论文检索

Applications/Health

Qing Wu, Lixuan Chen, Ce Wang, Hongjiang Wei, S. Kevin Zhou, Jingyi Yu, Yuyao Zhang

Emerging neural reconstruction techniques based on tomography (e.g., NeRF, NeAT, and NeRP) have started showing unique capabilities in medical imaging. In this work, we present a novel Polychromatic neural representation (Polyner) to tackle the challenging problem of CT imaging when metallic implants exist within the human body. CT metal artifacts arise from the drastic variation of metal's attenuation coefficients at various energy levels of the X-ray spectrum, leading to a nonlinear metal effect in CT measurements. Recovering CT images from metal-affected measurements hence poses a complicated nonlinear inverse problem where empirical models adopted in previous metal artifact reduction (MAR) approaches lead to signal loss and strongly aliased reconstructions. Polyner instead models the MAR problem from a nonlinear inverse problem perspective. Specifically, we first derive a polychromatic forward model to accurately simulate the nonlinear CT acquisition process. Then, we incorporate our forward model into the implicit neural representation to accomplish reconstruction. Lastly, we adopt a regularizer to preserve the physical properties of the CT images across different energy levels while effectively constraining the solution space. Our Polyner is an unsupervised method and does not require any external training data. Experimenting with multiple datasets shows that our Polyner achieves comparable or better performance than supervised methods on in-domain datasets while demonstrating significant performance improvements on out-of-domain datasets. To the best of our knowledge, our Polyner is the first unsupervised MAR method that outperforms its supervised counterparts. The code for this work is available at: https://github.com/iwuqing/Polyner.

Probabilistic Methods/Bayesian Models and Methods

Mingxuan Zhang, Yan Sun, Faming Liang

Sparse deep learning has become a popular technique for improving the performance of deep neural networks in areas such as uncertainty quantification, variable selection, and large-scale network compression. However, most existing research has focused on problems where the observations are independent and identically distributed (i.i.d.), and there has been little work on the problems where the observations are dependent, such as time series data and sequential data in natural language processing. This paper aims to address this gap by studying the theory for sparse deep learning with dependent data. We show that sparse recurrent neural networks (RNNs) can be consistently estimated, and their predictions are asymptotically normally distributed under appropriate assumptions, enabling the prediction uncertainty to be correctly quantified. Our numerical results show that sparse deep learning outperforms state-of-the-art methods, such as conformal predictions, in prediction uncertainty quantification for time series data. Furthermore, our results indicate that the proposed method can consistently identify the autoregressive order for time series data and outperform existing methods in large-scale model compression. Our proposed method has important practical implications in fields such as finance, healthcare, and energy, where both accurate point estimates and prediction uncertainty quantification are of concern.

Miscellaneous Aspects of Machine Learning/Transfer, Multitask and Meta-learning

Sanket Vaibhav Mehta, Darshan Patil, Sarath Chandar, Emma Strubell

The lifelong learning paradigm in machine learning is an attractive alternative to the more prominent isolated learning scheme not only due to its resemblance to biological learning but also its potential to reduce energy waste by obviating excessive model re-training. A key challenge to this paradigm is the phenomenon of catastrophic forgetting. With the increasing popularity and success of pre-trained models in machine learning, we pose the question: What role does pre-training play in lifelong learning, specifically with respect to catastrophic forgetting? We investigate existing methods in the context of large, pre-trained models and evaluate their performance on a variety of text and image classification tasks, including a large-scale study using a novel data set of 15 diverse NLP tasks. Across all settings, we observe that generic pre-training implicitly alleviates the effects of catastrophic forgetting when learning multiple tasks sequentially compared to randomly initialized models. We then further investigate why pre-training alleviates forgetting in this setting. We study this phenomenon by analyzing the loss landscape, finding that pre-trained weights appear to ease forgetting by leading to wider minima. Based on this insight, we propose jointly optimizing for current task loss and loss basin sharpness to explicitly encourage wider basins during sequential fine-tuning. We show that this optimization approach outperforms several state-of-the-art task-sequential continual learning algorithms across multiple settings, occasionally even without retaining a memory that scales in size with the number of tasks.

