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Applications · Chemistry and Drug Discovery

Ishan Amin, Sanjeev Raja, Aditi Krishnapriyan

The foundation model (FM) paradigm is transforming Machine Learning Force Fields (MLFFs), leveraging general-purpose representations and scalable training to perform a variety of computational chemistry tasks. Although MLFF FMs have begun to close the accuracy gap relative to first-principles methods, there is still a strong need for faster inference speed. Additionally, while research is increasingly focused on general-purpose models which transfer across chemical space, practitioners typically only study a small subset of systems at a given time. At test time, MLFFs must also obey physical constraints unique to the downstream use case, such as energy conservation for molecular dynamics simulations. This underscores the need for fast, specialized MLFFs relevant to specific downstream applications, which preserve test-time physical soundness while maintaining train-time scalability. In this work, we introduce a method for transferring general-purpose representations from MLFF foundation models to smaller, faster MLFFs specialized to specific regions of chemical space. We formulate our approach as an architecture-agnostic knowledge distillation procedure, where the smaller "student" MLFF is trained to match the Hessians of the energy predictions of the "teacher" foundation model. We demonstrate our approach across multiple recent foundation models, large-scale datasets, chemical subsets, and downstream tasks. Our specialized MLFFs can be up to 20 times faster than the original foundation model, while retaining, and in some cases exceeding, its performance and that of undistilled models. We also show that distilling from a teacher model with a direct force parameterization into a student model trained with conservative forces (i.e., computed as derivatives of the potential energy) successfully leverages the representations from the large-scale teacher for improved accuracy, while maintaining energy conservation during test-time molecular dynamics simulations. More broadly, our work suggests a new paradigm for MLFF development, in which foundation models are released along with smaller, specialized simulation ``engines" for common chemical subsets. The implementation of our method is available at https://github.com/ASK-Berkeley/MLFF-distill.

Applications · Robotics

Leonardo Barcellona, Andrii Zadaianchuk, Davide Allegro, Samuele Papa, Stefano Ghidoni, Efstratios Gavves

A world model provides an agent with a representation of its environment, enabling it to predict the causal consequences of its actions. Current world models typically cannot directly and explicitly imitate the actual environment in front of a robot, often resulting in unrealistic behaviors and hallucinations that make them unsuitable for real-world robotics applications. To overcome those challenges, we propose to rethink robot world models as learnable digital twins. We introduce DreMa, a new approach for constructing digital twins automatically using learned explicit representations of the real world and its dynamics, bridging the gap between traditional digital twins and world models.DreMa replicates the observed world and its structure by integrating Gaussian Splatting and physics simulators, allowing robots to imagine novel configurations of objects and to predict the future consequences of robot actions thanks to its compositionality.We leverage this capability to generate new data for imitation learning by applying equivariant transformations to a small set of demonstrations. Our evaluations across various settings demonstrate significant improvements in accuracy and robustness by incrementing actions and object distributions, reducing the data needed to learn a policy and improving the generalization of the agents. As a highlight, we show that a real Franka Emika Panda robot, powered by DreMa’s imagination, can successfully learn novel physical tasks from just a single example per task variation (one-shot policy learning).Our project page can be found in: https://dreamtomanipulate.github.io/.

Applications · Physics

Kanishk Bhatia, Felix Koehler, Nils Thuerey

The physics solvers employed for neural network training are primarily iterative, and hence, differentiating through them introduces a severe computational burden as iterations grow large. Inspired by works in bilevel optimization, we show that full accuracy of the network is achievable through physics significantly coarser than fully converged solvers. We propose *progressively refined differentiable physics* (PRDP), an approach that identifies the level of physics refinement sufficient for full training accuracy. By beginning with coarse physics, adaptively refining it during training, and stopping refinement at the level adequate for training, it enables significant compute savings without sacrificing network accuracy. Our focus is on differentiating iterative linear solvers for sparsely discretized differential operators, which are fundamental to scientific computing. PRDP is applicable to both unrolled and implicit differentiation. We validate its performance on a variety of learning scenarios involving differentiable physics solvers such as inverse problems, autoregressive neural emulators, and correction-based neural-hybrid solvers. In the challenging example of emulating the Navier-Stokes equations, we reduce training time by 62%.

