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Applications · Neuroscience, Cognitive Science

Arjun Karuvally, Pichsinee Lertsaroj, Terrence Sejnowski, Hava Siegelmann

The energy paradigm, exemplified by Hopfield networks, offers a principled framework for memory in neural systems by interpreting dynamics as descent on an energy surface. While powerful for static associative memories, it falls short in modeling sequential memory, where transitions between memories are essential. We introduce the Exponential Dynamic Energy Network (EDEN), a novel architecture that extends the energy paradigm to temporal domains by evolving the energy function over multiple timescales. EDEN combines a static high-capacity energy network with a slow, asymmetrically interacting modulatory population, enabling robust and controlled memory transitions. We formally derive short-timescale energy functions that govern local dynamics and use them to analytically compute memory escape times, revealing a phase transition between static and dynamic regimes. The analysis of capacity, defined as the number of memories that can be stored with minimal error rate as a function of the dimensions of the state space (number of feature neurons), for EDEN shows that it achieves exponential sequence memory capacity $\mathcal{O}(\gamma^N)$, outperforming the linear capacity $\mathcal{O}(N)$ of conventional models. Furthermore, EDEN's dynamics resemble the activity of time and ramping cells observed in the human brain during episodic memory tasks, grounding its biological relevance. By unifying static and sequential memory within a dynamic energy framework, EDEN offers a scalable and interpretable model for high-capacity temporal memory in both artificial and biological systems.

Applications · Chemistry and Drug Discovery

Michael Plainer, Hao Wu, Leon Klein, Stephan Günnemann, Frank Noe

In recent years, diffusion models trained on equilibrium molecular distributions have proven effective for sampling biomolecules. Beyond direct sampling, the score of such a model can also be used to derive the forces that act on molecular systems. However, while classical diffusion sampling usually recovers the training distribution, the corresponding energy-based interpretation of the learned score is often inconsistent with this distribution, even for low-dimensional toy systems. We trace this inconsistency to inaccuracies of the learned score at very small diffusion timesteps, where the model must capture the correct evolution of the data distribution. In this regime, diffusion models fail to satisfy the Fokker--Planck equation, which governs the evolution of the score. We interpret this deviation as the source of the observed inconsistencies and propose an energy-based diffusion model with a Fokker--Planck-derived regularization term to enforce consistency. We demonstrate our approach by sampling and simulating multiple biomolecular systems, including fast-folding proteins, and by introducing a state-of-the-art transferable Boltzmann emulator for dipeptides that supports simulation and achieves improved consistency and efficient sampling. Our code and self-contained JAX and PyTorch notebooks are available at https://github.com/noegroup/ScoreMD.

Deep Learning · Generative Models and Autoencoders

Vivek Jayaram, Ira Kemelmacher-Shlizerman, Steve Seitz, John Thickstun

We introduce Linearly Constrained Diffusion Implicit Models (CDIM), a fast and accurate approach to solving noisy linear inverse problems using diffusion models. Traditional diffusion-based inverse methods rely on numerous projection steps to enforce measurement consistency in addition to unconditional denoising steps. CDIM achieves a 10–50× reduction in projection steps by dynamically adjusting the number and size of projection steps to align a residual measurement energy with its theoretical distribution under the forward diffusion process. This adaptive alignment preserves measurement consistency while substantially accelerating constrained inference. For noise-free linear inverse problems, CDIM exactly satisfies the measurement constraints with few projection steps, even when existing methods fail. We demonstrate CDIM’s effectiveness across a range of applications, including super-resolution, denoising, inpainting, deblurring, and 3D point cloud reprojection.

