Protein complex formation, a pivotal challenge in contemporary biology, has recently gained interest from the machine learning community, particularly concerning protein-ligand docking tasks. In this paper, we delve into the equally crucial but comparatively under-investigated domain of protein-protein docking. Specifically, we propose a geometric deep learning framework, termed EBMDock, which employs statistical potential as its energy function. This approach produces a probability distribution over docking poses, such that the identified docking pose aligns with a minimum point in the energy landscape. We employ a differential algorithm grounded in Langevin dynamics to efficiently sample from the docking pose distribution. Additionally, we incorporate energy-based training using contrastive divergence, enhancing both performance and stability. Empirical results demonstrate that our approach achieves superior performance on two benchmark datasets DIPS and DB5.5. Furthermore, the results suggest EBMDock can serve as an orthogonal enhancement to existing methods.
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Applications · Physics
Battery degradation remains a pivotal concern in the energy storage domain, with machine learning emerging as a potent tool to drive forward insights and solutions. However, this intersection of electrochemical science and machine learning poses complex challenges. Machine learning experts often grapple with the intricacies of battery science, while battery researchers face hurdles in adapting intricate models tailored to specific datasets. Beyond this, a cohesive standard for battery degradation modeling, inclusive of data formats and evaluative benchmarks, is conspicuously absent. Recognizing these impediments, we present BatteryML—a one-step, all-encompass, and open-source platform designed to unify data preprocessing, feature extraction, and the implementation of both traditional and state-of-the-art models. This streamlined approach promises to enhance the practicality and efficiency of research applications. BatteryML seeks to fill this void, fostering an environment where experts from diverse specializations can collaboratively contribute, thus elevating the collective understanding and advancement of battery research.
Deep Learning · Self-Supervised Learning
High accuracy, low latency and high energy efficiency represent a set of contradictory goals when searching for system solutions for image classification and detection. While high-quality images naturally result in more precise detection and classification, they also result in a heavier computational workload for imaging and processing, reduce camera refresh rates, and increase the volume of data communication between the camera and processor. Taking inspiration from the foveal-peripheral sampling mechanism, saccade mechanism observed in the human visual system and the filling-in phenomena of brain, we have developed an active scene reconstruction architecture based on multiple foveal views. This model stitches together information from foveal and peripheral vision, which are sampled from multiple glances. Assisted by a reinforcement learning-based saccade mechanism, our model reduces the required input pixels by over 90\% per frame while maintaining the same level of performance in image recognition as with the original images. We evaluated the effectiveness of our model using the GTSRB dataset and the ImageNet dataset. Using an equal number of input pixels, our study demonstrates a 5\% higher image recognition accuracy compared to state-of-the-art foveal-peripheral vision systems. Furthermore, we demonstrate that our foveal sampling/saccadic scene reconstruction model exhibits significantly lower complexity and higher data efficiency during the training phase compared to existing approaches.
Probabilistic Methods · Monte Carlo and Sampling Methods
Bayesian deep learning counts on the quality of posterior distribution estimation. However, the posterior of deep neural networks is highly multi-modal in nature, with local modes exhibiting varying generalization performance. Given a practical budget, targeting at the original posterior can lead to suboptimal performance, as some samples may become trapped in "bad" modes and suffer from overfitting. Leveraging the observation that "good" modes with low generalization error often reside in flat basins of the energy landscape, we propose to bias sampling on the posterior toward these flat regions. Specifically, we introduce an auxiliary guiding variable, the stationary distribution of which resembles a smoothed posterior free from sharp modes, to lead the MCMC sampler to flat basins. By integrating this guiding variable with the model parameter, we create a simple joint distribution that enables efficient sampling with minimal computational overhead. We prove the convergence of our method and further show that it converges faster than several existing flatness-aware methods in the strongly convex setting. Empirical results demonstrate that our method can successfully sample from flat basins of the posterior, and outperforms all compared baselines on multiple benchmarks including classification, calibration, and out-of-distribution detection.