Nilo Schwencke, Cyril Furtlehner

In the recent years, Physics Informed Neural Networks (PINNs) have received strong interest as a method to solve PDE driven systems, in particular for data assimilation purpose. This method is still in its infancy, with many shortcomings and failures that remain not properly understood.In this paper we propose a natural gradient approach to PINNs which contributes to speed-up and improve the accuracy of the training.Based on an in depth analysis of the differential geometric structures of the problem, we come up with two distinct contributions:(i) a new natural gradient algorithm that scales as $\min(P^2S, S^2P)$, where $P$ is the number of parameters, and $S$ the batch size;(ii) a mathematically principled reformulation of the PINNs problem that allows the extension of natural gradient to it, with proved connections to Green's function theory.

Applications · Genetics, Cell Biology, Health, etc

Xikun ZHANG, Dongjin Song, Yushan Jiang, Yixin Chen, Dacheng Tao

Observation-based trajectory prediction for systems with unknown dynamics is essential in fields such as physics and biology. Most existing approaches are limited to learning within a single system with fixed dynamics patterns. However, many real-world applications require learning across systems with evolving dynamics patterns, a challenge that has been largely overlooked. To address this, we systematically investigate the problem of Continual Dynamics Learning (CDL), examining task configurations and evaluating the applicability of existing techniques, while identifying key challenges. In response, we propose the Mode-switching Graph ODE (MS-GODE) model, which integrates the strengths LG-ODE and sub-network learning with a mode-switching module, enabling efficient learning over varying dynamics. Moreover, we construct a novel benchmark of biological dynamic systems for CDL, Bio-CDL, featuring diverse systems with disparate dynamics and significantly enriching the research field of machine learning for dynamic systems. Our code available at \url{https://github.com/QueuQ/MS-GODE}.

Applications · Physics

Yusen Wu, Bujiao Wu, Yanqi Song, Xiao Yuan, Jingbo Wang

Quantifying the complexity of quantum states is a longstanding key problem in various subfields of science, ranging from quantum computing to the black-hole theory. The lower bound on quantum pure state complexity has been shown to grow linearly with system size [J. Haferkamp et al., 2022, *Nat. Phys.*]. However, extending this result to noisy circuit environments, which better reflect real quantum devices, remains an open challenge. In this paper, we explore the complexity of weakly noisy quantum states via the quantum learning method. We present an efficient learning algorithm, that leverages the classical shadow representation of target quantum states, to predict the circuit complexity of weakly noisy quantum states. Our algorithm is proved to be optimal in terms of sample complexity accompanied with polynomial classical processing time. Our result builds a bridge between the learning algorithm and quantum state complexity, meanwhile highlighting the power of learning algorithm in characterizing intrinsic properties of quantum states.

Applications · Chemistry and Drug Discovery

KISHALAY DAS, Subhojyoti Khastagir, Pawan Goyal, Seung-Cheol Lee, Satadeep Bhattacharjee, Niloy Ganguly

Equivariant diffusion models have emerged as the prevailing approach for generat-ing novel crystal materials due to their ability to leverage the physical symmetriesof periodic material structures. However, current models do not effectively learn thejoint distribution of atom types, fractional coordinates, and lattice structure of thecrystal material in a cohesive end-to-end diffusion framework. Also, none of thesemodels work under realistic setups, where users specify the desired characteristicsthat the generated structures must match. In this work, we introduce TGDMat, anovel text-guided diffusion model designed for 3D periodic material generation.Our approach integrates global structural knowledge through textual descriptionsat each denoising step while jointly generating atom coordinates, types, and latticestructure using a periodic-E(3)-equivariant graph neural network (GNN). Extensiveexperiments using popular datasets on benchmark tasks reveal that TGDMat out-performs existing baseline methods by a good margin. Notably, for the structureprediction task, with just one generated sample, TGDMat outperforms all baselinemodels, highlighting the importance of text-guided diffusion. Further, in the genera-tion task, TGDMat surpasses all baselines and their text-fusion variants, showcasingthe effectiveness of the joint diffusion paradigm. Additionally, incorporating textualknowledge reduces overall training and sampling computational overhead whileenhancing generative performance when utilizing real-world textual prompts fromexperts. Code is available at https://github.com/kdmsit/TGDMat

Applications · Physics

Yusei Ito, Tatsunori Taniai, Ryo Igarashi, Yoshitaka Ushiku, Kanta Ono

Crystal structure modeling with graph neural networks is essential for various applications in materials informatics, and capturing SE(3)-invariant geometric features is a fundamental requirement for these networks. A straightforward approach is to model with orientation-standardized structures through structure-aligned coordinate systems, or “frames.” However, unlike molecules, determining frames for crystal structures is challenging due to their infinite and highly symmetric nature. In particular, existing methods rely on a statically fixed frame for each structure, determined solely by its structural information, regardless of the task under consideration. Here, we rethink the role of frames, *questioning whether such simplistic alignment with the structure is sufficient*, and propose the concept of *dynamic frames*. While accommodating the infinite and symmetric nature of crystals, these frames provide each atom with a dynamic view of its local environment, focusing on actively interacting atoms. We demonstrate this concept by utilizing the attention mechanism in a recent transformer-based crystal encoder, resulting in a new architecture called **CrystalFramer**. Extensive experiments show that CrystalFramer outperforms conventional frames and existing crystal encoders in various crystal property prediction tasks.

