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Applications · Chemistry and Drug Discovery

Noémie Bergues, Arthur Carré, Paul Join-Lambert, Brice Hoffmann, Arnaud Blondel, Hamza Tajmouati

Predicting the 3D conformation of small molecules within protein binding sites is a key challenge in drug design. When a crystallized reference ligand (template) is available, it provides geometric priors that can guide 3D pose prediction. We present a two-stage method for ligand conformation generation guided by such templates. In the first stage, we introduce a molecular alignment approach based on flow-matching to generate 3D coordinates for the ligand, using the template structure as a reference. In the second stage, a differentiable pose optimization procedure refines this conformation based on shape and pharmacophore similarities, internal energy, and, optionally, the protein binding pocket. We introduce a new benchmark of ligand pairs co-crystallized with the same target to evaluate our approach and show that it outperforms standard docking tools and open-access alignment methods, especially in cases involving low similarity to the template or high ligand flexibility.

Applications · Health

Yanlong Chen, Mattia Orlandi, Pierangelo Rapa, Simone Benatti, Luca Benini, Yawei Li

Physiological signals are often corrupted by motion artifacts, baseline drift, and other low-SNR disturbances, posing significant challenges for analysis. Additionally, these signals exhibit strong non-stationarity, with sharp peaks and abrupt changes that evolve continuously, making them difficult to represent using traditional time-domain or filtering methods. To address these issues, a novel wavelet-based approach for physiological signal analysis is presented, aimed at capturing multi-scale time-frequency features across various physiological signals. Leveraging this technique, two large-scale pretrained models specific to EMG and ECG are introduced for the first time, achieving superior performance and setting new baselines in downstream tasks. Additionally, a unified multi-modal framework is constructed by integrating a pretrained EEG model, where each modality is guided through its dedicated branch and fused via learnable weighted fusion. This design effectively addresses challenges such as low signal-to-noise ratio, high inter-subject variability, and device mismatch, outperforming existing methods on multi-modal tasks. The proposed wavelet-based architecture lays a solid foundation for the analysis of diverse physiological signals, while the multi-modal design points to next-generation physiological signal processing with potential impacts on wearable health monitoring, clinical diagnostics, and broader biomedical applications. Code and data are available at: github.com/ForeverBlue816/PhysioWave

Computer Vision · Vision Models & Multimodal

Thanh-Dat Truong, Christophe Bobda, Nitin Agarwal, Khoa Luu

Multimodal learning has gained much success in recent years. However, current multimodal fusion methods adopt the attention mechanism of Transformers to implicitly learn the underlying correlation of multimodal features. As a result, the multimodal model cannot capture the essential features of each modality, making it difficult to comprehend complex structures and correlations of multimodal inputs. This paper introduces a novel Multimodal Attention-based Normalizing Flow (MANGO) approach to developing explicit, interpretable, and tractable multimodal fusion learning. In particular, we propose a new Invertible Cross-Attention (ICA) layer to develop the Normalizing Flow-based Model for multimodal data. To efficiently capture the complex, underlying correlations in multimodal data in our proposed invertible cross-attention layer, we propose three new cross-attention mechanisms: Modality-to-Modality Cross-Attention (MMCA), Inter-Modality Cross-Attention (IMCA), and Learnable Inter-Modality Cross-Attention (LICA). Finally, we introduce a new Multimodal Attention-based Normalizing Flow to enable the scalability of our proposed method to high-dimensional multimodal data. Our experimental results on three different multimodal learning tasks, i.e., semantic segmentation, image-to-image translation, and movie genre classification, have illustrated the state-of-the-art (SoTA) performance of the proposed approach.

Probabilistic Methods

Hongyu Shen, Zhizhen Jane Zhao

Recent advances in false discovery rate (FDR)-controlled feature selection methods have improved reliability by effectively limiting false positives, making them well-suited for complex applications. A popular FDR-controlled framework called data splitting uses the "mirror statistics" to select features. However, we find that the unit variance assumption on mirror statistics could potentially limit the feature selection power. To address this, we generalize the mirror statistics in the Gaussian mirror framework and introduce a new approach called "generalized Gaussian mirror" ($\text{G}^2\text{M}$), which adaptively learns the variance and forms new test statistics. We demonstrate both theoretically and empirically that the proposed test statistics achieve higher power than those of Gaussian mirror and data splitting. Comparisons with other FDR-controlled frameworks on synthetic, semi-synthetic, and real datasets highlight the superior performance of the $\text{G}^2\text{M}$ method in achieving higher power while maintaining FDR control. These findings suggest the potential for the $\text{G}^2\text{M}$ method for practical applications in real-world problems. Code is available in https://github.com/skyve2012/G2M.

