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Deep Learning · Graph Neural Networks

Olga Solodova, Nick Richardson, Deniz Oktay, Ryan P Adams

Graph neural networks (GNNs) appear to be powerful tools to learn state representations for agents in distributed, decentralized multi-agent systems, but generate catastrophically incorrect predictions when nodes update asynchronously during inference. This failure under asynchrony effectively excludes these architectures from many potential applications where synchrony is difficult or impossible to enforce, e.g., robotic swarms or sensor networks. In this work we identify ''implicitly-defined'' GNNs as a class of architectures which is provably robust to asynchronous ''hogwild'' inference, adapting convergence guarantees from work in asynchronous and distributed optimization. We then propose a novel implicitly-defined GNN architecture, which we call an energy GNN. We show that this architecture outperforms other GNNs from this class on a variety of synthetic tasks inspired by multi-agent systems.

Applications · Physics

Haoxiang Wang, Tao Yu, Hui Qiao, Qionghai Dai

Incompressible fluid on the surface is an interesting research area in the fluid simulation, which is the fundamental building block in visual effects, design of liquid crystal films, scientific analyses of atmospheric and oceanic phenomena, etc. The task brings two key challenges: the extension of the physical laws on 3D surfaces and the preservation of the energy and volume. Traditional methods rely on grids or meshes for spatial discretization, which leads to high memory consumption and a lack of robustness and adaptivity for various mesh qualities and representations. Many implicit representations based simulators like INSR are proposed for the storage efficiency and continuity, but they face challenges in the surface simulation and the energy dissipation. We propose a neural physical simulation framework on the surface with the implicit neural representation. Our method constructs a parameterized vector field with the exterior calculus and Closest Point Method on the surfaces, which guarantees the divergence-free property and enables the simulation on different surface representations (e.g. implicit neural represented surfaces). We further adopt a corresponding covariant derivative based advection process for surface flow dynamics and energy preservation. Our method shows higher accuracy, flexibility and memory-efficiency in the simulations of various surfaces with low energy dissipation. Numerical studies also highlight the potential of our framework across different practical applications such as vorticity shape generation and vector field Helmholtz decomposition.

Kangrui Du, Yuhang Wu, Shikuang Deng, Shi Gu

Spiking Neural Networks (SNNs), models inspired by neural mechanisms in the brain, allow for energy-efficient implementation on neuromorphic hardware. However, SNNs trained with current direct training approaches are constrained to a specific time step. This "temporal inflexibility" 1) hinders SNNs' deployment on time-step-free fully event-driven chips and 2) prevents energy-performance balance based on dynamic inference time steps. In this study, we first explore the feasibility of training SNNs that generalize across different time steps. We then introduce Mixed Time-step Training (MTT), a novel method that improves the temporal flexibility of SNNs, making SNNs adaptive to diverse temporal structures. During each iteration of MTT, random time steps are assigned to different SNN stages, with spikes transmitted between stages via communication modules. After training, the weights are deployed and evaluated on both time-stepped and fully event-driven platforms. Experimental results show that models trained by MTT gain remarkable temporal flexibility, friendliness for both event-driven and clock-driven deployment (nearly lossless on N-MNIST and 10.1\% higher than standard methods on CIFAR10-DVS), enhanced network generalization, and near SOTA performance. To the best of our knowledge, this is the first work to report the results of large-scale SNN deployment on fully event-driven scenarios.

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.

Guancheng Wan, Zitong Shi, Wenke Huang, Guibin Zhang, Dacheng Tao, Mang Ye

Federated Graph Learning is rapidly evolving as a privacy-preserving collaborative approach. However, backdoor attacks are increasingly undermining federated systems by injecting carefully designed triggers that lead to the model making incorrect predictions. Trigger structures and injection locations in Federated Graph Learning are more diverse, making traditional federated defense methods less effective. In our work, we propose an effective Federated Graph Backdoor Defense using Topological Graph Energy (FedTGE). At the local client level, it injects distribution knowledge into the local model, assigning low energy to benign samples and high energy to the constructed malicious substitutes, and selects benign clients through clustering. At the global server level, the energy elements uploaded by each client are treated as new nodes to construct a global energy graph for energy propagation, making the selected clients' energy elements more similar and further adjusting the aggregation weights. Our method can handle high data heterogeneity, does not require a validation dataset, and is effective under both small and large malicious proportions. Extensive results on various settings of federated graph scenarios under backdoor attacks validate the effectiveness of this approach.