Miscellaneous Aspects of Machine Learning/Transfer, Multitask and Meta-learning

Shengzhuang Chen, Long-Kai Huang, Jonathan Richard Schwarz, Yilun Du, Ying Wei

The success of meta-learning on out-of-distribution (OOD) tasks in the wild has proved to be hit-and-miss.To safeguard the generalization capability of the meta-learned prior knowledge to OOD tasks, in particularly safety-critical applications, necessitates detection of an OOD task followed by adaptation of the task towards the prior. Nonetheless, the reliability of estimated uncertainty on OOD tasks by existing Bayesian meta-learning methods is restricted by incomplete coverage of the feature distribution shift and insufficient expressiveness of the meta-learned prior. Besides, they struggle to adapt an OOD task, running parallel to the line of cross-domain task adaptation solutions which are vulnerable to overfitting.To this end, we build a single coherent framework that supports both detection and adaptation of OOD tasks, while remaining compatible with off-the-shelf meta-learning backbones. The proposed Energy-Based Meta-Learning (EBML) framework learns to characterize any arbitrary meta-training task distribution with the composition of two expressive neural-network-based energy functions. We deploy the sum of the two energy functions, being proportional to the joint distribution of a task, as a reliable score for detecting OOD tasks; during meta-testing, we adapt the OOD task to in-distribution tasks by energy minimization.Experiments on four regression and classification datasets demonstrate the effectiveness of our proposal.

Applications/Chemistry and Drug Discovery

Namkyeong Lee, Heewoong Noh, Sungwon Kim, Dongmin Hyun, Gyoung S. Na, Chanyoung Park

The density of states (DOS) is a spectral property of crystalline materials, which provides fundamental insights into various characteristics of the materials.While previous works mainly focus on obtaining high-quality representations of crystalline materials for DOS prediction, we focus on predicting the DOS from the obtained representations by reflecting the nature of DOS: DOS determines the general distribution of states as a function of energy.That is, DOS is not solely determined by the crystalline material but also by the energy levels, which has been neglected in previous works.In this paper, we propose to integrate heterogeneous information obtained from the crystalline materials and the energies via a multi-modal transformer, thereby modeling the complex relationships between the atoms in the crystalline materials and various energy levels for DOS prediction.Moreover, we propose to utilize prompts to guide the model to learn the crystal structural system-specific interactions between crystalline materials and energies.Extensive experiments on two types of DOS, i.e., Phonon DOS and Electron DOS, with various real-world scenarios demonstrate the superiority of DOSTransformer.The source code for DOSTransformer is available at https://github.com/HeewoongNoh/DOSTransformer.

Applications/Physics

Wai Tong Chung, Bassem Akoush, Pushan Sharma, Alex Tamkin, Ki Sung Jung, Jacqueline Chen, Jack Guo, Davy Brouzet, Mohsen Talei, Bruno Savard 等

Analysis of compressible turbulent flows is essential for applications related to propulsion, energy generation, and the environment. Here, we present BLASTNet 2.0, a 2.2 TB network-of-datasets containing 744 full-domain samples from 34 high-fidelity direct numerical simulations, which addresses the current limited availability of 3D high-fidelity reacting and non-reacting compressible turbulent flow simulation data. With this data, we benchmark a total of 49 variations of five deep learning approaches for 3D super-resolution - which can be applied for improving scientific imaging, simulations, turbulence models, as well as in computer vision applications. We perform neural scaling analysis on these models to examine the performance of different machine learning (ML) approaches, including two scientific ML techniques. We demonstrate that (i) predictive performance can scale with model size and cost, (ii) architecture matters significantly, especially for smaller models, and (iii) the benefits of physics-based losses can persist with increasing model size. The outcomes of this benchmark study are anticipated to offer insights that can aid the design of 3D super-resolution models, especially for turbulence models, while this data is expected to foster ML methods for a broad range of flow physics applications. This data is publicly available with download links and browsing tools consolidated at https://blastnet.github.io.