Optimization · Optimization and Learning under Uncertainty

Xiang Li, Yunai Li, Huiying Zhong, Lihua Lei, Zhun Deng

Performativity of predictions refers to the phenomenon where prediction-informed decisions influence the very targets they aim to predict—a dynamic commonly observed in policy-making, social sciences, and economics. In this paper, we initiate an end-to-end framework of statistical inference under performativity. Our contributions are twofold. First, we establish a central limit theorem for estimation and inference in the performative setting, enabling standard inferential tasks such as constructing confidence intervals and conducting hypothesis tests in policy-making contexts. Second, we leverage this central limit theorem to study prediction-powered inference (PPI) under performativity. This approach yields more precise estimates and tighter confidence regions for the model parameters (i.e., policies) of interest in performative prediction. We validate the effectiveness of our framework through numerical experiments. To the best of our knowledge, this is the first work to establish a complete statistical inference under performativity, introducing new challenges and inference settings that we believe will provide substantial value to policy-making, statistics, and machine learning.

Theory · Learning Theory

BaoLinh Tran, Van Vu

The matrix recovery (completion) problem, a central problem in data science, involves recovering a matrix $A$ from a relatively small random set of entries. While such a task is generally impossible, it has been shown that one can recover $A$ exactly in polynomial time, with high probability, under three basic and necessary assumptions: (1) the rank of $A$ is very small compared to its dimensions (low rank), (2) $A$ has delocalized singular vectors (incoherence), and (3) the sample size is sufficiently large. Various algorithms address this task, including convex optimization by Candes, Recht, and Tao (2009, 2010), alternating projection by Hardt and Wooters (2014), and low-rank approximation with gradient descent by Keshavan, Montanari, and Oh (2009, 2010). In applications, Candes and Plan (2009) noted that it is more realistic to assume noisy observations. In such cases, the above approaches provide approximate recovery with small root mean square error, which is difficult to convert into exact recovery. Recently, results by Abbe et al. (2017) and Bhardwaj et al. (2023) on approximation in the infinity norm showed that one can recover $A$ even in the noisy case, provided $A$ has bounded precision. However, beyond the three basic assumptions, they either required that the condition number of $A$ be small (2017) or that the gaps between consecutive singular values be large (2023). These additional assumptions conflict, with one requiring singular values to be close together and the other suggesting they should be far apart. It is thus natural to conjecture that neither is necessary. In this paper, we demonstrate that this is indeed the case. We propose a simple algorithm for exact recovery of noisy data, relying solely on the three basic assumptions. The core step of the algorithm is a straightforward truncated singular value decomposition, which is highly efficient. To analyze the algorithm, we prove a new infinity norm version of the classical Davis-Kahan perturbation theorem, improving an earlier result in (2023). Our proof employs a combinatorial contour integration argument and is entirely distinct from all previous approaches.

Deep Learning · Generative Models and Autoencoders

Bartlomiej Sobieski, Matthew Tivnan, Yuang Wang, Siyeop yoon, Pengfei Jin, Dufan Wu, Quanzheng Li, Przemyslaw Biecek

Solving inverse problems—recovering signals from incomplete or noisy measurements—is fundamental in science and engineering. Score-based generative models (SGMs) have recently emerged as a powerful framework for this task. Two main paradigms have formed: unsupervised approaches that adapt pretrained generative models to inverse problems, and supervised bridge methods that train stochastic processes conditioned on paired clean and corrupted data. While the former typically assume knowledge of the measurement model, the latter have largely overlooked this structural information. We introduce System-embedded Diffusion Bridge Models (SDBs), a new class of supervised bridge methods that explicitly embed the known linear measurement system into the coefficients of a matrix-valued SDE. This principled integration yields consistent improvements across diverse linear inverse problems and demonstrates robust generalization under system misspecification between training and deployment, offering a promising solution to real-world applications.