Probabilistic Methods · Bayesian Models and Methods

Yogesh Verma, Ayush Bharti, Vikas Garg

Simulation-based inference (SBI) methods typically require fully observed data to infer parameters of models with intractable likelihood functions. However, datasets often contain missing values due to incomplete observations, data corruptions (common in astrophysics), or instrument limitations (e.g., in high-energy physics applications). In such scenarios, missing data must be imputed before applying any SBI method. We formalize the problem of missing data in SBI and demonstrate that naive imputation methods can introduce bias in the estimation of SBI posterior. We also introduce a novel amortized method that addresses this issue by jointly learning the imputation model and the inference network within a neural posterior estimation (NPE) framework. Extensive empirical results on SBI benchmarks show that our approach provides robust inference outcomes compared to standard baselines for varying levels of missing data. Moreover, we demonstrate the merits of our imputation model on two real-world bioactivity datasets (Adrenergic and Kinase assays). Code is available at https://github.com/Aalto-QuML/RISE.

Applications · Chemistry and Drug Discovery

Lirong Wu, Yunfan Liu, Haitao Lin, Yufei Huang, Guojiang Zhao, Zhifeng Gao, Stan Z Li

The proteins that exist today have been optimized over billions of years of natural evolution, during which nature creates random mutations and selects them. The discovery of functionally promising mutations is challenged by the limited evolutionary accessible regions, i.e., only a small region on the fitness landscape is beneficial. There have been numerous priors used to constrain protein evolution to regions of landscapes with high-fitness variants, among which the change in binding free energy ($\Delta\Delta G$) of protein complexes upon mutations is one of the most commonly used priors. However, the huge mutation space poses two challenges: (1) how to improve the efficiency of $\Delta\Delta G$ prediction for fast mutation screening; and (2) how to explain mutation preferences and efficiently explore accessible evolutionary regions. To address these challenges, we propose a lightweight $\Delta\Delta G$ predictor (Light-DDG), which adopts a structure-aware Transformer as the backbone and enhances it by knowledge distilled from existing powerful but computationally heavy $\Delta\Delta G$ predictors. Additionally, we augmented, annotated, and released a large-scale dataset containing millions of mutation data for pre-training Light-DDG. We find that such a simple yet effective Light-DDG can serve as a good unsupervised antibody optimizer and explainer. For the target antibody, we propose a novel Mutation Explainer to learn mutation preferences, which accounts for the marginal benefit of each mutation per residue. To further explore accessible evolutionary regions, we conduct preference-guided antibody optimization and evaluate antibody candidates quickly using Light-DDG to identify desirable mutations. Extensive experiments have demonstrated the effectiveness of Light-DDG in terms of test generalizability, noise robustness, and inference practicality, e.g., 89.7$\times$ inference acceleration and 15.45\% performance gains over previous state-of-the-art baselines. A case study of SARS-CoV-2 further demonstrates the crucial role of Light-DDG for mutation explanation and antibody optimization.

Applications · Chemistry and Drug Discovery

Yunyang Li, Zaishuo Xia, Lin Huang, Xinran Wei, Samuel Harshe, Han Yang, Erpai Luo, Zun Wang, Jia Zhang, Chang Liu 等

Density Functional Theory (DFT) is a pivotal method within quantum chemistry and materials science, with its core involving the construction and solution of the Kohn-Sham Hamiltonian. Despite its importance, the application of DFT is frequently limited by the substantial computational resources required to construct the Kohn-Sham Hamiltonian. In response to these limitations, current research has employed deep-learning models to efficiently predict molecular and solid Hamiltonians, with roto-translational symmetries encoded in their neural networks. However, the scalability of prior models may be problematic when applied to large molecules, resulting in non-physical predictions of ground-state properties. In this study, we generate a substantially larger training set (PubChemQH) than used previously and use it to create a scalable model for DFT calculations with physical accuracy. For our model, we introduce a loss function derived from physical principles, which we call Wavefunction Alignment Loss (WALoss). WALoss involves performing a basis change on the predicted Hamiltonian to align it with the observed one; thus, the resulting differences can serve as a surrogate for orbital energy differences, allowing models to make better predictions for molecular orbitals and total energies than previously possible. WALoss also substantially accelerates self-consistent-field (SCF) DFT calculations. Here, we show it achieves a reduction in total energy prediction error by a factor of 1347 and an SCF calculation speed-up by a factor of 18\%. These substantial improvements set new benchmarks for achieving accurate and applicable predictions in larger molecular systems.

