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Deep Learning · Sequential Models, Time series

Yu Chen, Nathalia Céspedes, Payam Barnaghi

Time-series forecasting is crucial across various domains, including finance, healthcare, and energy. Transformer models, originally developed for natural language processing, have demonstrated significant potential in addressing challenges associated with time-series data. These models utilize different tokenization strategies, point-wise, patch-wise, and variate-wise, to represent time-series data, each resulting in different scope of attention maps. Despite the emergence of sophisticated architectures, simpler transformers consistently outperform their more complex counterparts in widely used benchmarks. This study examines why point-wise transformers are generally less effective, why intra- and inter-variate attention mechanisms yield similar outcomes, and which architectural components drive the success of simpler models. By analyzing mutual information and evaluating models on synthetic datasets, we demonstrate that intra-variate dependencies are the primary contributors to prediction performance on benchmarks, while inter-variate dependencies have a minor impact. Additionally, techniques such as Z-score normalization and skip connections are also crucial. However, these results are largely influenced by the self-dependent and stationary nature of benchmark datasets. By validating our findings on real-world healthcare data, we provide insights for designing more effective transformers for practical applications.

Social Aspects · Security

Cheng Zhang, Hanna Foerster, Robert Mullins, Yiren Zhao, Ilia Shumailov

It is now a common business practice to buy access to large language model (LLM) inference rather than self-host, because of significant upfront hardware infrastructure and energy costs. However, as a buyer, there is no mechanism to verify the authenticity of the advertised service including the serving hardware platform, e.g. that it is actually being served using an NVIDIA H100. Furthermore, there are reports suggesting that model providers may deliver models that differ slightly from the advertised ones, often to make them run on less expensive hardware. That way, a client pays premium for a capable model access on more expensive hardware, yet ends up being served by a (potentially less capable) cheaper model on cheaper hardware. In this paper we introduce ***hardware and software platform inference (HSPI)*** -- a method for identifying the underlying GPU architecture and software stack of a (black-box) machine learning model solely based on its input-output behavior. Our method leverages the inherent differences of various GPU architectures and compilers to distinguish between different GPU types and software stacks. By analyzing the numerical patterns in the model's outputs, we propose a classification framework capable of accurately identifying the GPU used for model inference as well as the underlying software configuration. Our findings demonstrate the feasibility of inferring GPU type from black-box models. We evaluate HSPI against models served on different real hardware and find that in a white-box setting we can distinguish between different GPUs with between 83.9% and 100% accuracy. Even in a black-box setting we are able to achieve results that are up to three times higher than random guess accuracy.

Deep Learning · Sequential Models, Time series

Jiaqi Yan, Changping Wang, De Ma, Huajin Tang, Qian Zheng, Gang Pan

Spiking Neural Networks (SNNs) are considered promising energy-efficient models due to their dynamic capability to process spatial-temporal spike information. Existing work has demonstrated that SNNs exhibit temporal heterogeneity, which leads to diverse outputs of SNNs at different time steps and has the potential to enhance their performance. Although SNNs obtained by direct training methods achieve state-of-the-art performance, current methods introduce limited temporal heterogeneity through the dynamics of spiking neurons or network structures. They lack the improvement of temporal heterogeneity through the lens of the gradient. In this paper, we first conclude that the diversity of the temporal logit gradients in current methods is limited. This leads to insufficient temporal heterogeneity and results in temporally miscalibrated SNNs with degraded performance. Based on the above analysis, we propose a Temporal Model Calibration (TMC) method, which can be seen as a logit gradient rescaling mechanism across time steps. Experimental results show that our method can improve the temporal logit gradient diversity and generate temporally calibrated SNNs with enhanced performance. In particular, our method achieves state-of-the-art accuracy on ImageNet, DVSCIFAR10, and N-Caltech101. Codes are available at https://github.com/zju-bmi-lab/TMC.

Applications · Neuroscience, Cognitive Science

Lusen Zhao, Zihan Huang, Ding Jianhao, Zhaofei Yu

ANN-to-SNN conversion has emerged as a key approach to train Spiking Neural Networks (SNNs), particularly for Transformer architectures, as it maps pre-trained ANN parameters to SNN equivalents without requiring retraining, thereby preserving ANN accuracy while eliminating training costs. Among various coding methods used in ANN-to-SNN conversion, time-to-first-spike (TTFS) coding, which allows each neuron to at most one spike, offers significantly lower energy consumption. However, while previous TTFS-based SNNs have achieved comparable performance with convolutional ANNs, the attention mechanism and nonlinear layers in Transformer architectures remains a challenge by existing SNNs with TTFS coding. This paper proposes a new neuron structure for TTFS coding that expands its representational range and enhances the capability to process nonlinear functions, along with detailed designs of nonlinear neurons for different layers in Transformer. Experimental results on different models demonstrate that our proposed method can achieve high accuracy with significantly lower energy consumption. To the best of our knowledge, this is the first work to focus on converting Transformer to SNN with TTFS coding.