Applications/Physics

Artur Toshev, Gianluca Galletti, Fabian Fritz, Stefan Adami, Nikolaus Adams

Machine learning has been successfully applied to grid-based PDE modeling in various scientific applications. However, learned PDE solvers based on Lagrangian particle discretizations, which are the preferred approach to problems with free surfaces or complex physics, remain largely unexplored. We present LagrangeBench, the first benchmarking suite for Lagrangian particle problems, focusing on temporal coarse-graining. In particular, our contribution is: (a) seven new fluid mechanics datasets (four in 2D and three in 3D) generated with the Smoothed Particle Hydrodynamics (SPH) method including the Taylor-Green vortex, lid-driven cavity, reverse Poiseuille flow, and dam break, each of which includes different physics like solid wall interactions or free surface, (b) efficient JAX-based API with various recent training strategies and three neighbor search routines, and (c) JAX implementation of established Graph Neural Networks (GNNs) like GNS and SEGNN with baseline results. Finally, to measure the performance of learned surrogates we go beyond established position errors and introduce physical metrics like kinetic energy MSE and Sinkhorn distance for the particle distribution. Our codebase is available under the URL: [https://github.com/tumaer/lagrangebench](https://github.com/tumaer/lagrangebench).

Deep Learning/Generative Models and Autoencoders

Davide Carbone, Mengjian Hua, Simon Coste, Eric Vanden-Eijnden

Energy-based models (EBMs) are generative models inspired by statistical physics with a wide range of applications in unsupervised learning. Their performance is well measured by the cross-entropy (CE) of the model distribution relative to the data distribution. Using the CE as the objective for training is however challenging because the computation of its gradient with respect to the model parameters requires sampling the model distribution. Here we show how results for nonequilibrium thermodynamics based on Jarzynski equality together with tools from sequential Monte-Carlo sampling can be used to perform this computation efficiently and avoid the uncontrolled approximations made using the standard contrastive divergence algorithm. Specifically, we introduce a modification of the unadjusted Langevin algorithm (ULA) in which each walker acquires a weight that enables the estimation of the gradient of the cross-entropy at any step during GD, thereby bypassing sampling biases induced by slow mixing of ULA. We illustrate these results with numerical experiments on Gaussian mixture distributions as well as the MNIST and CIFAR-10 datasets. We show that the proposed approach outperforms methods based on the contrastive divergence algorithm in all the considered situations.

Deep Learning/Attention Mechanisms

Benjamin Hoover, Yuchen Liang, Bao Pham, Rameswar Panda, Hendrik Strobelt, Duen Horng Chau, Mohammed Zaki, Dmitry Krotov

Our work combines aspects of three promising paradigms in machine learning, namely, attention mechanism, energy-based models, and associative memory. Attention is the power-house driving modern deep learning successes, but it lacks clear theoretical foundations. Energy-based models allow a principled approach to discriminative and generative tasks, but the design of the energy functional is not straightforward. At the same time, Dense Associative Memory models or Modern Hopfield Networks have a well-established theoretical foundation, and allow an intuitive design of the energy function. We propose a novel architecture, called the Energy Transformer (or ET for short), that uses a sequence of attention layers that are purposely designed to minimize a specifically engineered energy function, which is responsible for representing the relationships between the tokens. In this work, we introduce the theoretical foundations of ET, explore its empirical capabilities using the image completion task, and obtain strong quantitative results on the graph anomaly detection and graph classification tasks.

Applications/Chemistry and Drug Discovery

Shiwei Liu, Tian Zhu, Milong Ren, Chungong Yu, Dongbo Bu, Haicang Zhang

Many crucial biological processes rely on networks of protein-protein interactions. Predicting the effect of amino acid mutations on protein-protein binding is important in protein engineering, including therapeutic discovery. However, the scarcity of annotated experimental data on binding energy poses a significant challenge for developing computational approaches, particularly deep learning-based methods. In this work, we propose SidechainDiff, a novel representation learning-based approach that leverages unlabelled experimental protein structures. SidechainDiff utilizes a Riemannian diffusion model to learn the generative process of side-chain conformations and can also give the structural context representations of mutations on the protein-protein interface. Leveraging the learned representations, we achieve state-of-the-art performance in predicting the mutational effects on protein-protein binding. Furthermore, SidechainDiff is the first diffusion-based generative model for side-chains, distinguishing it from prior efforts that have predominantly focused on the generation of protein backbone structures.

