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Applications · Computer Vision

Haiyang Jiang, Tetsuichi Wazawa, Imari Sato, Takeharu Nagai, Yinqiang Zheng

Electron-multiplying charge-coupled device (EMCCD) has been instrumental in sensitive observations under low-light situations including astronomy, material science, and biology. Despite its ingenious designs to enhance target signals overcoming read-out circuit noises, produced images are not completely noise free, which could still cast a cloud on desired experiment outcomes, especially in fluorescence microscopy.Existing studies on EMCCD's noise model have been focusing on statistical characteristics in theory, yet unable to incorporate latest advancements in the field of computational photography, where physics-based noise models are utilized to guide deep learning processes, creating adaptive denoising algorithms for ordinary image sensors.Still, those models are not directly applicable to EMCCD.In this paper, we intend to pioneer EMCCD denoising by introducing a systematic study on physics-based noise model calibration procedures for an EMCCD camera, accurately estimating statistical features of observable noise components in experiments, which are then utilized to generate substantial amount of authentic training samples for one of the most recent neural networks.A first real-world test image dataset for EMCCD is captured, containing both images of ordinary daily scenes and those of microscopic contents.Benchmarking upon the testset and authentic microscopic images, we demonstrate distinct advantages of our model against previous methods for EMCCD and physics-based noise modeling, forging a promising new path for EMCCD denoising.

Deep Learning · Generative Models and Autoencoders

Enrico Ventura, Beatrice Achilli, Gianluigi Silvestri, Carlo Lucibello, Luca Ambrogioni

In this paper, we investigate the latent geometry of generative diffusion models under the manifold hypothesis. For this purpose, we analyze the spectrum of eigenvalues (and singular values) of the Jacobian of the score function, whose discontinuities (gaps) reveal the presence and dimensionality of distinct sub-manifolds. Using a statistical physics approach, we derive the spectral distributions and formulas for the spectral gaps under several distributional assumptions, and we compare these theoretical predictions with the spectra estimated from trained networks. Our analysis reveals the existence of three distinct qualitative phases during the generative process: a trivial phase; a manifold coverage phase where the diffusion process fits the distribution internal to the manifold; a consolidation phase where the score becomes orthogonal to the manifold and all particles are projected on the support of the data. This `division of labor' between different timescales provides an elegant explanation of why generative diffusion models are not affected by the manifold overfitting phenomenon that plagues likelihood-based models, since the internal distribution and the manifold geometry are produced at different time points during generation.

Deep Learning · Sequential Models, Time series

Filip Matzner, František Mráz

Echo State Networks (ESNs) are a class of recurrent neural networks in which only a small readout regression layer is trained, while the weights of the recurrent network, termed the reservoir, are randomly assigned and remain fixed. Our work introduces the Locally Connected ESN (LCESN), a novel ESN variant with a locally connected reservoir, forced memory, and a weight adaptation strategy. LCESN significantly reduces the asymptotic time and space complexities compared to the conventional ESN, enabling substantially larger networks. LCESN also improves the memory properties of ESNs without affecting network stability. We evaluate LCESN's performance on the NARMA10 benchmark task and compare it to state-of-the-art models on nine real-world datasets. Despite the simplicity of our model and its one-shot training approach, LCESN achieves competitive results, even surpassing several state-of-the-art models. LCESN introduces a fresh approach to real-world time series forecasting and demonstrates that large, well-tuned random recurrent networks can rival complex gradient-trained feedforward models. We provide our GPU-based implementation of LCESN as an open-source library.

Deep Learning · Other Representation Learning

Katharina Friedl, Noémie Jaquier, Jens Lundell, Tamim Asfour, Danica Kragic

By incorporating physical consistency as inductive bias, deep neural networks display increased generalization capabilities and data efficiency in learning nonlinear dynamic models. However, the complexity of these models generally increases with the system dimensionality, requiring larger datasets, more complex deep networks, and significant computational effort.We propose a novel geometric network architecture to learn physically-consistent reduced-order dynamic parameters that accurately describe the original high-dimensional system behavior.This is achieved by building on recent advances in model-order reduction and by adopting a Riemannian perspective to jointly learn a non-linear structure-preserving latent space and the associated low-dimensional dynamics.Our approach enables accurate long-term predictions of the high-dimensional dynamics of rigid and deformable systems with increased data efficiency by inferring interpretable and physically-plausible reduced Lagrangian models.