Computer Vision · 3D Rendering & Reconstruction

Jonathan Schmidt, Simon Giebenhain, Matthias Niessner

We introduce *BecomingLit*, a novel method for reconstructing relightable, high-resolution head avatars that can be rendered from novel viewpoints at interactive rates. Therefore, we propose a new low-cost light stage capture setup, tailored specifically towards capturing faces. Using this setup, we collect a novel dataset consisting of diverse multi-view sequences of numerous subjects under varying illumination conditions and facial expressions. By leveraging our new dataset, we introduce a new relightable avatar representation based on 3D Gaussian primitives that we animate with a parametric head model and an expression-dependent dynamics module. We propose a new hybrid neural shading approach, combining a neural diffuse BRDF with an analytical specular term. Our method reconstructs disentangled materials from our dynamic light stage recordings and enables all-frequency relighting of our avatars with both point lights and environment maps. In addition, our avatars can easily be animated and controlled from monocular videos. We validate our approach in extensive experiments on our dataset, where we consistently outperform existing state-of-the-art methods in relighting and reenactment by a significant margin.

Reinforcement Learning · Deep RL

Harshit Sushil Sikchi, Siddhant Agarwal, Pranaya Jajoo, Samyak Parajuli, Caleb Chuck, Max Rudolph, Peter Stone, Amy Zhang, Scott Niekum

The reward hypothesis states that all goals and purposes can be understood as the maximization of a received scalar reward signal. However, in practice, defining such a reward signal is notoriously difficult, as humans are often unable to predict the optimal behavior corresponding to a reward function. Natural language offers an intuitive alternative for instructing reinforcement learning (RL) agents, yet previous language-conditioned approaches either require costly supervision or test-time training given a language instruction. In this work, we present a new approach that uses a pretrained RL agent trained using only unlabeled, offline interactions—without task-specific supervision or labeled trajectories—to get zero-shot test-time policy inference from arbitrary natural language instructions. We introduce a framework comprising three steps: *imagine*, *project*, and *imitate*. First, the agent imagines a sequence of observations corresponding to the provided language description using video generative models. Next, these imagined observations are projected into the target environment domain. Finally, an agent pretrained in the target environment with unsupervised RL instantly imitates the projected observation sequence through a closed-form solution. To the best of our knowledge, our method, RLZero, is the first approach to show direct language-to-behavior generation abilities on a variety of tasks and environments without any in-domain supervision. We further show that components of RLZero can be used to generate policies zero-shot from cross-embodied videos, such as those available on YouTube, even for complex embodiments like humanoids.

Theory · Learning Theory

Yuchen Liang, Yingbin Liang, Lifeng LAI, Ness Shroff

Discrete diffusion models have recently gained significant prominence in applications involving natural language and graph data. A key factor influencing their effectiveness is the efficiency of discretized samplers. Among these, $\tau$-leaping samplers have become particularly popular due to their theoretical and empirical success. However, existing theoretical analyses of $\tau$-leaping often rely on somewhat restrictive and difficult-to-verify regularity assumptions, and their convergence bounds contain quadratic dependence on the vocabulary size. In this work, we introduce a new analytical approach for discrete diffusion models that removes the need for such assumptions. For the standard $\tau$-leaping method, we establish convergence guarantees in KL divergence that scale linearly with vocabulary size, improving upon prior results with quadratic dependence. Our approach is also more broadly applicable: it provides the first convergence guarantees for other widely used samplers, including the Euler method and Tweedie $\tau$-leaping. Central to our approach is a novel technique based on differential inequalities, offering a more flexible alternative to the traditional Girsanov change-of-measure methods. This technique may also be of independent interest for the analysis of other stochastic processes.