Deep Learning · Large Language Models

Yilong Li, Jingyu Liu, Hao Zhang, Badri Narayanan Murali Krishnan, Utkarsh Sharma, Shuai Zhang, Yijing Zeng, Jayaram Raghuram, Suman Banerjee

Deploying large language models (LLMs) locally on mobile devices is advantageous in scenarios where transmitting data to remote cloud servers is either undesirable due to privacy concerns or impractical due to network connection. Recent advancements have facilitated the local deployment of LLMs. However, local deployment also presents challenges, particularly in balancing quality (generative performance), latency, and throughput within the hardware constraints of mobile devices. In this paper, we introduce our lightweight, all-in-one automated benchmarking framework that allows users to evaluate LLMs on mobile devices. We provide a comprehensive benchmark of various popular LLMs with different quantization configurations (both weights and activations) across multiple mobile platforms with varying hardware capabilities. Unlike traditional benchmarks that assess full-scale models on high-end GPU clusters, we focus on evaluating resource efficiency (memory and power consumption) and harmful output for compressed models on mobile devices. Our key observations include: i) differences in energy efficiency and throughput across mobile platforms; ii) the impact of quantization on memory usage, GPU execution time, and power consumption; and iii) accuracy and performance degradation of quantized models compared to their non-quantized counterparts; and iv) the frequency of hallucinations and toxic content generated by compressed LLMs onmobile devices.

Deep Learning · Everything Else

Cyan Subhra Mishra, Deeksha Chaudhary, Jack Sampson, Mahmut Kandemir, Chita Das

The deployment of Deep Neural Networks (DNNs) in energy-constrained environments, such as Energy Harvesting Wireless Sensor Networks (EH-WSNs), introduces significant challenges due to the intermittent nature of power availability. This study introduces NExUME, a novel training methodology designed specifically for DNNs operating under such constraints. We propose a dynamic adjustment of training parameters—dropout rates and quantization levels—that adapt in real-time to the available energy, which varies in energy harvesting scenarios.This approach utilizes a model that integrates the characteristics of the network architecture and the specific energy harvesting profile. It dynamically adjusts training strategies, such as the intensity and timing of dropout and quantization, based on predictions of energy availability. This method not only conserves energy but also enhances the network’s adaptability, ensuring robust learning and inference capabilities even under stringent power constraints. Our results show a 6% to 22% improvement in accuracy over current methods, with an increase of less than 5% in computational overhead. This paper details the development of the adaptive training framework, describes the integration of energy profiles with dropout and quantization adjustments, and presents a comprehensive evaluation using real-world data. Additionally, we introduce a novel dataset aimed at furthering the application of energy harvesting in computational settings.

Applications · Chemistry and Drug Discovery

Kiyoung Seong, Seonghyun Park, Seonghwan Kim, Woo Youn Kim, Sungsoo Ahn

Understanding transition pathways between two meta-stable states of a molecular system is crucial to advance drug discovery and material design. However, unbiased molecular dynamics (MD) simulations are computationally infeasible because of the high energy barriers that separate these states. Although recent machine learning techniques are proposed to sample rare events, they are often limited to simple systems and rely on collective variables (CVs) derived from costly domain expertise. In this paper, we introduce a novel approach that trains diffusion path samplers (DPS) to address the transition path sampling (TPS) problem without requiring CVs. We reformulate the problem as an amortized sampling from the transition path distribution by minimizing the log-variance divergence between the path distribution induced by DPS and the transition path distribution. Based on the log-variance divergence, we propose learnable control variates to reduce the variance of gradient estimators and the off-policy training objective with replay buffers and simulated annealing techniques to improve sample efficiency and diversity. We also propose a scale-based equivariant parameterization of the bias forces to ensure scalability for large systems. We extensively evaluate our approach, termed TPS-DPS, on a synthetic system, small peptide, and challenging fast-folding proteins, demonstrating that it produces more realistic and diverse transition pathways than existing baselines. We also provide links to [project page](https://kiyoung98.github.io/tps-dps/) and [code](https://github.com/kiyoung98/tps-dps).