Applications · Physics

Jiyan Qiu, Lyulin Kuang, Guan Wang, Yichen Xu, Leiyao Cui, Shaotong Fu, Yixin Zhu, Rita Zhang

Vehicle aerodynamics optimization has become critical for automotive electrification, where drag reduction directly determines electric vehicle range and energy efficiency. Traditional approaches face an intractable trade-off: computationally expensive Computational Fluid Dynamics (CFD) simulations requiring weeks per design iteration, or simplified models that sacrifice production-grade accuracy. While machine learning offers transformative potential, existing datasets exhibit fundamental limitations -- inadequate mesh resolution, missing vehicle components, and validation errors exceeding 5% -- preventing deployment in industrial workflows. We present DrivAerStar, comprising 12,000 industrial-grade automotive CFD simulations generated using STAR-CCM+${}^{\textregistered}$ software. The dataset systematically explores three vehicle configurations through 20 Computer Aided Design (CAD) parameters via Free Form Deformation (FFD) algorithms, including complete engine compartments and cooling systems with realistic internal airflow. DrivAerStar achieves wind tunnel validation accuracy below 1.04% -- a five-fold improvement over existing datasets -- through refined mesh strategies with strict wall $y^+$ control. Benchmarks demonstrate that models trained on this data achieve production-ready accuracy while reducing computational costs from weeks to minutes. This represents the first dataset bridging academic machine learning research and industrial CFD practice, establishing a new standard for data-driven aerodynamic optimization in automotive development. Beyond automotive applications, DrivAerStar demonstrates a paradigm for integrating high-fidelity physics simulations with Artificial Intelligence (AI) across engineering disciplines where computational constraints currently limit innovation.

Applications · Physics

Jinlin Xiang, Minho Choi, Yubo Zhang, Zhihao Zhou, Arka Majumdar, Eli Shlizerman

Hybrid Optical Neural Networks (ONNs, typically consisting of an optical frontend and a digital backend) offer an energy-efficient alternative to fully digital deep networks for real-time, power-constrained systems. However, their adoption is limited by two main challenges: the accuracy gap compared to large-scale networks during training, and discrepancies between simulated and fabricated systems that further degrade accuracy. While previous work has proposed end-to-end optimizations for specific datasets (e.g., MNIST) and optical systems, these approaches typically lack generalization across tasks and hardware designs. To address these limitations, we propose a task-agnostic and hardware-agnostic pipeline that supports image classification and segmentation across diverse optical systems. To assist optical system design before training, we design the metasurface layout based on fabrication constraints. For training, we introduce Neural Tangent Knowledge Distillation (NTKD), which aligns optical models with electronic teacher networks, thereby narrowing the accuracy gap. After fabrication, NTKD also guides fine-tuning of the digital backend to compensate for implementation errors. Experiments on multiple datasets (e.g., MNIST, CIFAR, Carvana Masking) and hardware configurations show that our pipeline consistently improves ONN performance and enables practical deployment in both pre-fabrication simulations and physical implementations.

Applications · Chemistry and Drug Discovery

Yihang Zhou, Chen Wei, Minghao Sun, Jin Song, Yang Li, Lin Wang, Yang Zhang

Understanding the conformational landscape of proteins is essential for elucidating protein function and facilitating drug design. However, existing protein conformation benchmarks fail to capture the full energy landscape, limiting their ability to evaluate the diversity and physical plausibility of AI-generated structures. We introduce ProteinConformers, a large-scale benchmark dataset comprising over 381,000 physically realistic conformations for 87 CASP targets. These were derived from more than 40,000 structural decoys via extensive all-atom molecular dynamics simulations totaling over 6 million CPU hours. Using this dataset, we propose novel metrics to evaluate conformational diversity and plausibility, and systematically benchmark six protein conformation generative models. Our results highlight that leveraging large-scale protein sequence data can enhance a model’s ability to explore conformational space, potentially reducing reliance on MD-derived data. Additionally, we find that PDB and MD datasets influence model performance differently, current models perform well on inter-atomic distance prediction but struggle with inter-residue orientation generation. Overall, our dataset, evaluation metrics, and benchmarking results provide the first comprehensive foundation for assessing generative models in protein conformational modeling. Dataset and instructions are available at https://huggingface.co/ datasets/Jim990908/ProteinConformers/tree/main. Codes are stored at https://github.com/auroua/ProteinConformers. An interactive website locates at https://zhanggroup.org/ProteinConformers.