Applications · Genetics, Cell Biology, Health, etc

Lazar Atanackovic, Xi (Nicole) Zhang, Brandon Amos, Mathieu Blanchette, Leo J Lee, Yoshua Bengio, Alexander Tong, Kirill Neklyudov

Numerous biological and physical processes can be modeled as systems of interacting entities evolving continuously over time, e.g. the dynamics of communicating cells or physical particles. Learning the dynamics of such systems is essential for predicting the temporal evolution of populations across novel samples and unseen environments. Flow-based models allow for learning these dynamics at the population level - they model the evolution of the entire distribution of samples. However, current flow-based models are limited to a single initial population and a set of predefined conditions which describe different dynamics. We argue that multiple processes in natural sciences have to be represented as vector fields on the Wasserstein manifold of probability densities. That is, the change of the population at any moment in time depends on the population itself due to the interactions between samples. In particular, this is crucial for personalized medicine where the development of diseases and their respective treatment response depend on the microenvironment of cells specific to each patient. We propose *Meta Flow Matching* (MFM), a practical approach to integrate along these vector fields on the Wasserstein manifold by amortizing the flow model over the initial populations. Namely, we embed the population of samples using a Graph Neural Network (GNN) and use these embeddings to train a Flow Matching model. This gives MFM the ability to generalize over the initial distributions, unlike previously proposed methods. We demonstrate the ability of MFM to improve the prediction of individual treatment responses on a large-scale multi-patient single-cell drug screen dataset.

Applications · Chemistry and Drug Discovery

Jiarui Lu, Xiaoyin Chen, Stephen Lu, Chence Shi, Hongyu Guo, Yoshua Bengio, Jian Tang

Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Traditional physics-based simulation methods often struggle with sampling equilibrium conformations and are computationally expensive. Recently, deep generative models have shown promise in generating protein conformations as a more efficient alternative. However, these methods predominantly rely on the diffusion process within a 3D geometric space, which typically centers around the vicinity of metastable states and is often inefficient in terms of runtime. In this paper, we introduce Structure Language Modeling (SLM) as a novel framework for efficient protein conformation generation. Specifically, the protein structures are first encoded into a compact latent space using a discrete variational auto-encoder, followed by conditional language modeling that effectively captures sequence-specific conformation distributions. This enables a more efficient and interpretable exploration of diverse ensemble modes compared to existing methods. Based on this general framework, we instantiate SLM with various popular LM architectures as well as proposing the ESMDiff, a novel BERT-like structure language model fine-tuned from ESM3 with masked diffusion. We verify our approach in various scenarios, including the equilibrium dynamics of BPTI, conformational change pairs, and intrinsically disordered proteins. SLM provides a highly efficient solution, offering a 20-100x speedup than existing methods in generating diverse conformations, shedding light on promising avenues for future research.

Applications · Computer Vision

Haiwen Feng, Michael J Black, Weiyang Liu, Peter Kulits, Victoria Abrevaya

Inverse graphics -- the task of inverting an image into physical variables that, when rendered, enable reproduction of the observed scene -- is a fundamental challenge in computer vision and graphics. Successfully disentangling an image into its constituent elements, such as the shape, color, and material properties of the objects of the 3D scene that produced it, requires a comprehensive understanding of the environment. This complexity limits the ability of existing carefully engineered approaches to generalize across domains. Inspired by the zero-shot ability of large language models (LLMs) to generalize to novel contexts, we investigate the possibility of leveraging the broad world knowledge encoded in such models to solve inverse-graphics problems. To this end, we propose the Inverse-Graphics Large Language Model (IG-LLM), an inverse-graphics framework centered around an LLM, that autoregressively decodes a visual embedding into a structured, compositional 3D-scene representation. We incorporate a frozen pre-trained visual encoder and a continuous numeric head to enable end-to-end training. Through our investigation, we demonstrate the potential of LLMs to facilitate inverse graphics through next-token prediction, without the application of image-space supervision. Our analysis enables new possibilities for precise spatial reasoning about images that exploit the visual knowledge of LLMs. We release our code and data at https://ig-llm.is.tue.mpg.de/ to ensure the reproducibility of our investigation and to facilitate future research.