Probabilistic Methods
Nature performs complex computations constantly at clearly lower cost and higher performance than digital computers. It is crucial to understand how to harness the unique computational power of nature in Machine Learning (ML). In the past decade, besides the development of Neural Networks (NNs), the community has also relentlessly explored nature-powered ML paradigms. Although most of them are still predominantly theoretical, a new practical paradigm enabled by the recent advent of CMOS-compatible room-temperature nature-based computers has emerged. By harnessing a dynamical system's intrinsic behavior of chasing the lowest energy state, this paradigm can solve some simple binary problems delivering considerable speedup and energy savings compared with NNs, while maintaining comparable accuracy. Regrettably, its values to the real world are highly constrained by its binary nature. A clear pathway to its extension to real-valued problems remains elusive. This paper aims to unleash this pathway by proposing a novel end-to-end Nature-Powered Graph Learning (NP-GL) framework. Specifically, through a three-dimensional co-design, NP-GL can leverage the spontaneous energy decrease in nature to efficiently solve real-valued graph learning problems. Experimental results across 4 real-world applications with 6 datasets demonstrate that NP-GL delivers, on average, $6.97\times 10^3$ speedup and $10^5$ energy consumption reduction with comparable or even higher accuracy than Graph Neural Networks (GNNs).
Deep Learning · Everything Else
Large Vision-Language Models (LVLMs) can understand the world comprehensively by integrating rich information from different modalities, achieving remarkable performance improvements on various multimodal downstream tasks. However, deploying LVLMs is often problematic due to their massive computational/energy costs and carbon consumption, making it infeasible to adopt conventional iterative global pruning, which is costly due to computing the Hessian matrix of the entire large model for sparsification. Alternatively, several studies have recently proposed layer-wise pruning approaches to avoid the expensive computation of global pruning and efficiently compress model weights according to their importance within a layer. However, these methods often suffer from suboptimal model compression due to their lack of a global perspective. To address this limitation in recent efficient pruning methods for large models, we propose Efficient Coarse-to-Fine Layer-Wise Pruning (ECoFLaP), a two-stage coarse-to-fine weight pruning approach for LVLMs. We first determine the sparsity ratios of different layers or blocks by leveraging the global importance score, which is efficiently computed based on the zeroth-order approximation of the global model gradients. Then, the multimodal model performs layer-wise unstructured weight pruning. We validate our proposed method across various multi-modal and single-modal models and datasets, demonstrating significant performance improvements over prevalent pruning techniques in the high-sparsity regime.
Applications
Lattices are architected metamaterials whose properties strongly depend on their geometrical design. The analogy between lattices and graphs enables the use of graph neural networks (GNNs) as a faster surrogate model compared to traditional methods such as finite element modelling. In this work, we generate a big dataset of structure-property relationships for strut-based lattices. The dataset is made available to the community which can fuel the development of methods anchored in physical principles for the fitting of fourth-order tensors. In addition, we present a higher-order GNN model trained on this dataset. The key features of the model are (i) SE(3) equivariance, and (ii) consistency with the thermodynamic law of conservation of energy. We compare the model to non-equivariant models based on a number of error metrics and demonstrate its benefits in terms of predictive performance and reduced training requirements. Finally, we demonstrate an example application of the model to an architected material design task. The methods which we developed are applicable to fourth-order tensors beyond elasticity such as piezo-optical tensor etc.
Applications · Physics
Inverse design, where we seek to design input variables in order to optimize an underlying objective function, is an important problem that arises across fields such as mechanical engineering to aerospace engineering. Inverse design is typically formulated as an optimization problem, with recent works leveraging optimization across learned dynamics models. However, as models are optimized they tend to fall into adversarial modes, preventing effective sampling. We illustrate that by instead optimizing over the learned energy function captured by the diffusion model, we can avoid such adversarial examples and significantly improve design performance. We further illustrate how such a design system is compositional, enabling us to combine multiple different diffusion models representing subcomponents of our desired system to design systems with every specified component. In an N-body interaction task and a challenging 2D multi-airfoil design task, we demonstrate that by composing the learned diffusion model at test time, our method allows us to design initial states and boundary shapes that are more complex than those in the training data. Our method generalizes to more objects for N-body dataset and discovers formation flying to minimize drag in the multi-airfoil design task. Project website and code can be found at https://github.com/AI4Science-WestlakeU/cindm.
Applications · Neuroscience, Cognitive Science
Spiking Neural Networks (SNNs) have received widespread attention in academic communities due to their superior spatio-temporal processing capabilities and energy-efficient characteristics. With further in-depth application in various fields, the vulnerability of SNNs under adversarial attack has become a focus of concern. In this paper, we draw inspiration from two mainstream learning algorithms of SNNs and observe that SNN models reserve both rate and temporal information. To better understand the capabilities of these two types of information, we conduct a quantitative analysis separately for each. In addition, we note that the retention degree of temporal information is related to the parameters and input settings of spiking neurons. Building on these insights, we propose a hybrid adversarial attack based on rate and temporal information (HART), which allows for dynamic adjustment of the rate and temporal attributes. Experimental results demonstrate that compared to previous works, HART attack can achieve significant superiority under different attack scenarios, data types, network architecture, time-steps, and model hyper-parameters. These findings call for further exploration into how both types of information can be effectively utilized to enhance the reliability of SNNs. Code is available at [https://github.com/hzc1208/HART_Attack](https://github.com/hzc1208/HART_Attack).