Applications · Physics

Oumar Kaba, Kusha Sareen, Daniel Levy, Siamak Ravanbakhsh

Effectively leveraging prior knowledge of a system’s physics is crucial for applications of machine learning to scientific domains. Previous approaches mostly focused on incorporating physical insights at the architectural level. In this paper, we propose a framework to leverage physical information directly into the loss function for prediction and generative modeling tasks on systems like molecules and spins. We derive energy loss functions assuming that each data sample is in thermal equilibrium with respect to an approximate energy landscape. By using the reverse KL divergence with a Boltzmann distribution around the data, we obtain the loss as an energy difference between the data and the model predictions. This perspective also recasts traditional objectives like MSE as energy-based, but with a physically meaningless energy. In contrast, our formulation yields physically grounded loss functions with gradients that better align with valid configurations, while being architecture-agnostic and computationally efficient. The energy loss functions also inherently respect physical symmetries. We demonstrate our approach on molecular generation and spin ground-state prediction and report significant improvements over baselines.

XINGYANG LI, Muyang Li, Tianle Cai, Haocheng Xi, Shuo Yang, Yujun Lin, Lvmin Zhang, Songlin Yang, Jinbo Hu, Kelly Peng 等

Recent advances in diffusion models have enabled high-quality video generation, but the additional temporal dimension significantly increases computational costs, making training and inference on long videos prohibitively expensive. In this paper, we identify a phenomenon we term Spatiotemporal Energy Decay in video diffusion models: post-softmax attention scores diminish as spatial and temporal distance between tokens increase, akin to the physical decay of signal or waves over space and time in nature. Motivated by this, we propose Radial Attention, a scalable sparse attention mechanism with $\mathcal{O}(n \log n)$ complexity that translates energy decay into exponentially decaying compute density, which is significantly more efficient than standard $\mathcal{O}(n^2)$ dense attention and more expressive than linear attention. Specifically, Radial Attention employs a simple, static attention mask where each token attends to spatially nearby tokens, with the attention window size shrinking with temporal distance. Moreover, it allows pre-trained video diffusion models to extend their generation length with efficient LoRA-based fine-tuning. Extensive experiments show that \method maintains video quality across Wan2.1-14B, HunyuanVideo, and Mochi 1, achieving up to a 1.9× speedup over the original dense attention. With minimal tuning, it enables video generation up to 4× longer while reducing training costs by up to 4.4× compared to direct fine-tuning and accelerating inference by up to 3.7× compared to dense attention inference. Code is released at https://github.com/mit-han-lab/radial-attention.

General Machine Learning · Everything Else

Alexandru Oarga, Yilun Du

Generalization is a key challenge in machine learning, specifically in reasoning tasks, where models are expected to solve problems more complex than those encountered during training. Existing approaches typically train reasoning models in an end-to-end fashion, directly mapping input instances to solutions. While this allows models to learn useful heuristics from data, it often results in limited generalization beyond the training distribution. In this work, we propose a novel approach to reasoning generalization by learning energy landscapes over the solution spaces of smaller, more tractable subproblems. At test time, we construct a global energy landscape for a given problem by combining the energy functions of multiple subproblems. This compositional approach enables the incorporation of additional constraints during inference, allowing the construction of energy landscapes for problems of increasing difficulty. To improve the sample quality from this newly constructed energy landscape, we introduce Parallel Energy Minimization (PEM). We evaluate our approach on a wide set of reasoning problems. Our method outperforms existing state-of-the-art methods, demonstrating its ability to generalize to larger and more complex problems. Project website can be found at: https://alexoarga.github.io/compositional_reasoning/

Applications · Health

Ke Liu, Shangde Gao, Yichao Fu, Shangqi Gao

Retinal vessel segmentation is critical for medical diagnosis, yet existing models often struggle to generalize across domains due to appearance variability, limited annotations, and complex vascular morphology. We propose GraphSeg, a variational Bayesian framework that integrates anatomical graph priors with structure-aware image decomposition to enhance cross-domain segmentation. GraphSeg factorizes retinal images into structure-preserved and structure-degraded components, enabling domain-invariant representation. A deformable graph prior, derived from a statistical retinal atlas, is incorporated via a differentiable alignment and guided by an unsupervised energy function. Experiments on three public benchmarks (CHASE, DRIVE, HRF) show that GraphSeg consistently outperforms existing methods under domain shifts. These results highlight the importance of jointly modeling anatomical topology and image structure for robust generalizable vessel segmentation.