Optimization · Large Scale, Parallel and Distributed

Yury Demidovich, Petr Ostroukhov, Grigory Malinovsky, Samuel Horváth, Martin Takáč, Peter Richtarik, Eduard Gorbunov

Non-convex Machine Learning problems typically do not adhere to the standard smoothness assumption. Based on empirical findings, Zhang et al. (2020b) proposed a more realistic generalized $(L_0,L_1)$-smoothness assumption, though it remains largely unexplored. Many existing algorithms designed for standard smooth problems need to be revised. However, in the context of Federated Learning, only a few works address this problem but rely on additional limiting assumptions. In this paper, we address this gap in the literature: we propose and analyze new methods with local steps, partial participation of clients, and Random Reshuffling without extra restrictive assumptions beyond generalized smoothness. The proposed methods are based on the proper interplay between clients' and server's stepsizes and gradient clipping. Furthermore, we perform the first analysis of these methods under the Polyak-Łojasiewicz condition. Our theory is consistent with the known results for standard smooth problems, and our experimental results support the theoretical insights.

Applications · Chemistry and Drug Discovery

Yurou Liu, Jiahao Chen, Rui Jiao, Jiangmeng Li, Wenbing Huang, Bing Su

Denoising learning of 3D molecules learns molecular representations by imposing noises into the equilibrium conformation and predicting the added noises to recover the equilibrium conformation, which essentially captures the information of molecular force fields. Due to the specificity of Potential Energy Surfaces, the probabilities of physically reasonable noises for each atom in different molecules are different. However, existing methods apply the shared heuristic hand-crafted noise sampling strategy to all molecules, resulting in inaccurate force field learning. In this paper, we propose a novel 3D molecular pre-training method, namely DenoiseVAE, which employs a Noise Generator to acquire atom-specific noise distributions for different molecules. It utilizes the stochastic reparameterization technique to sample noisy conformations from the generated distributions, which are inputted into a Denoising Module for denoising. The Noise Generator and the Denoising Module are jointly learned in a manner conforming with the paradigm of Variational Auto Encoder. Consequently, the sampled noisy conformations can be more diverse, adaptive, and informative, and thus DenoiseVAE can learn representations that better reveal the molecular force fields. Extensive experiments show that DenoiseVAE outperforms the current state-of-the-art methods on various molecular property prediction tasks, demonstrating the effectiveness of it.

Miscellaneous Aspects of Machine Learning · Online Learning, Active Learning and Bandits

Evgenii Dzhivelikian, Petr Kuderov, Aleksandr Panov

This paper presents a novel approach to address the challenge of online sequence learning for decision making under uncertainty in non-stationary, partially observable environments. The proposed algorithm, Distributed Hebbian Temporal Memory (DHTM), is based on the factor graph formalism and a multi-component neuron model. DHTM aims to capture sequential data relationships and make cumulative predictions about future observations, forming Successor Features (SFs). Inspired by neurophysiological models of the neocortex, the algorithm uses distributed representations, sparse transition matrices, and local Hebbian-like learning rules to overcome the instability and slow learning of traditional temporal memory algorithms such as RNN and HMM. Experimental results show that DHTM outperforms LSTM, RWKV and a biologically inspired HMM-like algorithm, CSCG, on non-stationary data sets. Our results suggest that DHTM is a promising approach to address the challenges of online sequence learning and planning in dynamic environments.

Deep Learning · Generative Models and Autoencoders

John Vastola

How diffusion models generalize beyond their training set is not known, and is somewhat mysterious given two facts: the optimum of the denoising score matching (DSM) objective usually used to train diffusion models is the score function of the training distribution; and the networks usually used to learn the score function are expressive enough to learn this score to high accuracy. We claim that a certain feature of the DSM objective—the fact that its target is not the training distribution's score, but a noisy quantity only equal to it in expectation—strongly impacts whether and to what extent diffusion models generalize. In this paper, we develop a mathematical theory that partly explains this 'generalization through variance' phenomenon. Our theoretical analysis exploits a physics-inspired path integral approach to compute the distributions typically learned by a few paradigmatic under- and overparameterized diffusion models. We find that the distributions diffusion models effectively learn to sample from resemble their training distributions, but with `gaps' filled in, and that this inductive bias is due to the covariance structure of the noisy target used during training. We also characterize how this inductive bias interacts with feature-related inductive biases.