Social Aspects · Fairness, Equity, Justice and Safety
Although transformers demonstrate impressive capabilities in a variety of tasks, the fairness issue remains a significant concern when deploying these models. Existing works to address fairness issues in transformers require sensitive labels (such as age, gender, etc.), which can raise privacy concerns or violate legal regulations. An alternative way is through fairness without demographics. However, existing works that improve Rawlsian Max-Min fairness may impose overly restrictive constraints. Other methods that use auxiliary networks could be parameter inefficient. In this paper, we present a new approach to debiasing transformers by leveraging their inherent structure. By reconsidering the roles of important components (queries, keys, and values) in the attention mechanism, we introduce a simple yet effective debiasing strategy from two perspectives: 1) Grounded in theoretical analysis, we normalize and apply absolute value operations to queries and keys to minimize the bias in attention weight allocation; 2) We reduce the bias within values through local alignment via contrastive learning. Throughout the entire process, our approach does not require any sensitive labels. Furthermore, to enhance memory efficiency in the training phase, we propose a strategy that debias only the last encoder to improve fairness in pre-trained models. We conduct experiments in computer vision and natural language processing tasks and show that our method is comparable and even outperforms the state-of-the-art method with substantially lower energy consumption.
Deep Learning · Generative Models and Autoencoders
Modern distribution matching algorithms for training diffusion or flow models directly prescribe the time evolution of the marginal distributions between two boundary distributions. In this work, we consider a generalized distribution matching setup, where these marginals are only implicitly described as a solution to some task-specific objective function. The problem setup, known as the Generalized Schrödinger Bridge (GSB), appears prevalently in many scientific areas both within and without machine learning. We propose Generalized Schödinger Bridge Matching (GSBM), a new matching algorithm inspired by recent advances, generalizing them beyond kinetic energy minimization and to account for nonlinear state costs. We show that such a generalization can be cast as solving conditional stochastic optimal control, for which efficient variational approximations can be used, and further debiased with the aid of path integral theory. Compared to prior methods for solving GSB problems, our GSBM algorithm always preserves a feasible transport map between the boundary distributions throughout training, thereby enabling stable convergence and significantly improved scalability. We empirically validate our claims on an extensive suite of experimental setups, including crowd navigation, opinion depolarization, LiDAR manifolds, and image domain transfer. Our work brings new algorithmic opportunities for training diffusion models enhanced with task-specific optimality structures.
Social Aspects · Accountability, Transparency and Interpretability
Existing methods, such as concept bottleneck models (CBMs), have been successful in providing concept-based interpretations for black-box deep learning models. They typically work by predicting concepts given the input and then predicting the final class label given the predicted concepts. However, (1) they often fail to capture the high-order, nonlinear interaction between concepts, e.g., correcting a predicted concept (e.g., “yellow breast”) does not help correct highly correlated concepts (e.g., “yellow belly”), leading to suboptimal final accuracy; (2) they cannot naturally quantify the complex conditional dependencies between different concepts and class labels (e.g., for an image with the class label “Kentucky Warbler” and a concept “black bill”, what is the probability that the model correctly predicts another concept “black crown”), therefore failing to provide deeper insight into how a black-box model works. In response to these limitations, we propose Energy-based Concept Bottleneck Models (ECBMs). Our ECBMs use a set of neural networks to define the joint energy of candidate (input, concept, class) tuples. With such a unified interface, prediction, concept correction, and conditional dependency quantification are then represented as conditional probabilities, which are generated by composing different energy functions. Our ECBMs address both limitations of existing CBMs, providing higher accuracy and richer concept interpretations. Empirical results show that our approach outperforms the state-of-the-art on real-world datasets.