Applications · Physics

Razmik Khosrovian, Takaharu Yaguchi, Hiroaki Yoshimura, Takashi Matsubara

Deep learning has achieved great success in modeling dynamical systems, providing data-driven simulators to predict complex phenomena, even without known governing equations. However, existing models have two major limitations: their narrow focus on mechanical systems and their tendency to treat systems as monolithic. These limitations reduce their applicability to dynamical systems in other domains, such as electrical and hydraulic systems, and to coupled systems. To address these limitations, we propose Poisson-Dirac Neural Networks (PoDiNNs), a novel framework based on the Dirac structure that unifies the port-Hamiltonian and Poisson formulations from geometric mechanics. This framework enables a unified representation of various dynamical systems across multiple domains as well as their interactions and degeneracies arising from couplings. Our experiments demonstrate that PoDiNNs offer improved accuracy and interpretability in modeling unknown coupled dynamical systems from data.

Deep Learning · Large Language Models

Clemencia Siro, Guy Gur-Ari, Gaurav Mishra, Stuart Shieber, Jason Phang, Zijie Wang, Kory Mathewson, Giorgio Mariani, Allen Nie, James Y Zou 等

Language models demonstrate both quantitative improvement and new qualitative capabilities with increasing scale. Despite their potentially transformative impact, these new capabilities are as yet poorly characterized. In order to inform future research, prepare for disruptive new model capabilities, and ameliorate socially harmful effects, it is vital that we understand the present and near-future capabilities and limitations of language models. To address this challenge, we introduce the Beyond the Imitation Game benchmark (BIG- bench). BIG-bench currently consists of 204 tasks, contributed by 450 authors across 132 institutions. Task topics are diverse, drawing problems from linguistics, childhood develop- ment, math, common-sense reasoning, biology, physics, social bias, software development, and beyond. BIG-bench focuses on tasks that are believed to be beyond the capabilities of current language models. We evaluate the behavior of OpenAI's GPT models, Google- internal dense transformer architectures, and Switch-style sparse transformers on BIG-bench, across model sizes spanning millions to hundreds of billions of parameters. In addition, a team of human expert raters performed all tasks in order to provide a strong baseline. Findings include: model performance and calibration both improve with scale, but are poor in absolute terms (and when compared with rater performance); performance is remarkably similar across model classes, though with benefits from sparsity; tasks that improve gradually and predictably commonly involve a large knowledge or memorization component, whereas tasks that exhibit "breakthrough" behavior at a critical scale often involve multiple steps or components, or brittle metrics; social bias typically increases with scale in settings with ambiguous context, but this can be improved with prompting.

Applications · Physics

Daniel Musekamp, Marimuthu Kalimuthu, David Holzmüller, Makoto Takamoto, Mathias Niepert

Solving partial differential equations (PDEs) is a fundamental problem in engineering and science. While neural PDE solvers can be more efficient than established numerical solvers, they often require large amounts of training data that is costly to obtain. Active learning (AL) could help surrogate models reach the same accuracy with smaller training sets by querying classical solvers with more informative initial conditions and PDE parameters. While AL is more common in other domains, it has yet to be studied extensively for neural PDE solvers. To bridge this gap, we introduce AL4PDE, a modular and extensible active learning benchmark. It provides multiple parametric PDEs and state-of-the-art surrogate models for the solver-in-the-loop setting, enabling the evaluation of existing and the development of new AL methods for PDE solving. We use the benchmark to evaluate batch active learning algorithms such as uncertainty- and feature-based methods. We show that AL reduces the average error by up to 71\% compared to random sampling and significantly reduces worst-case errors. Moreover, AL generates similar datasets across repeated runs, with consistent distributions over the PDE parameters and initial conditions. The acquired datasets are reusable, providing benefits for surrogate models not involved in the data generation.