Deep Learning · Attention Mechanisms

Svetha Venkatesh, Kien Do, Hung Le, Truyen Tran, Dung Nguyen

We introduce Pointer-Augmented Neural Memory (PANM), a versatile module designed to enhance neural networks' ability to process symbols and extend their capabilities to longer data sequences. PANM integrates an external neural memory utilizing novel physical addresses and pointer manipulation techniques, emulating human and computer-like symbol processing abilities. PANM facilitates operations like pointer assignment, dereferencing, and arithmetic by explicitly employing physical pointers for memory access. This module can be trained end-to-end on sequence data, empowering various sequential models, from simple recurrent networks to large language models (LLMs). Our experiments showcase PANM's exceptional length extrapolation capabilities and its enhancement of recurrent neural networks in symbol processing tasks, including algorithmic reasoning and Dyck language recognition. PANM enables Transformers to achieve up to 100% generalization accuracy in compositional learning tasks and significantly improves performance in mathematical reasoning, question answering, and machine translation. Notably, the generalization effectiveness scales with stronger backbone models, as evidenced by substantial performance gains when we test LLMs finetuned with PANM for tasks up to 10-100 times longer than the training data.

Applications · Physics

Thomas Hehn, Markus Peschl, Tribhuvanesh Orekondy, Arash Behboodi, Johann Brehmer

Modelling the propagation of electromagnetic wireless signals is critical for designing modern communication systems. Wireless ray tracing simulators model signal propagation based on the 3D geometry and other scene parameters, but their accuracy is fundamentally limited by underlying modelling assumptions and correctness of parameters. In this work, we introduce Wi-GATr, a fully-learnable neural simulation surrogate designed to predict the channel observations based on scene primitives (e. g., surface mesh, antenna position and orientation). Recognizing the inherently geometric nature of these primitives, Wi-GATr leverages an equivariant Geometric Algebra Transformer that operates on a tokenizer specifically tailored for wireless simulation. We evaluate our approach on a range of tasks (i. e., signal strength and delay spread prediction, receiver localization, and geometry reconstruction) and find that Wi-GATr is accurate, fast, sample-efficient, and robust to symmetry-induced transformations. Remarkably, we find our results also translate well to the real world: Wi-GATr demonstrates more than 35% lower error than hybrid techniques, and 70% lower error than a calibrated wireless tracer.

Miscellaneous Aspects of Machine Learning · Causality

Arvind Raghavan, Elias Bareinboim

It is commonly believed that, in a real-world environment, samples can only be drawn from observational and interventional distributions, corresponding to Layers 1 and 2 of the *Pearl Causal Hierarchy*. Layer 3, representing counterfactual distributions, is believed to be inaccessible by definition. However, Bareinboim, Forney, and Pearl (2015) introduced a procedure that allows an agent to sample directly from a counterfactual distribution, leaving open the question of what other counterfactual quantities can be estimated directly via physical experimentation. We resolve this by introducing a formal definition of realizability, the ability to draw samples from a distribution, and then developing a complete algorithm to determine whether an arbitrary counterfactual distribution is realizable given fundamental physical constraints, such as the inability to go back in time and subject the same unit to a different experimental condition. We illustrate the implications of this new framework for counterfactual data collection using motivating examples from causal fairness and causal reinforcement learning. While the baseline approach in these motivating settings typically follows an interventional or observational strategy, we show that a counterfactual strategy provably dominates both.

Deep Learning · Large Language Models

Chunting Zhou, Lili Yu, Arun Babu, Kushal Tirumala, Michihiro Yasunaga, Leonid Shamis, Jacob Kahn, Xuezhe Ma, Luke Zettlemoyer, Omer Levy

We introduce Transfusion, a recipe for training a multi-modal model over discrete and continuous data.Transfusion combines the language modeling loss function (next token prediction) with diffusion to train a single transformer over mixed-modality sequences.We pretrain multiple Transfusion models up to 7B parameters from scratch on a mixture of text and image data, establishing scaling laws with respect to a variety of uni- and cross-modal benchmarks.Our experiments show that Transfusion scales significantly better than quantizing images and training a language model over discrete image tokens.By introducing modality-specific encoding and decoding layers, we can further improve the performance of Transfusion models, and even compress each image to just 16 patches.We further demonstrate that scaling our Transfusion recipe to 7B parameters and 2T multi-modal tokens produces a model that can generate images and text on a par with similar scale diffusion models and language models, reaping the benefits of both worlds.