Deep Learning · Generative Models and Autoencoders

Guhao Feng, Yihan Geng, Jian Guan, Wei Wu, Liwei Wang, Di He

Diffusion language models have emerged as a new approach for text generation. By enabling the parallel sampling of multiple tokens in each diffusion step, they appear to offer a more efficient alternative to auto-regressive models. However, our observations show that current open-sourced diffusion language models require more sampling steps to achieve comparable accuracy on representative tasks--resulting in even higher inference costs than their auto-regressive counterparts. To investigate whether this is an inherent limitation, we conduct a rigorous theoretical analysis of a widely adopted variant: the Masked Diffusion Model (MDM). Surprisingly, our analysis reveals that the conclusion is highly sensitive to the choice of evaluation metric. Under mild conditions, we prove that when the target is near-optimal perplexity, MDMs can achieve this goal in a constant number of sampling steps, independent of sequence length. This result demonstrates that efficiency can, in principle, be attained without compromising generation quality. However, when targeting low sequence error rate--which is important for assessing the ``correctness" of a generated sequence, such as a reasoning chain--we show that in the worst case, the required sampling steps must scale linearly with sequence length, thereby eliminating the efficiency advantage. Our analysis establishes the first theoretical foundation for understanding the comparative strengths and limitations of MDMs, offering practical guidance on when to favor MDMs over the auto-regressive models and vice versa.

Applications · Everything Else

Azim Ospanov, Farzan Farnia, Roozbeh Yousefzadeh

Formal reasoning and automated theorem proving constitute a challenging subfield of machine learning, in which machines are tasked with proving mathematical theorems using formal languages like Lean. A formal verification system can check whether a formal proof is correct or not almost instantaneously, but generating a completely correct formal proof with large language models (LLMs) remains a formidable task. The usual approach in the literature is to prompt the LLM many times (up to several thousands) until one of the generated proofs passes the verification system. In this work, we present APOLLO (**A**utomated **P**r**O**of repair via**L**LM and **L**ean c**O**llaboration), a modular, model‑agnostic agentic framework that combines the strengths of the Lean compiler with an LLM’s reasoning abilities to achieve better proof‐generation results at a low token and sampling budgets. _Apollo_ directs a fully automated process in which the LLM generates proofs for theorems, a set of agents analyze the proofs, fix the syntax errors, identify the mistakes in the proofs using Lean, isolate failing sub‑lemmas, utilize automated solvers, and invoke an LLM on each remaining goal with a low top‑K budget. The repaired sub‑proofs are recombined and reverified, iterating up to a user‑controlled maximum number of attempts. On the miniF2F benchmark, we establish a new state‑of‑the‑art accuracy of 84.9% among sub 8B‑parameter models (as of August 2025) while keeping the sampling budget below one hundred. Moreover, _Apollo_ raises the state‑of‑the‑art accuracy for Goedel‑Prover‑SFT to 65.6% while cutting sample complexity from 25,600 to a few hundred. General‑purpose models (o3‑mini, o4‑mini) jump from 3–7% to over 40% accuracy. Our results demonstrate that targeted, compiler‑guided repair of LLM outputs yields dramatic gains in both efficiency and correctness, suggesting a general paradigm for scalable automated theorem proving. The codebase is available at https://github.com/aziksh-ospanov/APOLLO

Deep Learning · Graph Neural Networks

Yonghao Liu, Yajun Wang, Chunli Guo, Wei Pang, Ximing Li, Fausto Giunchiglia, Xiaoyue Feng, Renchu Guan

Graph few-shot learning has attracted increasing attention due to its ability to rapidly adapt models to new tasks with only limited labeled nodes. Despite the remarkable progress made by existing graph few-shot learning methods, several key limitations remain. First, most current approaches rely on predefined and unified graph filters (e.g., low-pass or high-pass filters) to globally enhance or suppress node frequency signals. Such fixed spectral operations fail to account for the heterogeneity of local topological structures inherent in real-world graphs. Moreover, these methods often assume that the support and query sets are drawn from the same distribution. However, under few-shot conditions, the limited labeled data in the support set may not sufficiently capture the complex distribution of the query set, leading to suboptimal generalization. To address these challenges, we propose GRACE, a novel Graph few-shot leaRning framework that integrates Adaptive spectrum experts with Cross-sEt distribution calibration techniques. Theoretically, the proposed approach enhances model generalization by adapting to both local structural variations and cross-set distribution calibration. Empirically, GRACE consistently outperforms state-of-the-art baselines across a wide range of experimental settings. Our code can be found here.

