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Probabilistic Methods · Gaussian Processes

David Dalton, Dirk Husmeier, Hao Gao

Physics-informed machine learning (PIML) has established itself as a new scientific paradigm which enables the seamless integration of observational data with partial differential equation (PDE) based physics models. A powerful tool for the analysis, reduction and solution of PDEs is the Lie symmetry method. Nevertheless, only recently has the integration of such symmetries into PIML frameworks begun to be explored. The present work adds to this growing literature by introducing an approach for incorporating a Lie symmetry into a physics-informed Gaussian process (GP) model. The symmetry is introduced as a constraint on the GP; either in a soft manner via virtual observations of an induced PDE called the invariant surface condition, or explicitly through the design of the kernel. Experimental results demonstrate that the use of symmetry constraints improves the performance of the GP for both forward and inverse problems, and that our approach offers competitive performance with neural networks in the low-data environment.

Deep Learning · Large Language Models

Junhong Shen, Neil Tenenholtz, James Hall, David Alvarez-Melis, Nicolò Fusi

Large Language Models (LLMs) have demonstrated remarkable proficiency in understanding and generating natural language. However, their capabilities wane in highly specialized domains underrepresented in the pretraining corpus, such as physical and biomedical sciences. This work explores how to repurpose general LLMs into effective task solvers for specialized domains. We introduce a novel, model-agnostic framework for learning custom input tags, which are parameterized as continuous vectors appended to the LLM’s embedding layer, to condition the LLM. We design two types of input tags: domain tags are used to delimit specialized representations (e.g., chemical formulas) and provide domain-relevant context; function tags are used to represent specific functions (e.g., predicting molecular properties) and compress function-solving instructions. We develop a three-stage protocol to learn these tags using auxiliary data and domain knowledge. By explicitly disentangling task domains from task functions, our method enables zero-shot generalization to unseen problems through diverse combinations of the input tags. It also boosts LLM’s performance in various specialized domains, such as predicting protein or chemical properties and modeling drug-target interactions, outperforming expert models tailored to these tasks.

Deep Learning · Generative Models and Autoencoders

raghav singhal, Mark Goldstein, Rajesh Ranganath

Reversing a diffusion process by learning its score forms the heart of diffusion-based generative modeling and for estimating properties of scientific systems. The diffusion processes that are tractable center on linear processes with a Gaussian stationary distribution, limiting the kinds of models that can be built to those that target a Gaussian prior or more generally limits the kinds of problems that can be generically solved to those that have conditionally linear score functions. In this work, we introduce a family of tractable denoising score matching objectives, called local-DSM, built using local increments of the diffusion process. We show how local-DSM melded with Taylor expansions enables automated training and score estimation with nonlinear diffusion processes. To demonstrate these ideas, we use automated-DSM to train generative models using non-Gaussian priors on challenging low dimensional distributions and the CIFAR10 image dataset. Additionally, we use the automated-DSM to learn the scores for nonlinear processes studied in statistical physics.

Applications · Physics

Zhongzhan Huang, Mingfu Liang, Shanshan Zhong, Liang Lin

We propose the attention-inspired numerical solver (AttNS), a concise method that helps the generalization and robustness issues faced by the AI-Hybrid numerical solver in solving differential equations due to limited data. AttNS is inspired by the effectiveness of attention modules in Residual Neural Networks (ResNet) in enhancing model generalization and robustness for conventional deep learning tasks. Drawing from the dynamical system perspective of ResNet, We seamlessly incorporate attention mechanisms into the design of numerical methods tailored for the characteristics of solving differential equations. Our results on benchmarks, ranging from high-dimensional problems to chaotic systems, showcase AttNS consistently enhancing various numerical solvers without any intricate model crafting. Finally, we analyze AttNS experimentally and theoretically, demonstrating its ability to achieve strong generalization and robustness while ensuring the convergence of the solver. This includes requiring less data compared to other advanced methods to achieve comparable generalization errors and better prevention of numerical explosion issues when solving differential equations.

Deep Learning · Other Representation Learning

Rui Wang, Elyssa Hofgard, Han Gao, Robin Walters, Tess Smidt

Modeling symmetry breaking is essential for understanding the fundamental changes in the behaviors and properties of physical systems, from microscopic particle interactions to macroscopic phenomena like fluid dynamics and cosmic structures. Thus, identifying sources of asymmetry is an important tool for understanding physical systems. In this paper, we focus on learning asymmetries of data using relaxed group convolutions. We provide both theoretical and empirical evidence that this flexible convolution technique allows the model to maintain the highest level of equivariance that is consistent with data and discover the subtle symmetry-breaking factors in various physical systems. We employ various relaxed group convolution architectures to uncover various symmetry-breaking factors that are interpretable and physically meaningful in different physical systems, including the phase transition of crystal structure, the isotropy and homogeneity breaking in turbulent flow, and the time-reversal symmetry breaking in pendulum systems.