Applications · Everything Else

Can Rong, Jingtao Ding, Yan Liu, Yong Li

Commuting Origin-Destination~(OD) flows are critical inputs for urban planning and transportation, providing crucial information about the population residing in one region and working in another within an interested area. Due to the high cost of data collection, researchers have developed physical and computational models to generate commuting OD flows using readily available urban attributes, such as sociodemographics and points of interest, for cities lacking historical OD flows \textemdash commuting OD flow generation. Existing works developed models based on different techniques and achieved improvement on different datasets with different evaluation metrics, which hinderes establishing a unified standard for comparing model performance. To bridge this gap, we introduce a large-scale dataset containing commuting OD flows for 3,333 areas including a wide range of urban environments around the United States. Based on that, we benchmark widely used models for commuting OD flow generation. We surprisingly find that the network-based generative models achieve the optimal performance in terms of both precision and generalization ability, which may inspire new research directions of graph generative modeling in this field. The dataset and benchmark are available at https://anonymous.4open.science/r/CommutingODGen-Dataset-0D4C/.

Deep Learning · Large Language Models

Eunice Yiu, Maan Qraitem, Anisa Majhi, Charlie Wong, Yutong Bai, Shiry Ginosar, Alison Gopnik, Kate Saenko

This paper investigates visual analogical reasoning in large multimodal models (LMMs) compared to human adults and children. A “visual analogy” is an abstract rule inferred from one image and applied to another. While benchmarks exist for testing visual reasoning in LMMs, they require advanced skills and omit basic visual analogies that even young children can make. Inspired by developmental psychology, we propose a new benchmark of 4,300 visual transformations of everyday objects to test LMMs on visual analogical reasoning and compare them to children (ages three to five) and to adults. We structure the evaluation into three stages: identifying what changed (e.g., color, number, etc.), how it changed (e.g., added one object), and applying the rule to new scenarios. Our findings show that while GPT-o1, GPT-4V, LLaVA-1.5, and MANTIS identify the “what” effectively, they struggle with quantifying the “how” and extrapolating this rule to new objects. In contrast, children and adults exhibit much stronger analogical reasoning at all three stages. Additionally, the strongest tested model, GPT-o1, performs better in tasks involving simple surface-level visual attributes like color and size, correlating with quicker human adult response times. Conversely, more complex tasks such as number, rotation, and reflection, which necessitate extensive cognitive processing and understanding of extrinsic spatial properties in the physical world, present more significant challenges. Altogether, these findings highlight the limitations of training models on data that primarily consists of 2D images and text.

Applications · Physics

Youssef Shehata, Benjamin Holzschuh, Nils Thuerey

State-of-the-art Denoising Diffusion Probabilistic Models (DDPMs) rely on an expensive sampling process with a large Number of Function Evaluations (NFEs) to provide high-fidelity predictions. This computational bottleneck renders diffusion models less appealing as surrogates for the spatio-temporal prediction of physics-based problems with long rollout horizons. We propose Truncated Sampling Models, enabling single-step and few-step sampling with elevated fidelity by simple truncation of the diffusion process, reducing the gap between DDPMs and deterministic single-step approaches. We also introduce a novel approach, Iterative Refinement, to sample pre-trained DDPMs by reformulating the generative process as a refinement process with few sampling steps. Both proposed methods enable significant improvements in accuracy compared to DDPMs, DDIMs, and EDMs with NFEs $\leq$ 10 on a diverse set of experiments, including incompressible and compressible turbulent flow and airfoil flow uncertainty simulations. Our proposed methods provide stable predictions for long rollout horizons in time-dependent problems and are able to learn all modes of the data distribution in steady-state problems with high uncertainty.