David Ruhe, Johannes Brandstetter, Patrick Forré

We introduce Clifford Group Equivariant Neural Networks: a novel approach for constructing $\mathrm{O}(n)$- and $\mathrm{E}(n)$-equivariant models. We identify and study the *Clifford group*: a subgroup inside the Clifford algebra tailored to achieve several favorable properties. Primarily, the group's action forms an orthogonal automorphism that extends beyond the typical vector space to the entire Clifford algebra while respecting the multivector grading. This leads to several non-equivalent subrepresentations corresponding to the multivector decomposition. Furthermore, we prove that the action respects not just the vector space structure of the Clifford algebra but also its multiplicative structure, i.e., the geometric product. These findings imply that every polynomial in multivectors, including their grade projections, constitutes an equivariant map with respect to the Clifford group, allowing us to parameterize equivariant neural network layers. An advantage worth mentioning is that we obtain expressive layers that can elegantly generalize to inner-product spaces of any dimension. We demonstrate, notably from a single core implementation, state-of-the-art performance on several distinct tasks, including a three-dimensional $n$-body experiment, a four-dimensional Lorentz-equivariant high-energy physics experiment, and a five-dimensional convex hull experiment.

Probabilistic Methods

Lorenzo Loconte, Nicola Di Mauro, Robert Peharz, Antonio Vergari

Some of the most successful knowledge graph embedding (KGE) models for link prediction – CP, RESCAL, TuckER, ComplEx – can be interpreted as energy-based models. Under this perspective they are not amenable for exact maximum-likelihood estimation (MLE), sampling and struggle to integrate logical constraints. This work re-interprets the score functions of these KGEs as circuits – constrained computational graphs allowing efficient marginalisation. Then, we design two recipes to obtain efficient generative circuit models by either restricting their activations to be non-negative or squaring their outputs. Our interpretation comes with little or no loss of performance for link prediction, while the circuits framework unlocks exact learning by MLE, efficient sampling of new triples, and guarantee that logical constraints are satisfied by design. Furthermore, our models scale more gracefully than the original KGEs on graphs with millions of entities.

Applications/Chemistry and Drug Discovery

Mathias Schreiner, Ole Winther, Simon Olsson

Computing properties of molecular systems rely on estimating expectations of the (unnormalized) Boltzmann distribution. Molecular dynamics (MD) is a broadly adopted technique to approximate such quantities. However, stable simulations rely on very small integration time-steps ($10^{-15}\,\mathrm{s}$), whereas convergence of some moments, e.g. binding free energy or rates, might rely on sampling processes on time-scales as long as $10^{-1}\, \mathrm{s}$, and these simulations must be repeated for every molecular system independently. Here, we present Implicit Transfer Operator (ITO) Learning, a framework to learn surrogates of the simulation process with multiple time-resolutions. We implement ITO with denoising diffusion probabilistic models with a new SE(3) equivariant architecture and show the resulting models can generate self-consistent stochastic dynamics across multiple time-scales, even when the system is only partially observed. Finally, we present a coarse-grained CG-SE3-ITO model which can quantitatively model all-atom molecular dynamics using only coarse molecular representations. As such, ITO provides an important step towards multiple time- and space-resolution acceleration of MD. Code is available at \href{https://github.com/olsson-group/ito}{https://github.com/olsson-group/ito}.

Theory/Online Learning and Bandits

Zhiyu Zhang, Ashok Cutkosky, Yannis Paschalidis

Motivated by the challenge of nonstationarity in sequential decision making, we study Online Convex Optimization (OCO) under the coupling of two problem structures: the domain is unbounded, and the comparator sequence $u_1,\ldots,u_T$ is arbitrarily time-varying. As no algorithm can guarantee low regret simultaneously against all comparator sequences, handling this setting requires moving from minimax optimality to comparator adaptivity. That is, sensible regret bounds should depend on certain complexity measures of the comparator relative to one's prior knowledge. This paper achieves a new type of such adaptive regret bounds leveraging a sparse coding framework. The complexity of the comparator is measured by its energy and its sparsity on a user-specified dictionary, which offers considerable versatility. For example, equipped with a wavelet dictionary, our framework improves the state-of-the-art bound (Jacobsen & Cutkosky, 2022) by adapting to both ($i$) the magnitude of the comparator average $||\bar u||=||\sum_{t=1}^Tu_t/T||$, rather than the maximum $\max_t||u_t||$; and ($ii$) the comparator variability $\sum_{t=1}^T||u_t-\bar u||$, rather than the uncentered sum $\sum_{t=1}^T||u_t||$. Furthermore, our proof is simpler due to decoupling function approximation from regret minimization.