Deep Learning · Everything Else

Eliahu Horwitz, Asaf Shul, Yedid Hoshen

The number of models shared online has recently skyrocketed, with over one million public models available on Hugging Face. Sharing models allows other users to build on existing models, using them as initialization for fine-tuning, improving accuracy, and saving compute and energy. However, it also raises important intellectual property issues, as fine-tuning may violate the license terms of the original model or that of its training data. A Model Tree, i.e., a tree data structure rooted at a foundation model and having directed edges between a parent model and other models directly fine-tuned from it (children), would settle such disputes by making the model heritage explicit. Unfortunately, current models are not well documented, with most model metadata (e.g., "model cards") not providing accurate information about heritage. In this paper, we introduce the task of Unsupervised Model Tree Heritage Recovery (Unsupervised MoTHer Recovery) for collections of neural networks. For each pair of models, this task requires: i) determining if they are directly related, and ii) establishing the direction of the relationship. Our hypothesis is that model weights encode this information, the challenge is to decode the underlying tree structure given the weights. We discover several properties of model weights that allow us to perform this task. By using these properties, we formulate the MoTHer Recovery task as finding a directed minimal spanning tree. In extensive experiments we demonstrate that our method successfully reconstructs complex Model Trees.

Han Li, Shaohui Li, Wenrui Dai, Maida Cao, Nuowen Kan, Chenglin Li, Junni Zou, Hongkai Xiong

Learned image compression (LIC) has demonstrated superior rate-distortion (R-D) performance compared to traditional codecs, but is challenged by training inefficiency that could incur more than two weeks to train a state-of-the-art model from scratch. Existing LIC methods overlook the slow convergence caused by compacting energy in learning nonlinear transforms. In this paper, we first reveal that such energy compaction consists of two components, \emph{i.e.}, feature decorrelation and uneven energy modulation. On such basis, we propose a linear auxiliary transform (AuxT) to disentangle energy compaction in training nonlinear transforms. The proposed AuxT obtains coarse approximation to achieve efficient energy compaction such that distribution fitting with the nonlinear transforms can be simplified to fine details. We then develop wavelet-based linear shortcuts (WLSs) for AuxT that leverages wavelet-based downsampling and orthogonal linear projection for feature decorrelation and subband-aware scaling for uneven energy modulation. AuxT is lightweight and plug-and-play to be integrated into diverse LIC models to address the slow convergence issue. Experimental results demonstrate that the proposed approach can accelerate training of LIC models by 2 times and simultaneously achieves an average 1\% BD-rate reduction. To our best knowledge, this is one of the first successful attempt that can significantly improve the convergence of LIC with comparable or superior rate-distortion performance.

Deep Learning · Robustness

Wonjeong Choi, Do-Yeon Kim, Jungwuk Park, JungMoon Lee, Younghyun Park, Dong-Jun Han, Jaekyun Moon

In response to the increasing demand for tackling out-of-domain (OOD) scenarios, test-time adaptation (TTA) has garnered significant research attention in recent years. To adapt a source pre-trained model to target samples without getting access to their labels, existing approaches have typically employed entropy minimization (EM) loss as a primary objective function. In this paper, we propose an adaptive energy alignment (AEA) solution that achieves fast online TTA. We start from the re-interpretation of the EM loss by decomposing it into two energy-based terms with conflicting roles, showing that the EM loss can potentially hinder the assertive model adaptation. Our AEA addresses this challenge by strategically reducing the energy gap between the source and target domains during TTA, aiming to effectively align the target domain with the source domains and thus to accelerate adaptation. We specifically propose two novel strategies, each contributing a necessary component for TTA: (i) aligning the energy level of each target sample with the energy zone of the source domain that the pre-trained model is already familiar with, and (ii) precisely guiding the direction of the energy alignment by matching the class-wise correlations between the source and target domains. Our approach demonstrates its effectiveness on various domain shift datasets including CIFAR10-C, CIFAR100-C, and TinyImageNet-C.

Applications · Everything Else

Yunfei Teng, Yuxuan Ren, Kai Chen, Xi Chen, Zhaoming Chen, Qiwei Ye

Cryogenic electron tomography (Cryo-ET) is a powerful technique for visualizing subcellular structures in their native states. Nonetheless, its effectiveness is compromised by anisotropic resolution artifacts caused by the missing-wedge effect. To address this, IsoNet, a deep learning-based method, proposes iteratively reconstructing the missing-wedge information. While successful, IsoNet's dependence on recursive prediction updates often leads to training instability and model divergence. In this study, we introduce CryoGEN—an energy-based probabilistic model that not only mitigates resolution anisotropy but also removes the need for recursive subtomogram averaging, delivering an approximate *10*$\times$ speedup for training. Evaluations across various biological datasets, including immature HIV-1 virions and ribosomes, demonstrate that CryoGEN significantly enhances structural completeness and interpretability of the reconstructed samples.