Applications · Physics

Tianyi Bao, Xinyu Ye, Hang Ruan, Chang Liu, Wenjie Wu, Junchi Yan

Despite the progress in quantum computing, one major bottleneck against the practical utility is its susceptibility to noise, which frequently occurs in current quantum systems. Existing quantum error mitigation (QEM) methods either lack generality to noise and circuit types or fail to capture the global dependencies of entire systems in addition to circuit structure. In this work, we first propose a unique circuit-to-graph encoding scheme with qubit-wise noisy measurement aggregated. Then, we introduce GTranQEM, a non-message passing graph transformer designed to mitigate errors in expected circuit measurement outcomes effectively. GTranQEM is equipped with a quantum-specific positional encoding, a structure matrix as attention bias guiding nonlocal aggregation, and a virtual quantum-representative node to further grasp graph representations, which guarantees to model the long-range entanglement. Experimental evaluations demonstrate that GTranQEM outperforms state-of-the-art QEM methods on both random and structured quantum circuits across noise types and scales among diverse settings.

Applications · Computer Vision

Zhongpai Gao, Benjamin Planche, Meng Zheng, Anwesa Choudhuri, Terrence Chen, Ziyan Wu

Novel view synthesis has advanced significantly with the development of neural radiance fields (NeRF) and 3D Gaussian splatting (3DGS). However, achieving high quality without compromising real-time rendering remains challenging, particularly for physically-based rendering using ray/path tracing with view-dependent effects. Recently, N-dimensional Gaussians (N-DG) introduced a 6D spatial-angular representation to better incorporate view-dependent effects, but the Gaussian representation and control scheme are sub-optimal. In this paper, we revisit 6D Gaussians and introduce 6D Gaussian Splatting (6DGS), which enhances color and opacity representations and leverages the additional directional information in the 6D space for optimized Gaussian control. Our approach is fully compatible with the 3DGS framework and significantly improves real-time radiance field rendering by better modeling view-dependent effects and fine details. Experiments demonstrate that 6DGS significantly outperforms 3DGS and N-DG, achieving up to a 15.73 dB improvement in PSNR with a reduction of 66.5\% Gaussian points compared to 3DGS. The project page is: https://gaozhongpai.github.io/6dgs/.

Applications · Physics

Bin Cao, Yang Liu, Zinan Zheng, Ruifeng Tan, Jia Li, Tong-Yi Zhang

Powder X-ray diffraction (XRD) patterns are highly effective for crystal identification and play a pivotal role in materials discovery. While machine learning (ML) has advanced the analysis of powder XRD patterns, progress has been constrained by the limited availability of training data and established benchmarks. To address this, we introduce SimXRD, the largest open-source simulated XRD pattern dataset to date, aimed at accelerating the development of crystallographic informatics. We developed a novel XRD simulation method that incorporates comprehensive physical interactions, resulting in a high-fidelity database. SimXRD comprises 4,065,346 simulated powder XRD patterns, representing 119,569 unique crystal structures under 33 simulated conditions that reflect real-world variations. We benchmark 21 sequence models in both in-library and out-of-library scenarios and analyze the impact of class imbalance in long-tailed crystal label distributions. Remarkably, we find that: (1) current neural networks struggle with classifying low-frequency crystals, particularly in out-of-library situations; (2) models trained on SimXRD can generalize to real experimental data.

Applications · Physics

Zihan Zhou, Xiaoxue Wang, Tianshu Yu

Generating physically feasible dynamics in a data-driven context is challenging, especially when adhering to physical priors expressed in specific equations or formulas. Existing methodologies often overlook the integration of ''physical priors'', resulting in violation of basic physical laws and suboptimal performance. In this paper, we introduce a novel framework that seamlessly incorporates physical priors into diffusion-based generative models to address this limitation. Our approach leverages two categories of priors: 1) distributional priors, such as roto-translational invariance, and 2) physical feasibility priors, including energy and momentum conservation laws and PDE constraints. By embedding these priors into the generative process, our method can efficiently generate physically realistic dynamics, encompassing trajectories and flows. Empirical evaluations demonstrate that our method produces high-quality dynamics across a diverse array of physical phenomena with remarkable robustness, underscoring its potential to advance data-driven studies in AI4Physics. Our contributions signify a substantial advancement in the field of generative modeling, offering a robust solution to generate accurate and physically consistent dynamics.