Deep Learning · Generative Models and Autoencoders
Training energy-based models (EBMs) on high-dimensional data can be both challenging and time-consuming, and there exists a noticeable gap in sample quality between EBMs and other generative frameworks like GANs and diffusion models. To close this gap, inspired by the recent efforts of learning EBMs by maximimizing diffusion recovery likelihood (DRL), we propose cooperative diffusion recovery likelihood (CDRL), an effective approach to tractably learn and sample from a series of EBMs defined on increasingly noisy versons of a dataset, paired with an initializer model for each EBM. At each noise level, the two models are jointly estimated within a cooperative training framework: Samples from the initializer serve as starting points that are refined by a few MCMC sampling steps from the EBM. The EBM is then optimized by maximizing recovery likelihood, while the initializer model is optimized by learning from the difference between the refined samples and the initial samples. In addition, we made several practical designs for EBM training to further improve the sample quality. Combining these advances, we significantly boost the generation performance compared to existing EBM methods on CIFAR-10 and ImageNet 32x32. And we have shown that CDRL has great potential to largely reduce the sampling time. We also demonstrate the effectiveness of our models for several downstream tasks, including classifier-free guided generation, compositional generation, image inpainting and out-of-distribution detection.
Applications · Chemistry and Drug Discovery
Equivariant Transformers such as Equiformer have demonstrated the efficacy of applying Transformers to the domain of 3D atomistic systems. However, they are limited to small degrees of equivariant representations due to their computational complexity. In this paper, we investigate whether these architectures can scale well to higher degrees. Starting from Equiformer, we first replace $SO(3)$ convolutionswith eSCN convolutions to efficiently incorporate higher-degree tensors. Then, to better leverage the power of higher degrees, we propose three architectural improvements – attention re-normalization, separable $S^2$ activation and separable layer normalization. Putting these all together, we propose EquiformerV2, which outperforms previous state-of-the-art methods on large-scale OC20 dataset by up to 9% on forces, 4% on energies, offers better speed-accuracy trade-offs, and 2$\times$ reduction in DFT calculations needed for computing adsorption energies. Additionally, EquiformerV2 trained on only OC22 dataset outperforms GemNet-OC trained on both OC20 and OC22 datasets, achieving much better data efficiency. Finally, we compare EquiformerV2 with Equiformer on QM9 and OC20 S2EF-2Mdatasets to better understand the performance gain brought by higher degrees.
Reinforcement Learning
Learning expressive stochastic policies instead of deterministic ones has been proposed to achieve better stability, sample complexity and robustness. Notably, in Maximum Entropy reinforcement learning (MaxEnt RL), the policy is modeled as an expressive energy-based model (EBM) over the Q-values. However, this formulation requires the estimation of the entropy of such EBM distributions which is an open problem. To address this, previous MaxEnt RL methods either implicitly estimate the entropy, yielding high computational complexity and variance (SQL), or follow a variational inference approach that fits simplified distributions (e.g., Gaussian) for tractability (SAC). We propose Sein Soft Actor-Critic (S$^2$AC), a MaxEnt RL algorithm that learns expressive policies without compromising efficiency. S$^2$AC uses parameterized Stein Variational Gradient Descent (SVGD) as the underlying policy. At the core of S$^2$AC is a new solution to the above open challenge of entropy computation for EBMs. Our entropy formula is computationally efficient and only depends on first-order derivatives and vector products. Empirical results show that S$^2$AC yields more optimal solutions to the MaxEnt objective than SQL and SAC in the multi-goal environment, and outperforms SAC and SQL on the MuJoCo benchmark. Our code is available at: https://anonymous.4open.science/r/Stein-Soft-Actor-Critic/
Deep Learning · Graph Neural Networks
While contrastive self-supervised learning has become the de-facto learning paradigm for graph neural networks, the pursuit of higher task accuracy requires a larger hidden dimensionality to learn informative and discriminative full-precision representations, raising concerns about computation, memory footprint, and energy consumption burden (largely overlooked) for real-world applications. This work explores a promising direction for graph contrastive learning (GCL) with spiking neural networks (SNNs), which leverage sparse and binary characteristics to learn more biologically plausible and compact representations. We propose SpikeGCL, a novel GCL framework to learn binarized 1-bit representations for graphs, making balanced trade-offs between efficiency and performance. We provide theoretical guarantees to demonstrate that SpikeGCL has comparable expressiveness with its full-precision counterparts. Experimental results demonstrate that, with nearly 32x representation storage compression, SpikeGCL is either comparable to or outperforms many fancy state-of-the-art supervised and self-supervised methods across several graph benchmarks.