Applications/Neuroscience, Cognitive Science

Dayong Ren, Zhe Ma, Yuanpei Chen, Weihang Peng, Xiaode Liu, Yuhan Zhang, Yufei Guo

Recently, Spiking Neural Networks (SNNs), enjoying extreme energy efficiency, have drawn much research attention on 2D visual recognition and shown gradually increasing application potential. However, it still remains underexplored whether SNNs can be generalized to 3D recognition. To this end, we present Spiking PointNet in the paper, the first spiking neural model for efficient deep learning on point clouds. We discover that the two huge obstacles limiting the application of SNNs in point clouds are: the intrinsic optimization obstacle of SNNs that impedes the training of a big spiking model with large time steps, and the expensive memory and computation cost of PointNet that makes training a big spiking point model unrealistic. To solve the problems simultaneously, we present a trained-less but learning-more paradigm for Spiking PointNet with theoretical justifications and in-depth experimental analysis. In specific, our Spiking PointNet is trained with only a single time step but can obtain better performance with multiple time steps inference, compared to the one trained directly with multiple time steps. We conduct various experiments on ModelNet10, ModelNet40 to demonstrate the effectiveness of Sipiking PointNet. Notably, our Spiking PointNet even can outperform its ANN counterpart, which is rare in the SNN field thus providing a potential research direction for the following work. Moreover, Spiking PointNet shows impressive speedup and storage saving in the training phase. Our code is open-sourced at https://github.com/DayongRen/Spiking-PointNet.

Applications/Neuroscience, Cognitive Science

Man Yao, JiaKui Hu, Zhaokun Zhou, Li Yuan, Yonghong Tian, Bo Xu, Guoqi Li

Spiking Neural Networks (SNNs) provide an energy-efficient deep learning option due to their unique spike-based event-driven (i.e., spike-driven) paradigm. In this paper, we incorporate the spike-driven paradigm into Transformer by the proposed Spike-driven Transformer with four unique properties: (1) Event-driven, no calculation is triggered when the input of Transformer is zero; (2) Binary spike communication, all matrix multiplications associated with the spike matrix can be transformed into sparse additions; (3) Self-attention with linear complexity at both token and channel dimensions; (4) The operations between spike-form Query, Key, and Value are mask and addition. Together, there are only sparse addition operations in the Spike-driven Transformer. To this end, we design a novel Spike-Driven Self-Attention (SDSA), which exploits only mask and addition operations without any multiplication, and thus having up to $87.2\times$ lower computation energy than vanilla self-attention. Especially in SDSA, the matrix multiplication between Query, Key, and Value is designed as the mask operation. In addition, we rearrange all residual connections in the vanilla Transformer before the activation functions to ensure that all neurons transmit binary spike signals. It is shown that the Spike-driven Transformer can achieve 77.1\% top-1 accuracy on ImageNet-1K, which is the state-of-the-art result in the SNN field.

Adam Cobb, Anirban Roy, Daniel Elenius, Frederick Heim, Brian Swenson, Sydney Whittington, James Walker, Theodore Bapty, Joseph Hite, Karthik Ramani 等

We present AircraftVerse, a publicly available aerial vehicle design dataset. Aircraft design encompasses different physics domains and, hence, multiple modalities of representation. The evaluation of these designs requires the use of scientific analytical and simulation models ranging from computer-aided design tools for structural and manufacturing analysis, computational fluid dynamics tools for drag and lift computation, battery models for energy estimation, and simulation models for flight control and dynamics. AircraftVerse contains $27{,}714$ diverse air vehicle designs - the largest corpus of designs with this level of complexity. Each design comprises the following artifacts: a symbolic design tree describing topology, propulsion subsystem, battery subsystem, and other design details; a STandard for the Exchange of Product (STEP) model data; a 3D CAD design using a stereolithography (STL) file format; a 3D point cloud for the shape of the design; and evaluation results from high fidelity state-of-the-art physics models that characterize performance metrics such as maximum flight distance and hover-time. We also present baseline surrogate models that use different modalities of design representation to predict design performance metrics, which we provide as part of our dataset release. Finally, we discuss the potential impact of this dataset on the use of learning in aircraft design, and more generally, in the emerging field of deep learning for scientific design. AircraftVerse is accompanied by a datasheet as suggested in the recent literature, and it is released under Creative Commons Attribution-ShareAlike (CC BY-SA) license. The dataset with baseline models are hosted at http://doi.org/10.5281/zenodo.6525446, code at https://github.com/SRI-CSL/AircraftVerse, and the dataset description at https://uavdesignverse.onrender.com/.