Hongchi Xia, Chih-Hao Lin, Hao-Yu Hsu, Quentin Leboutet, Katelyn Gao, Michael Paulitsch, Benjamin Ummenhofer, Shenlong Wang

Digitizing the physical world into accurate simulation‑ready virtual environments offers significant opportunities in a variety of fields such as augmented and virtual reality, gaming, and robotics. However, current 3D reconstruction and scene-understanding methods commonly fall short in one or more critical aspects, such as geometry completeness, object interactivity, physical plausibility, photorealistic rendering, or realistic physical properties for reliable dynamic simulation. To address these limitations, we introduce HoloScene, a novel interactive 3D reconstruction framework that simultaneously achieves these requirements. HoloScene leverages a comprehensive interactive scene-graph representation, encoding object geometry, appearance, and physical properties alongside hierarchical and inter-object relationships. Reconstruction is formulated as an energy-based optimization problem, integrating observational data, physical constraints, and generative priors into a unified, coherent objective. Optimization is efficiently performed via a hybrid approach combining sampling-based exploration with gradient-based refinement. The resulting digital twins exhibit complete and precise geometry, physical stability, and realistic rendering from novel viewpoints. Evaluations conducted on multiple benchmark datasets demonstrate superior performance, while practical use-cases in interactive gaming and real-time digital-twin manipulation illustrate HoloScene's broad applicability and effectiveness.

Deep Learning · Generative Models and Autoencoders

Florentin Guth, Zahra Kadkhodaie, Eero Simoncelli

Learning probability models from data is at the heart of many machine learning endeavors, but is notoriously difficult due to the curse of dimensionality. We introduce a new framework for learning \emph{normalized} energy (log probability) models that is inspired from diffusion generative models, which rely on networks optimized to estimate the score. We modify a score network architecture to compute an energy while preserving its inductive biases. The gradient of this energy network with respect to its input image is the score of the learned density, which can be optimized using a denoising objective. Importantly, the gradient with respect to the noise level provides an additional score that can be optimized with a novel secondary objective, ensuring consistent and normalized energies across noise levels. We train an energy network with this \emph{dual} score matching objective on the ImageNet64 dataset, and obtain a cross-entropy (negative log likelihood) value comparable to the state of the art. We further validate our approach by showing that our energy model \emph{strongly generalizes}: log probabilities estimated with two networks trained on non-overlapping data subsets are nearly identical. Finally, we demonstrate that both image probability and dimensionality of local neighborhoods vary substantially depending on image content, in contrast with conventional assumptions such as concentration of measure or support on a low-dimensional manifold.

Applications · Physics

Guillaume Pourcel, Maxence Ernoult

Deep State Space Models (SSMs) reignite physics-grounded compute paradigms, as RNNs could natively be embodied into dynamical systems. This calls for dedicated learning algorithms obeying to core physical principles, with efficient techniques to simulate these systems and guide their design. We propose \emph{Recurrent Hamiltonian Echo Learning} (RHEL), an algorithm which provably computes loss gradients as finite differences of physical trajectories of non-dissipative, \emph{Hamiltonian systems}. In ML terms, RHEL only requires three ``forward passes'' irrespective of model size, without explicit Jacobian computation, nor incurring any variance in the gradient estimation. Motivated by the potential to implement our algorithm in non-digital physical systems, we first introduce RHEL in \emph{continuous time} and demonstrate its formal equivalence with the continuous adjoint state method. To facilitate the simulation of Hamiltonian systems trained by RHEL, we propose a \emph{discrete-time} version of RHEL which is equivalent to Backpropagation Through Time (BPTT) when applied to a class of recurrent modules which we call \emph{Hamiltonian Recurrent Units} (HRUs). This setting allows us to demonstrate the scalability of RHEL by generalizing these results to hierarchies of HRUs, which we call \emph{Hamiltonian SSMs} (HSSMs). We apply RHEL to train HSSMs with linear and nonlinear dynamics on a variety of time-series tasks ranging from mid-range to long-range classification and regression with sequence length reaching $\sim 50k$. We show that RHEL consistently matches the performance of BPTT across all models and tasks. This work opens new doors for the design of scalable, energy-efficient physical systems endowed with self-learning capabilities for sequence modelling.