Applications · Computer Vision

Xihaier Luo, Xiaoning Qian, Byung-Jun Yoon

In this work, we present an arbitrary-scale super-resolution (SR) method to enhance the resolution of scientific data, which often involves complex challenges such as continuity, multi-scale physics, and the intricacies of high-frequency signals. Grounded in operator learning, the proposed method is resolution-invariant. The core of our model is a hierarchical neural operator that leverages a Galerkin-type self-attention mechanism, enabling efficient learning of mappings between function spaces. Sinc filters are used to facilitate the information transfer across different levels in the hierarchy, thereby ensuring representation equivalence in the proposed neural operator. Additionally, we introduce a learnable prior structure that is derived from the spectral resizing of the input data. This loss prior is model-agnostic and is designed to dynamically adjust the weighting of pixel contributions, thereby balancing gradients effectively across the model. We conduct extensive experiments on diverse datasets from different domains and demonstrate consistent improvements compared to strong baselines, which consist of various state-of-the-art SR methods.

Applications · Chemistry and Drug Discovery

YAN WANG, Lihao Wang, Yuning Shen, Yiqun Wang, Huizhuo Yuan, Yue Wu, Quanquan Gu

The conformational landscape of proteins is crucial to understanding their functionality in complex biological processes. Traditional physics-based computational methods, such as molecular dynamics (MD) simulations, suffer from rare event sampling and long equilibration time problems, hindering their applications in general protein systems. Recently, deep generative modeling techniques, especially diffusion models, have been employed to generate novel protein conformations. However, existing score-based diffusion methods cannot properly incorporate important physical prior knowledge to guide the generation process, causing large deviations in the sampled protein conformations from the equilibrium distribution. In this paper, to overcome these limitations, we propose a force-guided $\mathrm{SE}(3)$ diffusion model, ConfDiff, for protein conformation generation. By incorporating a force-guided network with a mixture of data-based score models, ConfDiff can generate protein conformations with rich diversity while preserving high fidelity. Experiments on a variety of protein conformation prediction tasks, including 12 fast-folding proteins and the Bovine Pancreatic Trypsin Inhibitor (BPTI), demonstrate that our method surpasses the state-of-the-art method.

Deep Learning · Sequential Models, Time series

Raunaq Bhirangi, Chenyu Wang, Venkatesh Pattabiraman, Carmel Majidi, Abhinav Gupta, Tess Hellebrekers, Lerrel Pinto

Reasoning from sequences of raw sensory data is a ubiquitous problem across fields ranging from medical devices to robotics. These problems often involve using long sequences of raw sensor data (e.g. magnetometers, piezoresistors) to predict sequences of desirable physical quantities (e.g. force, inertial measurements). While classical approaches are powerful for locally-linear prediction problems, they often fall short when using real-world sensors. These sensors are typically non-linear, are affected by extraneous variables (e.g. vibration), and exhibit data-dependent drift. For many problems, the prediction task is exacerbated by small labeled datasets since obtaining ground-truth labels requires expensive equipment. In this work, we present Hierarchical State-Space models (HiSS), a conceptually simple, new technique for continuous sequential prediction. HiSS stacks structured state-space models on top of each other to create a temporal hierarchy. Across six real-world sensor datasets, from tactile-based state prediction to accelerometer-based inertial measurement, HiSS outperforms state-of-the-art sequence models such as causal Transformers, LSTMs, S4, and Mamba by at least 23% on MSE. Our experiments further indicate that HiSS demonstrates efficient scaling to smaller datasets and is compatible with existing data-filtering techniques. Code, datasets and videos can be found on https://hiss-csp.github.io.