Deep Learning · Everything Else

Xisen Jin, Xiang Ren

Large Language models (LLMs) suffer from forgetting of upstream knowledge when fine-tuned. Despite efforts on mitigating forgetting, few have investigated how forgotten upstream examples are dependent on newly learned tasks. Insights on such dependencies enable efficient and targeted mitigation of forgetting. In this paper, we empirically analyze forgetting that occurs in $N$ upstream examples of language modeling or instruction-tuning after fine-tuning LLMs on one of $M$ new tasks, visualized in $M\times N$ matrices. We show that the matrices are often well-approximated with low-rank matrices, indicating the dominance of simple associations between the learned tasks and forgotten upstream examples. Leveraging the analysis, we predict forgetting of upstream examples when fine-tuning LLMs on unseen tasks with matrix completion over the empirical associations. This enables fast identification of most forgotten examples without expensive inference on the entire upstream data. Despite simplicity, the approach outperforms prior approaches that learn semantic relationships of learned tasks and upstream examples with LMs. We demonstrate the practical utility of our analysis by showing statistically significantly reduced forgetting as we upweight predicted examples for replay during fine-tuning.

General Machine Learning · Representation Learning

Giacomo Camposampiero, Pietro Barbiero, Michael Hersche, Roger Wattenhofer, Abbas Rahimi

Compositional generalization—a key open challenge in modern machine learning—requires models to predict unknown combinations of known concepts. However, assessing compositional generalization remains a fundamental challenge due to the lack of standardized evaluation protocols and the limitations of current benchmarks, which often favor efficiency over rigor. At the same time, general-purpose vision architectures lack the necessary inductive biases, and existing approaches to endow them compromise scalability. As a remedy, this paper introduces: 1) a rigorous evaluation framework that unifies and extends previous approaches while reducing computational requirements from combinatorial to constant; 2) an extensive and modern evaluation on the status of compositional generalization in supervised vision backbones, training more than 5000 models; 3) Attribute Invariant Networks, a class of models establishing a new Pareto frontier in compositional generalization, achieving a 23.43% accuracy improvement over baselines while reducing parameter overhead from 600% to 16% compared to fully disentangled counterparts.

Deep Learning · Algorithms

Jiaxing Wang, Deping Xiang, Jin Xu, Mingyang Yi, Guoqiang Gong, Zicheng Zhang, Haoran Li, Pengzhang Liu, Zhen Chen, Ke Zhang 等

The capabilities of large language models (LLMs) significantly depend on training data drawn from various domains. Optimizing domain-specific mixture ratios can be modeled as a bi-level optimization problem, which we simplify into a single-level penalized form and solve with twin networks: a proxy model trained on primary data and a dynamically updated reference model trained with additional data. Our proposed method, Twin Networks for bi-level DatA mixturE optiMization (TANDEM), measures the data efficacy through the difference between the twin models and up-weights domains that benefit more from the additional data. TANDEM provides theoretical guarantees and wider applicability, compared to prior approaches. Furthermore, our bi-level perspective suggests new settings to study domain reweighting such as data-restricted scenarios and supervised fine-tuning, where optimized mixture ratios significantly improve the performance. Extensive experiments validate TANDEM's effectiveness in all scenarios.

Applications · Language, Speech and Dialog

Liang Wang, Haonan Chen, Nan Yang, Xiaolong Huang, Zhicheng Dou, Furu Wei

This paper introduces an approach for training o1-like RAG models that retrieve and reason over relevant information step by step before generating the final answer. Conventional RAG methods usually perform a single retrieval step before the generation process, which limits their effectiveness in addressing complex queries due to imperfect retrieval results. In contrast, our proposed method, CoRAG (Chain-of-Retrieval Augmented Generation), allows the model to dynamically reformulate the query based on the evolving state. To train CoRAG effectively, we utilize rejection sampling to automatically generate intermediate retrieval chains, thereby augmenting existing RAG datasets that only provide the correct final answer. At test time, we propose various decoding strategies to scale the model's test-time compute by controlling the length and number of sampled retrieval chains. Experimental results across multiple benchmarks validate the efficacy of CoRAG, particularly in multi-hop question answering tasks, where we observe more than $10$ points improvement in EM score compared to strong baselines. On the KILT benchmark, CoRAG establishes a new state-of-the-art performance across a diverse range of knowledge-intensive tasks. Furthermore, we offer comprehensive analyses to understand the scaling behavior of CoRAG, laying the groundwork for future research aimed at developing factual and grounded foundation models.