Applications · Chemistry and Drug Discovery

Shriram Chennakesavalu, Frank Hu, Sebastian Ibarraran, Grant Rotskoff

Searching through chemical space is an exceptionally challenging problem because the number of possible molecules grows combinatorially with the number of atoms. Large, autoregressive models trained on databases of chemical compounds have yielded powerful generators, but we still lack robust strategies for generating molecules with desired properties. This molecular search problem closely resembles the "alignment" problem for large language models, though for many chemical tasks we have a specific and easily evaluable reward function. Here, we introduce an algorithm called energy rank alignment (ERA) that leverages an explicit reward function to produce a gradient-based objective that we use to optimize autoregressive policies. We show theoretically that this algorithm is closely related to proximal policy optimization (PPO) and direct preference optimization (DPO), but has a minimizer that converges to an ideal Gibbs-Boltzmann distribution with the reward playing the role of an energy function. Furthermore, this algorithm is highly scalable, does not require reinforcement learning, and performs well relative to DPO when the number of preference observations per pairing is small. We deploy this approach to align molecular transformers and protein language models to generate molecules and protein sequences, respectively, with externally specified properties and find that it does so robustly, searching through diverse parts of chemical space.

Applications · Physics

Wahid Bhimji, Ragansu Chakkappai, Po-Wen Chang, Yuan-Tang Chou, Sascha Diefenbacher, Jordan Dudley, Ibrahim Elsharkawy, Steven Farrell, Aishik Ghosh, Cristina Giordano 等

The FAIR Universe – HiggsML Uncertainty Challenge focused on measuring the physical properties of elementary particles with imperfect simulators. Participants were required to compute and report confidence intervals for a parameter of interest regarding the Higgs boson while accounting for various systematic (epistemic) uncertainties. The dataset is a tabular dataset of 28 features and 280 million instances. Each instance represents a simulated proton-proton collision as observed at CERN’s Large Hadron Collider in Geneva, Switzerland. The features of these simulations were chosen to capture key characteristics of different types of particles. These include primary attributes, such as the energy and three-dimensional momentum of the particles, as well as derived attributes, which are calculated from the primary ones using domain-specific knowledge. Additionally, a label feature designates each instance’s type of proton-proton collision, distinguishing the Higgs boson events of interest from three background sources. As outlined in this paper, the permanent dataset release allows long-term benchmarking of new techniques. The leading submissions, including Contrastive Normalising Flows and Density Ratios estimation through classification, are described. Our challenge has brought together the physics and machine learning communities to advance our understanding and methodologies in handling systematic uncertainties within AI techniques.

Theory · Game Theory

John Lazarsfeld, Georgios Piliouras, Ryann Sim, Stratis Skoulakis

This paper studies the *optimistic* variant of Fictitious Play for learning in two-player zero-sum games. While it is known that Optimistic FTRL -- a *regularized* algorithm with a bounded stepsize parameter -- obtains constant regret in this setting, we show for the first time that similar, optimal rates are also achievable *without* regularization: we prove for two-strategy games that Optimistic Fictitious Play (using *any* tiebreaking rule) obtains only *constant regret*, providing surprising new evidence on the ability of *non*-no-regret algorithms for fast learning in games. Our proof technique leverages a geometric view of Optimistic Fictitious Play in the dual space of payoff vectors, where we show a certain energy function of the iterates remains bounded over time. Additionally, we also prove a regret *lower bound* of $\Omega(\sqrt{T})$ for *Alternating* Fictitious Play. In the unregularized regime, this separates the ability of optimism and alternation in achieving $o(\sqrt{T})$ regret.