Applications · Physics

Yi Xiao, LEI BAI, Wei Xue, Hao Chen, Kun Chen, kang chen, Tao Han, Wanli Ouyang

Data-driven weather forecasting models are advancing rapidly, yet they rely on initial states (i.e., analysis states) typically produced by traditional data assimilation algorithms. Four-dimensional variational assimilation (4DVar) is one of the most widely adopted data assimilation algorithms in numerical weather prediction centers; it is accurate but computationally expensive. In this paper, we aim to couple the AI forecasting model, FengWu, with 4DVar to build a self-contained data-driven global weather forecasting framework, FengWu-4DVar. To achieve this, we propose an *AI-embedded* 4DVar algorithm that includes three components: (1) a 4DVar objective function embedded with the FengWu forecasting model and its error representation to enhance efficiency and accuracy; (2) a spherical-harmonic-transform-based (SHT-based) approximation strategy for capturing the horizontal correlation of background error; and (3) an auto-differentiation (AD) scheme for determining the optimal analysis fields. Experimental results show that under the ERA5 simulated observational data with varying proportions and noise levels, FengWu-4DVar can generate accurate analysis fields; remarkably, it has achieved stable self-contained global weather forecasts for an entire year for the first time, demonstrating its potential for real-world applications. Additionally, our framework is approximately 100 times faster than the traditional 4DVar algorithm under similar experimental conditions, highlighting its significant computational efficiency.

Applications · Physics

Andrey Bryutkin, Jiahao Huang, Zhongying Deng, Guang Yang, Carola-Bibiane Schönlieb, Angelica I Aviles-Rivero

We present a novel graph transformer framework, HAMLET, designed to address the challenges in solving partial differential equations (PDEs) using neural networks. The framework uses graph transformers with modular input encoders to directly incorporate differential equation information into the solution process. This modularity enhances parameter correspondence control, making HAMLET adaptable to PDEs of arbitrary geometries and varied input formats. Notably, HAMLET scales effectively with increasing data complexity and noise, showcasing its robustness. HAMLET is not just tailored to a single type of physical simulation, but can be applied across various domains. Moreover, it boosts model resilience and performance, especially in scenarios with limited data. We demonstrate, through extensive experiments, that our framework is capable of outperforming current techniques for PDEs.

Applications

Bodhisattwa Prasad Majumder, Harshit Surana, Dhruv Agarwal, Sanchaita Hazra, Ashish Sabharwal, Peter Clark

With the accumulation of data at an unprecedented rate, its potential to fuel scientific discovery is growing exponentially. This position paper urges the Machine Learning (ML) community to exploit the capabilities of large generative models (LGMs) to develop automated systems for end-to-end data-driven discovery—a paradigm encompassing the search and verification of hypotheses purely from a set of provided datasets, without the need for additional data collection or physical experiments. We first outline several desiderata for an ideal data-driven discovery system. Then, through DataVoyager, a proof-of-concept utilizing GPT-4, we demonstrate how LGMs fulfill several of these desiderata—a feat previously unattainable—while also highlighting important limitations in the current system that open up opportunities for novel ML research. We contend that achieving accurate, reliable, and robust end-to-end discovery systems solely through the current capabilities of LGMs is challenging. We instead advocate for fail-proof tool integration, along with active user moderation through feedback mechanisms, to foster data-driven scientific discoveries with efficiency and reproducibility.

Miscellaneous Aspects of Machine Learning · Representation Learning

Zhengqi Pei, Anran Zhang, Shuhui Wang, Xiangyang Ji, Qingming Huang

Neural models are equivalent to dynamic systems from a physics-inspired view, implying that computation on neural networks can be interpreted as the dynamical interactions between neurons. However, existing work models neuronal interaction as a weight-based linear transformation, and the nonlinearity comes from the nonlinear activation functions, which leads to limited nonlinearity and data-fitting ability of the whole neural model. Inspired by Riemannian geometry, we interpret neural structures by projecting neurons onto the Riemannian neuronal state space and model neuronal interaction with Riemannian metric (${\it RieM}$), which provides a more efficient neural representation with higher parameter efficiency. With ${\it RieM}$, we further design a novel data-free neural compression mechanism that does not require additional fine-tuning with real data. Using backbones like ResNet and Vision Transformer, we conduct extensive experiments on datasets such as MNIST, CIFAR-100, ImageNet-1k, and COCO object detection. Empirical results show that, under equal compression rates and computational complexity, models compressed with ${\it RieM}$ achieve superior inference accuracy compared to existing data-free compression methods.