Shree K. Nayar, Jeremy Klotz, Nikhil Nanda, Mikhail Fridberg

We present a sensor that can measure light and wirelessly communicate the measurement, without the need for an external power source or a battery. Our sensor, called cricket, harvests energy from incident light. It is asleep for most of the time and transmits a short and strong radio frequency chirp when its harvested energy reaches a specific level. The carrier frequency of each cricket is fixed and reveals its identity, and the duration between consecutive chirps is a measure of the incident light level. We have characterized the radiometric response function, signal-to-noise ratio and dynamic range of cricket. We have experimentally verified that cricket can be miniaturized at the expense of increasing the duration between chirps. We show that a cube with a cricket on each of its sides can be used to estimate the centroid of any complex illumination, which has value in applications such as solar tracking. We also demonstrate the use of crickets for creating untethered sensor arrays that can produce video and control lighting for energy conservation. Finally, we modified cricket's circuit to develop battery-free electronic sunglasses that can instantly adapt to environmental illumination.

Yuta Noma, Silvia Sellán, Nicholas Sharp, Karan Singh 0004, Alec Jacobson

We introduce a fast, robust, and user-controllable algorithm to generate surface-filling curves. We compute these curves through the gradient flow of a simple sparse energy, making our method several orders of magnitude faster than previous works. Our algorithm makes minimal assumptions on the topology and resolution of the input surface, achieving improved robustness. Our framework provides tuneable parameters that guide the shape of the output curve, making it ideal for interactive design applications.

Josua Sassen, Henrik Schumacher, Martin Rumpf, Keenan Crane

This paper develops a shape space framework for collision-aware geometric modeling, where basic geometric operations automatically avoid inter-penetration. Shape spaces are a powerful tool for surface modeling, shape analysis, nonrigid motion planning, and animation, but past formulations permit nonphysical intersections. Our framework augments an existing shape space using a repulsive energy such that collision avoidance becomes a first-class property, encoded in the Riemannian metric itself. In turn, tasks like intersection-free shape interpolation or motion extrapolation amount to simply computing geodesic paths via standard numerical algorithms. To make optimization practical, we develop an adaptive collision penalty that prevents mesh self-intersection, and converges to a meaningful limit energy under refinement. The final algorithms apply to any category of shape, and do not require a dataset of examples, training, rigging, nor any other prior information. For instance, to interpolate between two shapes we need only a single pair of meshes with the same connectivity. We evaluate our method on a variety of challenging examples from modeling and animation.

Etienne Corman

In this paper, we introduce a novel approach for computing conformal deformations in ℝ3 while minimizing curvature-based energies. Curvature-based energies serve as fundamental tools in geometry processing, essential for tasks such as surface fairing, deformation, and approximation using developable or cone metric surfaces. However, accurately computing the geometric embedding, especially for the latter, has been a challenging endeavor. The complexity arises from inherent numerical instabilities in curvature estimation and the intricate nature of differentiating these energies. To address these challenges, we concentrate on conformal deformations, leveraging the curvature tensor as the primary variable in our model. This strategic choice renders curvature-based energies easily applicable, mitigating previous manipulation difficulties. Our key contribution lies in identifying a previously unknown integrability condition that establishes a connection between conformal deformations and changes in curvature. We use this insight to deform surfaces of arbitrary genus, aiming to minimize bending energies or prescribe Gaussian curvature while sticking to positional constraints.

Vismay Modi, Nicholas Sharp, Or Perel, Shinjiro Sueda, David I. W. Levin

The proliferation of 3D representations, from explicit meshes to implicit neural fields and more, motivates the need for simulators agnostic to representation. We present a data-, mesh-, and grid-free solution for elastic simulation for any object in any geometric representation undergoing large, nonlinear deformations. We note that every standard geometric representation can be reduced to an occupancy function queried at any point in space, and we define a simulator atop this common interface. For each object, we fit a small implicit neural network encoding spatially varying weights that act as a reduced deformation basis. These weights are trained to learn physically significant motions in the object via random perturbations. Our loss ensures we find a weight-space basis that best minimizes deformation energy by stochastically evaluating elastic energies through Monte Carlo sampling of the deformation volume. At runtime, we simulate in the reduced basis and sample the deformations back to the original domain. Our experiments demonstrate the versatility, accuracy, and speed of this approach on data including signed distance functions, point clouds, neural primitives, tomography scans, radiance fields, Gaussian splats, surface meshes, and volume meshes, as well as showing a variety of material energies, contact models, and time integration schemes.