Computer Vision · Vision Models & Multimodal

Piyush Nitin Bagad, Andrew Zisserman

Our objective is to develop compact video representations that are sensitive to visual change over time. To measure such time-sensitivity, we introduce a new task: chiral action recognition, where one needs to distinguish between a pair of temporally opposite actions, such as “opening vs. closing a door", “approaching vs. moving away from something", “folding vs. unfolding paper", etc. Such actions (i) occur frequently in everyday life, (ii) require understanding of simple visual change over time (in object state, size, spatial position, count . . . ), and (iii) are known to be poorly represented by many video embeddings. Our goal is to build time aware video representations which offer linear separability between these chiral pairs. To that end, we propose a self-supervised adaptation recipe to inject time-sensitivity into a sequence of frozen image features. Our model is based on an auto-encoder with a latent space with inductive bias inspired by perceptual straightening. We show that this results in a compact but time-sensitive video representation for the proposed task across three datasets: Something-Something, EPIC-Kitchens, and Charade. Our method (i) outperforms much larger video models pre-trained on large-scale video datasets, and (ii) leads to an improvement in classification performance on standard benchmarks when combined with these existing models.

Optimization · Discrete Optimization

Nguyen Do, Bach Ngo, Youval Kashuv, Canh Pham, Hanghang Tong, My T. Thai

We study the Quality of Service Degradation (QoSD) problem, in which an adversary perturbs edge weights to degrade network performance. This setting arises in both network infrastructures and distributed ML systems, where communication quality, not just connectivity, determines functionality. While classical methods rely on combinatorial optimization, and recent ML approaches address only restricted linear variants with small-size networks, no prior model directly tackles the QoSD problem under nonlinear edge-weight functions. This work proposes Hephaestus, a self-reinforcing generative framework that synthesizes feasible solutions in latent space, to fill this gap. Our method includes three phases: (1) Forge: a Predictive Path-Stressing (PPS) algorithm that uses graph learning and approximation to produce feasible solutions with performance guarantee, (2) Morph: a new theoretically grounded training paradigm for Mixture of Conditional VAEs guided by an energy-based model to capture solution feature distributions, and (3) Refine: a reinforcement learning agent that explores this space to generate progressively near-optimal solutions using our designed differentiable reward function. Experiments on both synthetic and real-world networks show that our approach consistently outperforms classical and ML baselines, particularly in scenarios with nonlinear cost functions where traditional methods fail to generalize.

Applications · Neuroscience, Cognitive Science

Alexander Ratzan, Sidharth Goel, Junhao Wen, Christos Davatzikos, Erdem Varol

Spatial location and molecular interactions have long been linked to the connectivity patterns of neural circuits. Yet, at the macroscale of human brain networks, the interplay between spatial position, gene expression, and connectivity remains incompletely understood. Recent efforts to map the human transcriptome and connectome have yielded spatially resolved brain atlases, however modeling the relationship between high-dimensional transcriptomic data and connectivity while accounting for inherent spatial confounds presents a significant challenge. In this paper, we present the first deep learning approaches for predicting whole-brain functional connectivity from gene expression and regional spatial coordinates, including our proposed Spatiomolecular Transformer (SMT). SMT explicitly models biological context by tokenizing genes based on their transcription start site (TSS) order to capture multi-scale genomic organization, and incorporating regional 3D spatial location via a dedicated context [CLS] token within its multi-head self-attention mechanism. We rigorously benchmark context-aware neural networks, including SMT and a single-gene resolution Multilayer-Perceptron (MLP), to established rules-based and bilinear methods. Crucially, to ensure that learned relationships in any model are not mere artifacts of spatial proximity, we introduce novel spatiomolecular null maps, preserving both spatial and transcriptomic autocorrelation. Context-aware neural networks outperform linear methods, significantly exceed our stringent null shuffle models, and generalize across diverse connectomic datasets and parcellation resolutions. Together, these findings demonstrate a strong, predictable link between the spatial distributions of gene expression and functional brain network architecture, and establish a rigorously validated deep learning framework for decoding this relationship. Code to reproduce our results is available at: github.com/neuroinfolab/GeneEx2Conn.