Social Aspects · Trustworthy Machine Learning

Luca Masserano, Alexander Shen, Michele Doro, Tommaso Dorigo, Rafael Izbicki, Ann Lee

An open scientific challenge is how to classify events with reliable measures of uncertainty, when we have a mechanistic model of the data-generating process but the distribution over both labels and latent nuisance parameters is different between train and target data. We refer to this type of distributional shift as generalized label shift (GLS). Direct classification using observed data $\mathbf{X}$ as covariates leads to biased predictions and invalid uncertainty estimates of labels $Y$. We overcome these biases by proposing a new method for robust uncertainty quantification that casts classification as a hypothesis testing problem under nuisance parameters. The key idea is to estimate the classifier's receiver operating characteristic (ROC) across the entire nuisance parameter space, which allows us to devise cutoffs that are invariant under GLS. Our method effectively endows a pre-trained classifier with domain adaptation capabilities and returns valid prediction sets while maintaining high power. We demonstrate its performance on two challenging scientific problems in biology and astroparticle physics with data from realistic mechanistic models.

Optimization

Shirin Shoushtari, JIAMING LIU, Edward Chandler, Salman Asif, Ulugbek Kamilov

Plug-and-Play (PnP) priors is a widely-used family of methods for solving imaging inverse problems by integrating physical measurement models with image priors specified using image denoisers. PnP methods have been shown to achieve state-of-the-art performance when the prior is obtained using powerful deep denoisers. Despite extensive work on PnP, the topic of distribution mismatch between the training and testing data has often been overlooked in the PnP literature. This paper presents a set of new theoretical and numerical results on the topic of prior distribution mismatch and domain adaptation for the alternating direction method of multipliers (ADMM) variant of PnP. Our theoretical result provides an explicit error bound for PnP-ADMM due to the mismatch between the desired denoiser and the one used for inference. Our analysis contributes to the work in the area by considering the mismatch under nonconvex data-fidelity terms and expansive denoisers. Our first set of numerical results quantifies the impact of the prior distribution mismatch on the performance of PnP-ADMM on the problem of image super-resolution. Our second set of numerical results considers a simple and effective domain adaption strategy that closes the performance gap due to the use of mismatched denoisers. Our results suggest the relative robustness of PnP-ADMM to prior distribution mismatch, while also showing that the performance gap can be significantly reduced with only a few training samples from the desired distribution.

Applications · Chemistry and Drug Discovery

Bowen Jing, Bonnie Berger, Tommi Jaakkola

The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly accurate single-state predictors such as AlphaFold and ESMFold and fine-tune them under a custom flow matching framework to obtain sequence-conditioned generative models of protein structure called AlphaFlow and ESMFlow. When trained and evaluated on the PDB, our method provides a superior combination of precision and diversity compared to AlphaFold with MSA subsampling. When further trained on ensembles from all-atom MD, our method accurately captures conformational flexibility, positional distributions, and higher-order ensemble observables for unseen proteins. Moreover, our method can diversify a static PDB structure with faster wall-clock convergence to certain equilibrium properties than replicate MD trajectories, demonstrating its potential as a proxy for expensive physics-based simulations. Code is available at https://github.com/bjing2016/alphaflow.

Applications · Everything Else

Yoni Choukroun, Lior Wolf

Error correction codes are a crucial part of the physical communication layer, ensuring the reliable transfer of data over noisy channels. The design of optimal linear block codes capable of being efficiently decoded is of major concern, especially for short block lengths. While neural decoders have recently demonstrated their advantage over classical decoding techniques, the neural design of the codes remains a challenge. In this work, we propose for the first time a unified encoder-decoder training of binary linear block codes. To this end, we adapt the coding setting to support efficient and differentiable training of the code for end-to-end optimization over the order two Galois field. We also propose a novel Transformer model in which the self-attention masking is performed in a differentiable fashion for the efficient backpropagation of the code gradient. Our results show that (i) the proposed decoder outperforms existing neural decoding on conventional codes, (ii) the suggested framework generates codes that outperform the analogous conventional codes, and (iii) the codes we developed not only excel with our decoder but also show enhanced performance with traditional decoding techniques.

Sherry Yang, Jacob C Walker, Jack Parker-Holder, Yilun Du, Jake Bruce, Andre Barreto, Pieter Abbeel, Dale Schuurmans

Both text and video data are abundant on the internet and support large-scale self-supervised learning through next token or frame prediction. However, they have not been equally leveraged: language models have had significant real-world impact, whereas video generation has remained largely limited to media entertainment. Yet video data captures important information about the physical world that is difficult to express in language. To address this gap, we discuss an under-appreciated opportunity to extend video generation to solve tasks in the real world. We observe how, akin to language, video can serve as a unified interface that can absorb internet knowledge and represent diverse tasks. Moreover, we demonstrate how, like language models, video generation can serve as planners, agents, compute engines, and environment simulators through techniques such as in-context learning, planning and reinforcement learning. We identify major impact opportunities in domains such as robotics, self-driving, and science, supported by recent work that demonstrates how such advanced capabilities in video generation are plausibly within reach. Lastly, we identify key challenges in video generation that mitigate progress. Addressing these challenges will enable video generation models to demonstrate unique value alongside language models in a wider array of AI applications.