Deep Learning · Robustness

Jingyu Li, Pengwen Dai, Mingqing Zhu, Chengwei Wang, Haolong Liu, Xiaochun Cao

Recent work has shown that scene text recognition (STR) models are vulnerable to adversarial examples. Different from non-sequential vision tasks, the output sequence of STR models contains rich information. However, existing adversarial attacks against STR models can only lead to a few incorrect characters in the predicted text. These attack results still carry partial information about the original prediction and could be easily corrected by an external dictionary or a language model. Therefore, we propose the Multi-Population Coevolution Search (MPCS) method to attack each character in the image. We first decompose the global optimization objective into sub-objectives to solve the attack pixel concentration problem existing in previous attack methods. While this distributed optimization paradigm brings a new joint perturbation shift problem, we propose a novel coevolution energy function to solve it. Experiments on recent STR models show the superiority of our method. The code is available at \url{https://github.com/Lee-Jingyu/MPCS}.

Applications · Chemistry and Drug Discovery

Yihan Zhu, Gang Liu, Eric Inae, Tengfei Luo, Meng Jiang

Polymers are large macromolecules composed of repeating structural units known as monomers and are widely applied in fields such as energy storage, construction, medicine, and aerospace. However, existing graph neural network methods, though effective for small molecules, only model the single unit of polymers and fail to produce consistent vector representations for the true polymer structure with varying numbers of units. To address this challenge, we introduce Graph Repetition Invariance (GRIN), a novel method to learn polymer representations that are invariant to the number of repeating units in their graph representations. GRIN integrates a graph-based maximum spanning tree alignment with repeat-unit augmentation to ensure structural consistency. We provide theoretical guarantees for repetition‐invariance from both model and data perspectives, demonstrating that three repeating units are the minimal augmentation required for optimal invariant representation learning. GRIN outperforms state-of-the-art baselines on both homopolymer and copolymer benchmarks, learning stable, repetition-invariant representations that generalize effectively to polymer chains of unseen sizes.

Probabilistic Methods

SEOKJU HAHN, Junghye Lee

Diffusion models have demonstrated decent generation quality, yet their deployment in federated learning scenarios remains challenging. Due to data heterogeneity and a large number of parameters, conventional parameter averaging schemes often fail to achieve stable collaborative training of diffusion models. We reframe collaborative synthetic data generation as a cooperative sampling procedure from a mixture of decentralized distributions, each encoded by a pre-trained local diffusion model. This leverages the connection between diffusion and energy-based models, which readily supports compositional generation thereof. Consequently, we can directly obtain refined synthetic dataset, optionally with differential privacy guarantee, even without exchanging diffusion model parameters. Our framework reduces communication overhead while maintaining the generation quality, realized through an unadjusted Langevin algorithm with a convergence guarantee.

Applications · Neuroscience, Cognitive Science

Jieyuan (Eric) Zhang, Xiaolong Zhou, Shuai Wang, Wenjie Wei, Hanwen Liu, Qian Sun, Malu Zhang, Yang Yang, Haizhou Li

Spiking Neural Networks (SNNs) demonstrate significant potential for energy-efficient neuromorphic computing through an event-driven paradigm. While training methods and computational models have greatly advanced, SNNs struggle to achieve competitive performance in visual long-sequence modeling tasks. In artificial neural networks, the effective receptive field (ERF) serves as a valuable tool for analyzing feature extraction capabilities in visual long-sequence modeling. Inspired by this, we introduce the Spatio-Temporal Effective Receptive Field (ST-ERF) to analyze the ERF distributions across various Transformer-based SNNs. Based on the proposed ST-ERF, we reveal that these models suffer from establishing a robust global ST-ERF, thereby limiting their visual feature modeling capabilities. To overcome this issue, we propose two novel channel-mixer architectures: \underline{m}ulti-\underline{l}ayer-\underline{p}erceptron-based m\underline{ixer} (MLPixer) and \underline{s}plash-and-\underline{r}econstruct \underline{b}lock (SRB). These architectures enhance global spatial ERF through all timesteps in early network stages of Transformer-based SNNs, improving performance on challenging visual long-sequence modeling tasks. Extensive experiments conducted on the Meta-SDT variants and across object detection and semantic segmentation tasks further validate the effectiveness of our proposed method. Beyond these specific applications, we believe the proposed ST-ERF framework can provide valuable insights for designing and optimizing SNN architectures across a broader range of tasks. The code is available at \href{https://github.com/EricZhang1412/Spatial-temporal-ERF}{\faGithub~EricZhang1412/Spatial-temporal-ERF}.