Wei Chow, Jiageng Mao, Boyi Li, Daniel Seita, Vitor Campagnolo Guizilini, Yue Wang

Understanding the physical world is a fundamental challenge in embodied AI, critical for enabling agents to perform complex tasks and operate safely in real-world environments. While Vision-Language Models (VLMs) have shown great promise in reasoning and task planning for embodied agents, their ability to comprehend physical phenomena remains extremely limited.To close this gap, we introduce PhysBench, a comprehensive benchmark designed to evaluate VLMs' physical world understanding capability across a diverse set of tasks. PhysBench contains 10,002 entries of interleaved video-image-text data, categorized into four major domains: physical object properties, physical object relationships, physical scene understanding, and physics-based dynamics, further divided into 19 subclasses and 8 distinct capability dimensions.Our extensive experiments, conducted on 75 representative VLMs, reveal that while these models excel in common-sense reasoning, they struggle with understanding the physical world---likely due to the absence of physical knowledge in their training data and the lack of embedded physical priors.To tackle the shortfall, we introduce PhysAgent, a novel framework that combines the generalization strengths of VLMs with the specialized expertise of vision models, significantly enhancing VLMs' physical understanding across a variety of tasks, including an 18.4\% improvement on GPT-4o.Furthermore, our results demonstrate that enhancing VLMs' physical world understanding capabilities can help embodied agents such as MOKA.We believe that PhysBench and PhysAgent offer valuable insights and contribute to bridging the gap between VLMs and physical world understanding. [Project Page is here](https://physbench.github.io/)

Yongxing Zhang, Donglin Yang, Renjie Liao

The group of permutations $S_n$, also known as the finite symmetric groups, are essential in fields such as combinatorics, physics, and chemistry. However, learning a probability distribution over $S_n$ poses significant challenges due to its intractable size and discrete nature. In this paper, we introduce *SymmetricDiffusers*, a novel discrete diffusion model that simplifies the task of learning a complicated distribution over $S_n$ by decomposing it into learning simpler transitions of the reverse diffusion using deep neural networks. We identify the riffle shuffle as an effective forward transition and provide empirical guidelines for selecting the diffusion length based on the theory of random walks on finite groups. Additionally, we propose a generalized Plackett-Luce (PL) distribution for the reverse transition, which is provably more expressive than the PL distribution. We further introduce a theoretically grounded "denoising schedule" to improve sampling and learning efficiency. Extensive experiments show that our model achieves state-of-the-art or comparable performance on solving tasks including sorting 4-digit MNIST images, jigsaw puzzles, and traveling salesman problems. Our code is released at <https://github.com/DSL-Lab/SymmetricDiffusers>.

Applications · Physics

Honghui Wang, Shiji Song, Gao Huang

Significant advancements have been achieved in PDE modeling using neural fields. Despite their effectiveness, existing methods rely on global modulation, limiting their ability to reconstruct local details. While spatial modulation with vanilla grid-based representations offers a promising alternative, it struggles with inadequate global information modeling and over-fitting to the training spatial domain. To address these challenges, we propose GridMix, a novel approach that models spatial modulation as a mixture of grid-based representations. GridMix effectively explores global structures while preserving locality for fine-grained modulation. Furthermore, we introduce spatial domain augmentation to enhance the robustness of the modulated neural fields against spatial domain variations. With all these innovations,our comprehensive approach culminates in MARBLE, a framework that significantly advancing the capabilities of neural fields in PDE modeling. The effectiveness of MARBLE is extensivelyvalidated on diverse benchmarks encompassing dynamics modeling and geometric prediction.