Deep Learning/Generative Models and Autoencoders

Chen-Hao Chao, Wei-Fang Sun, Yen-Chang Hsu, Zsolt Kira, Chun-Yi Lee

In this paper, we establish a connection between the parameterization of flow-based and energy-based generative models, and present a new flow-based modeling approach called energy-based normalizing flow (EBFlow). We demonstrate that by optimizing EBFlow with score-matching objectives, the computation of Jacobian determinants for linear transformations can be entirely bypassed. This feature enables the use of arbitrary linear layers in the construction of flow-based models without increasing the computational time complexity of each training iteration from $\mathcal{O}(D^2L)$ to $\mathcal{O}(D^3L)$ for an $L$-layered model that accepts $D$-dimensional inputs. This makes the training of EBFlow more efficient than the commonly-adopted maximum likelihood training method. In addition to the reduction in runtime, we enhance the training stability and empirical performance of EBFlow through a number of techniques developed based on our analysis of the score-matching methods. The experimental results demonstrate that our approach achieves a significant speedup compared to maximum likelihood estimation while outperforming prior methods with a noticeable margin in terms of negative log-likelihood (NLL).

Applications/Chemistry and Drug Discovery

Geonu Kim, Byunggook Na, Gunhee Kim, Hyuntae Cho, Seungjin Kang, Hee Sun Lee, Saerom Choi, Heejae Kim, Seungwon Lee, Yongdeok Kim

As semiconductor devices become miniaturized and their structures become more complex, there is a growing need for large-scale atomic-level simulations as a less costly alternative to the trial-and-error approach during development.Although machine learning force fields (MLFFs) can meet the accuracy and scale requirements for such simulations, there are no open-access benchmarks for semiconductor materials.Hence, this study presents a comprehensive benchmark suite that consists of two semiconductor material datasets and ten MLFF models with six evaluation metrics. We select two important semiconductor thin-film materials silicon nitride and hafnium oxide, and generate their datasets using computationally expensive density functional theory simulations under various scenarios at a cost of 2.6k GPU days.Additionally, we provide a variety of architectures as baselines: descriptor-based fully connected neural networks and graph neural networks with rotational invariant or equivariant features.We assess not only the accuracy of energy and force predictions but also five additional simulation indicators to determine the practical applicability of MLFF models in molecular dynamics simulations.To facilitate further research, our benchmark suite is available at https://github.com/SAITPublic/MLFF-Framework.

Reinforcement Learning/Multi-agent

Pascal Leroy, Pablo G. Morato, Jonathan Pisane, Athanasios Kolios, Damien Ernst

We introduce IMP-MARL, an open-source suite of multi-agent reinforcement learning (MARL) environments for large-scale Infrastructure Management Planning (IMP), offering a platform for benchmarking the scalability of cooperative MARL methods in real-world engineering applications.In IMP, a multi-component engineering system is subject to a risk of failure due to its components' damage condition.Specifically, each agent plans inspections and repairs for a specific system component, aiming to minimise maintenance costs while cooperating to minimise system failure risk.With IMP-MARL, we release several environments including one related to offshore wind structural systems, in an effort to meet today's needs to improve management strategies to support sustainable and reliable energy systems.Supported by IMP practical engineering environments featuring up to 100 agents, we conduct a benchmark campaign, where the scalability and performance of state-of-the-art cooperative MARL methods are compared against expert-based heuristic policies. The results reveal that centralised training with decentralised execution methods scale better with the number of agents than fully centralised or decentralised RL approaches, while also outperforming expert-based heuristic policies in most IMP environments.Based on our findings, we additionally outline remaining cooperation and scalability challenges that future MARL methods should still address.Through IMP-MARL, we encourage the implementation of new environments and the further development of MARL methods.