Deep Learning · Large Language Models

Xiaoxuan Wang, ziniu hu, Pan Lu, Yanqiao Zhu, Jieyu Zhang, Satyen Subramaniam, Arjun Loomba, Shichang Zhang, Yizhou Sun, Wei Wang

Most existing Large Language Model (LLM) benchmarks on scientific problem reasoning focus on problems grounded in high-school subjects and are confined to elementary algebraic operations. To systematically examine the reasoning capabilities required for solving complex scientific problems, we introduce an expansive benchmark suite SciBench for LLMs. SciBench contains a carefully curated dataset featuring a range of collegiate-level scientific problems from mathematics, chemistry, and physics domains. Based on the dataset, we conduct an in-depth benchmarking study of representative open-source and proprietary LLMs with various prompting strategies. The results reveal that current LLMs fall short of delivering satisfactory performance, with the best overall score of merely 43.22%. Furthermore, through a detailed user study, we categorize the errors made by LLMs into ten problem-solving abilities. Our analysis indicates that no single prompting strategy significantly outperforms the others and some strategies that demonstrate improvements in certain problem-solving skills could result in declines in other skills. We envision that SciBench will catalyze further developments in the reasoning abilities of LLMs, thereby ultimately contributing to scientific research and discovery.

Deep Learning · Graph Neural Networks

Alexandre Duval, Victor Schmidt, Santiago Miret, Yoshua Bengio, Alex Hernandez-Garcia, David Rolnick

Mitigating the climate crisis requires a rapid transition towards lower-carbon energy. Catalyst materials play a crucial role in the electrochemical reactions involved in numerous industrial processes key to this transition, such as renewable energy storage and electrofuel synthesis. To reduce the energy spent on such activities, we must quickly discover more efficient catalysts to drive electrochemical reactions. Machine learning (ML) holds the potential to efficiently model materials properties from large amounts of data, accelerating electrocatalyst design. The Open Catalyst Project OC20 dataset was constructed to that end. However, ML models trained on OC20 are still neither scalable nor accurate enough for practical applications. In this paper, we propose task-specific innovations applicable to most architectures, enhancing both computational efficiency and accuracy. This includes improvements in (1) the graph creation step, (2) atom representations, (3) the energy prediction head, and (4) the force prediction head. We describe these contributions, referred to as PhAST, and evaluate them thoroughly on multiple architectures. Overall, PhAST improves energy MAE by 4 to 42% while dividing compute time by 3 to 8× depending on the targeted task/model. PhAST also enables CPU training, leading to 40× speedups in highly parallelized settings. Python package: https://phast.readthedocs.io.

Applications · Neuroscience, Cognitive Science

Tingting Dan, Ziquan Wei, Won Hwa Kim, Guorong Wu

The human brain is a complex inter-wired system that emerges spontaneous functional fluctuations. In spite of tremendous success in the experimental neuroscience field, a system-level understanding of how brain anatomy supports various neural activities remains elusive. Capitalizing on the unprecedented amount of neuroimaging data, we present a physics-informed deep model to uncover the coupling mechanism between brain structure and function through the lens of data geometry that is rooted in the widespread wiring topology of connections between distant brain regions. Since deciphering the puzzle of self-organized patterns in functional fluctuations is the gateway to understanding the emergence of cognition and behavior, we devise a geometric deep model to uncover manifold mapping functions that characterize the intrinsic feature representations of evolving functional fluctuations on the Riemannian manifold. In lieu of learning unconstrained mapping functions, we introduce a set of graph-harmonic scattering transforms to impose the brain-wide geometry on top of manifold mapping functions, which allows us to cast the manifold-based deep learning into a reminiscent of *MLP-Mixer* architecture (in computer vision) for Riemannian manifold. As a proof-of-concept approach, we explore a neural-manifold perspective to understand the relationship between (static) brain structure and (dynamic) function, challenging the prevailing notion in cognitive neuroscience by proposing that neural activities are essentially excited by brain-wide oscillation waves living on the geometry of human connectomes, instead of being confined to focal areas.