Deep Learning · Large Language Models

Chunting Zhou, Lili Yu, Arun Babu, Kushal Tirumala, Michihiro Yasunaga, Leonid Shamis, Jacob Kahn, Xuezhe Ma, Luke Zettlemoyer, Omer Levy

We introduce Transfusion, a recipe for training a multi-modal model over discrete and continuous data.Transfusion combines the language modeling loss function (next token prediction) with diffusion to train a single transformer over mixed-modality sequences.We pretrain multiple Transfusion models up to 7B parameters from scratch on a mixture of text and image data, establishing scaling laws with respect to a variety of uni- and cross-modal benchmarks.Our experiments show that Transfusion scales significantly better than quantizing images and training a language model over discrete image tokens.By introducing modality-specific encoding and decoding layers, we can further improve the performance of Transfusion models, and even compress each image to just 16 patches.We further demonstrate that scaling our Transfusion recipe to 7B parameters and 2T multi-modal tokens produces a model that can generate images and text on a par with similar scale diffusion models and language models, reaping the benefits of both worlds.

Itay Beit Halachmi, Ido Kaminer

Fundamental mathematical constants appear in nearly every field of science, from physics to biology. Formulas that connect different constants often bring great insight by hinting at connections between previously disparate fields.Discoveries of such relations, however, have remained scarce events, relying on sporadic strokes of creativity by human mathematicians.Recent developments of algorithms for automated conjecture generation have accelerated the discovery of formulas for specific constants.Yet, the discovery of connections between constants has not been addressed.In this paper, we present the first library dedicated to mathematical constants and their interrelations. This library can serve as a central repository of knowledge for scientists from different areas, and as a collaborative platform for development of new algorithms.The library is based on a new representation that we propose for organizing the formulas of mathematical constants: a hypergraph, with each node representing a constant and each edge representing a formula.Using this representation, we propose and demonstrate a systematic approach for automatically enriching this library using PSLQ, an integer relation algorithm based on QR decomposition and lattice construction. During its development and testing, our strategy led to the discovery of 75 previously unknown connections between constants, including a new formula for the `first continued fraction' constant $C_1$, novel formulas for natural logarithms, and new formulas connecting $\pi$ and $e$.The latter formulas generalize a century-old relation between $\pi$ and $e$ by Ramanujan, which until now was considered a singular formula and is now found to be part of a broader mathematical structure. The code supporting this library is a public, open-source API that can serve researchers in experimental mathematics and other fields of science.

Deep Learning · Graph Neural Networks

Mario Lino, Tobias Pfaff, Nils Thuerey

Physical systems with complex unsteady dynamics, such as fluid flows, are often poorly represented by a single mean solution. For many practical applications, it is crucial to access the full distribution of possible states, from which relevant statistics (e.g., RMS and two-point correlations) can be derived. Here, we propose a graph-based latent diffusion model that enables direct sampling of states from their equilibrium distribution, given a mesh discretization of the system and its physical parameters. This allows for the efficient computation of flow statistics without running long and expensive numerical simulations. The graph-based structure enables operations on unstructured meshes, which is critical for representing complex geometries with spatially localized high gradients, while latent-space diffusion modeling with a multi-scale GNN allows for efficient learning and inference of entire distributions of solutions. A key finding of our work is that the proposed networks can accurately learn full distributions even when trained on incomplete data from relatively short simulations. We apply this method to a range of fluid dynamics tasks, such as predicting pressure distributions on 3D wing models in turbulent flow, demonstrating both accuracy and computational efficiency in challenging scenarios. The ability to directly sample accurate solutions, and capturing their diversity from short ground-truth simulations, is highly promising for complex scientific modeling tasks.

Applications · Chemistry and Drug Discovery

Gyoung S. Na, Chanyoung Park

Physical properties derived from electronic distributions are essential information that determines molecular properties. However, the electron-level information is not accessible in most real-world complex molecules due to the extensive computational costs of determining uncertain electronic distributions. For this reason, existing methods for molecular property prediction have remained in regression models on simplified atom-level molecular descriptors, such as atomic structures and fingerprints. This paper proposes an efficient knowledge transfer method for electron-aware molecular representation learning. To this end, we devised a self-supervised diffusion method that estimates the electron-level information of real-world complex molecules without expensive quantum mechanical calculations. The proposed method achieved state-of-the-art prediction accuracy in the tasks of predicting molecular properties on extensive real-world molecular datasets.