monte Carlo inherently lack amortization; the computational cost of sampling must be paid in full for each system of interest. The widespread success of generative models has inspired interest towards overcoming this limitation through learning sampling algorithms. Despite performing competitively with conventional methods when trained on a single system, learned samplers have so far demonstrated limited ability to transfer across systems. We demonstrate that deep learning enables the design of scalable and transferable samplers by introducing Prose, a 285 million parameter all-atom transferable normalizing flow trained on a corpus of peptide molecular dynamics trajectories up to 8 residues in length. Prose draws zero-shot uncorrelated proposal samples for arbitrary peptide systems, achieving the previously intractable transferability across sequence length, whilst retaining the efficient likelihood evaluation of normalizing flows. Through extensive empirical evaluation we demonstrate the efficacy of Prose as a proposal for a variety of sampling algorithms, finding a simple importance sampling-based fine-tuning procedure to achieve competitive performance to established methods such as sequential Monte Carlo. We open-source the Prose codebase, model weights, and training dataset, to further stimulate research into amortized sampling methods and objectives.

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arXiv2025

Drag-and-Drop LLMs: Zero-Shot Prompt-to-Weights

Modern Parameter-Efficient Fine-Tuning (PEFT) methods such as low-rank adaptation (LoRA) reduce the cost of customizing large language models (LLMs), yet still require a separate optimization run for every downstream dataset. We introduce \textbf{Drag-and-Drop LLMs (\textit{DnD})}, a prompt-conditioned parameter generator that eliminates per-task training by mapping a handful of unlabeled task prompts directly to LoRA weight updates. A lightweight text encoder distills each prompt batch into condition embeddings, which are then transformed by a cascaded hyper-convolutional decoder into the full set of LoRA matrices. Once trained in a diverse collection of prompt-checkpoint pairs, DnD produces task-specific parameters in seconds, yielding i) up to \textbf{12,000$\times$} lower overhead than full fine-tuning, ii) average gains up to \textbf{30\%} in performance over the strongest training LoRAs on unseen common-sense reasoning, math, coding, and multimodal benchmarks, and iii) robust cross-domain generalization despite never seeing the target data or labels. Our results demonstrate that prompt-conditioned parameter generation is a viable alternative to gradient-based adaptation for rapidly specializing LLMs. Our project is available at \href{https://jerryliang24.github.io/DnD}{https://jerryliang24.github.io/DnD}.

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arXiv2025

HYPER: A Foundation Model for Inductive Link Prediction with Knowledge Hypergraphs

Inductive link prediction with knowledge hypergraphs is the task of predicting missing hyperedges involving completely novel entities (i.e., nodes unseen during training). Existing methods for inductive link prediction with knowledge hypergraphs assume a fixed relational vocabulary and, as a result, cannot generalize to knowledge hypergraphs with novel relation types (i.e., relations unseen during training). Inspired by knowledge graph foundation models, we propose HYPER as a foundation model for link prediction, which can generalize to any knowledge hypergraph, including novel entities and novel relations. Importantly, HYPER can learn and transfer across different relation types of varying arities, by encoding the entities of each hyperedge along with their respective positions in the hyperedge. To evaluate HYPER, we construct 16 new inductive datasets from existing knowledge hypergraphs, covering a diverse range of relation types of varying arities. Empirically, HYPER consistently outperforms all existing methods in both node-only and node-and-relation inductive settings, showing strong generalization to unseen, higher-arity relational structures.

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arXiv2025

Link Prediction with Relational Hypergraphs

Link prediction with knowledge graphs has been thoroughly studied in graph machine learning, leading to a rich landscape of graph neural network architectures with successful applications. Nonetheless, it remains challenging to transfer the success of these architectures to relational hypergraphs, where the task of link prediction is over $k$-ary relations, which is substantially harder than link prediction with knowledge graphs. In this paper, we propose a framework for link prediction with relational hypergraphs, unlocking applications of graph neural networks to fully relational structures. Theoretically, we conduct a thorough analysis of the expressive power of the resulting model architectures via corresponding relational Weisfeiler-Leman algorithms and also via logical expressiveness. Empirically, we validate the power of the proposed model architectures on various relational hypergraph benchmarks. The resulting model architectures substantially outperform every baseline for inductive link prediction, and lead to state-of-the-art results for transductive link prediction.

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arXiv2025

How Expressive are Knowledge Graph Foundation Models?

Knowledge Graph Foundation Models (KGFMs) are at the frontier for deep learning on knowledge graphs (KGs), as they can generalize to completely novel knowledge graphs with different relational vocabularies. Despite their empirical success, our theoretical understanding of KGFMs remains very limited. In this paper, we conduct a rigorous study of the expressive power of KGFMs. Specifically, we show that the expressive power of KGFMs directly depends on the motifs that are used to learn the relation representations. We then observe that the most typical motifs used in the existing literature are binary, as the representations are learned based on how pairs of relations interact, which limits the model's expressiveness. As part of our study, we design more expressive KGFMs using richer motifs, which necessitate learning relation representations based on, e.g., how triples of relations interact with each other. Finally, we empirically validate our theoretical findings, showing that the use of richer motifs results in better performance on a wide range of datasets drawn from different domains.

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