Applications · Neuroscience, Cognitive Science
Spiking Neural Networks (SNNs) have emerged as energy-efficient alternatives to Artificial Neural Networks (ANNs) when deployed on neuromorphic chips. While recent studies have demonstrated the impressive performance of deep SNNs on challenging tasks, their energy efficiency advantage has been diminished. Existing methods targeting energy consumption reduction do not fully exploit sparsity, whereas powerful pruning methods can achieve high sparsity but are not directly targeted at energy efficiency, limiting their effectiveness in energy saving. Furthermore, none of these works fully exploit the sparsity of neurons or the potential for unstructured neuron pruning in SNNs. In this paper, we propose a novel pruning framework that combines unstructured weight pruning with unstructured neuron pruning to maximize the utilization of the sparsity of neuromorphic computing, thereby enhancing energy efficiency. To the best of our knowledge, this is the first application of unstructured neuron pruning to deep SNNs. Experimental results demonstrate that our method achieves impressive energy efficiency gains. The sparse network pruned by our method with only 0.63\% remaining connections can achieve a remarkable 91 times increase in energy efficiency compared to the original dense network, requiring only 8.5M SOPs for inference, with merely 2.19\% accuracy loss on the CIFAR-10 dataset. Our work suggests that deep and dense SNNs exhibit high redundancy in energy consumption, highlighting the potential for targeted SNN sparsification to save energy.
Deep Learning · Generative Models and Autoencoders
Despite the recent advances in the field of computational Schrödinger Bridges (SB), most existing SB solvers are still heavy-weighted and require complex optimization of several neural networks. It turns out that there is no principal solver which plays the role of simple-yet-effective baseline for SB just like, e.g., $k$-means method in clustering, logistic regression in classification or Sinkhorn algorithm in discrete optimal transport. We address this issue and propose a novel fast and simple SB solver. Our development is a smart combination of two ideas which recently appeared in the field: (a) parameterization of the Schrödinger potentials with sum-exp quadratic functions and (b) viewing the log-Schrödinger potentials as the energy functions. We show that combined together these ideas yield a lightweight, simulation-free and theoretically justified SB solver with a simple straightforward optimization objective. As a result, it allows solving SB in moderate dimensions in a matter of minutes on CPU without a painful hyperparameter selection. Our light solver resembles the Gaussian mixture model which is widely used for density estimation. Inspired by this similarity, we also prove an important theoretical result showing that our light solver is a universal approximator of SBs. Furthemore, we conduct the analysis of the generalization error of our light solver. The code for our solver can be found at https://github.com/ngushchin/LightSB.
Probabilistic Methods · Bayesian Models and Methods
We propose conditional flows of the maximum mean discrepancy (MMD) with the negative distance kernel for posterior sampling and conditional generative modelling. This MMD, which is also known as energy distance, has several advantageous properties like efficient computation via slicing and sorting. We approximate the joint distribution of the ground truth and the observations using discrete Wasserstein gradient flows and establish an error bound for the posterior distributions. Further, we prove that our particle flow is indeed a Wasserstein gradient flow of an appropriate functional. The power of our method is demonstrated by numerical examples including conditional image generation and inverse problems like superresolution, inpainting and computed tomography in low-dose and limited-angle settings.
Deep Learning · Large Language Models
The fast growing capabilities of large-scale deep learning models, such as Bert, GPT and ViT, are revolutionizing the landscape of NLP, CV and many other domains. Training such models, however, poses an unprecedented demand for computing power, which incurs exponentially increasing energy cost and carbon dioxide emissions. It is thus critical to develop efficient training solutions to reduce the training costs. Motivated by a set of key observations of inter- and intra-layer similarities among feature maps and attentions that can be identified from typical training processes, we propose a multi-level framework for training acceleration. Specifically, the framework is based on three basic operators, Coalescing, De-coalescing and Interpolation, which can be orchestrated to build a multi-level training framework. The framework consists of a V-cycle training process, which progressively down- and up-scales the model size and projects the parameters between adjacent levels of models via coalescing and de-coalescing. The key idea is that a smaller model that can be trained for fast convergence and the trained parameters provides high-qualities intermediate solutions for the next level larger network. The interpolation operator is designed to break the symmetry of neurons incurred by de-coalescing for better convergence performance. Our experiments on transformer-based language models (e.g. Bert, GPT) as well as a vision model (e.g. DeiT) prove that the proposed framework reduces the computational cost by about 20% on training BERT/GPT-Base models and up to 51.6% on training the BERT-Large model while preserving the performance.