General Machine Learning · Representation Learning

Ziang Zhou, Zhihao DING, Jieming Shi, Qing Li, Shiqi Shen

Graph Neural Networks (GNNs) are pivotal in graph-based learning, particularly excelling in node classification. However, their scalability is hindered by the need for multi-hop data during inference, limiting their application in latency-sensitive scenarios. Recent efforts to distill GNNs into multi-layer perceptrons (MLPs) for faster inference often underutilize the layer-level insights of GNNs. In this paper, we present TINED, a novel approach that distills GNNs to MLPs on a layer-by-layer basis using Teacher Injection and Dirichlet Energy Distillation techniques.We focus on two key operations in GNN layers: feature transformation (FT) and graph propagation (GP). We recognize that FT is computationally equivalent to a fully-connected (FC) layer in MLPs. Thus, we propose directly transferring teacher parameters from an FT in a GNN to an FC layer in the student MLP, enhanced by fine-tuning. In TINED, the FC layers in an MLP replicate the sequence of FTs and GPs in the GNN. We also establish a theoretical bound for GP approximation.Furthermore, we note that FT and GP operations in GNN layers often exhibit opposing smoothing effects: GP is aggressive, while FT is conservative. Using Dirichlet energy, we develop a DE ratio to measure these effects and propose Dirichlet Energy Distillation to convey these characteristics from GNN layers to MLP layers. Extensive experiments show that TINED outperforms GNNs and leading distillation methods across various settings and seven datasets. Source code are available at https://github.com/scottjiao/TINED_ICML25/.

Applications · Neuroscience, Cognitive Science

Qi Xu, Junyang Zhu, Dongdong Zhou, Hao Chen, Yang Liu, Jiangrong Shen, Qiang Zhang

Deep neural networks (DNNs) excel in computer vision tasks, especially, few-shot learning (FSL), which is increasingly important for generalizing from limited examples. However, DNNs are computationally expensive with scalability issues in real world. Spiking Neural Networks (SNNs), with their event-driven nature and low energy consumption, are particularly efficient in processing sparse and dynamic data, though they still encounter difficulties in capturing complex spatiotemporal features and performing accurate cross-class comparisons. To further enhance the performance and efficiency of SNNs in few-shot learning, we propose a few-shot learning framework based on SNNs, which combines a self-feature extractor module and a cross-feature contrastive module to refine feature representation and reduce power consumption. We apply the combination of temporal efficient training loss and InfoNCE loss to optimize the temporal dynamics of spike trains and enhance the discriminative power. Experimental results show that the proposed FSL-SNN significantly improves the classification performance on the neuromorphic dataset N-Omniglot, and also achieves competitive performance to ANNs on static datasets such as CUB and miniImageNet with low power consumption.

Deep Learning · Large Language Models

Peijie Dong, Zhenheng Tang, Xiang Liu, Lujun Li, Xiaowen Chu, Bo Li

Post-training compression reduces the computational and memory costs of large language models (LLMs), enabling resource-efficient deployment. However, existing compression benchmarks focus narrowly on language modeling (e.g., perplexity) and natural language understanding tasks (e.g., GLUE accuracy), ignoring the agentic capabilities—workflow, tool use/function call, long-context understanding and real-world application. We introduce the Agent Compression Benchmark (ACBench), the first comprehensive benchmark for evaluating how compression impacts LLMs' agentic abilities. ACBench spans (1) 12 tasks across 4 capabilities (e.g., WorfBench for workflow generation, Needle-in-Haystack for long-context retrieval), (2) 4-bit quantization (GPTQ, AWQ) and 50% pruning (Wanda, SparseGPT), and (3) 15 models, including small (Gemma-2B), standard (Qwen2.5-7B), and distilled reasoning LLMs (DeepSeek-R1-Distill). Our experiments reveal compression tradeoffs: 4-bit quantization preserves workflow generation and tool use (1%--3% drop) but degrades real-world application accuracy by 10%--15%. We introduce ERank, Top-k Ranking Correlation and Energy to systematize analysis. ACBench provides actionable insights for optimizing LLM compression in agentic scenarios, bridging the gap between algorithmic efficiency and real-world applicability.

Social Aspects · Privacy

Xiuyuan Wang, Chaochao Chen, Weiming Liu, Xinting Liao, Fan Wang, Xiaolin Zheng

With growing privacy concerns and the enforcement of data protection regulations, machine unlearning has emerged as a promising approach for removing the influence of forget data while maintaining model performance on retain data. However, most existing unlearning methods require access to the original training data, which is often impractical due to privacy policies, storage constraints, and other limitations. This gives rise to the challenging task of source-free unlearning, where unlearning must be accomplished without accessing the original training data. Few existing source-free unlearning methods rely on knowledge distillation and model retraining, which impose substantial computational costs. In this work, we propose the Data Synthesis-based Discrimination-Aware (DSDA) unlearning framework, which enables efficient source-free unlearning in two stages: (1) Accelerated Energy-Guided Data Synthesis (AEGDS), which employs Langevin dynamics to model the training data distribution while integrating Runge–Kutta methods and momentum to enhance efficiency. (2) Discrimination-Aware Multitask Optimization (DAMO), which refines the feature distribution of retain data and mitigates the gradient conflicts among multiple unlearning objectives. Extensive experiments on three benchmark datasets demonstrate that DSDA outperforms existing unlearning methods, validating its effectiveness and efficiency in source-free unlearning.

Optimization

Michael Sander, Vincent Roulet, Tianlin Liu, Mathieu Blondel

Energy-based models (EBMs) offer a flexible framework for parameterizing probability distributions using neural networks.However, learning EBMs by exact maximum likelihood estimation (MLE) is generally intractable, due to the need to compute the partition function.In this paper, we propose a novel min-min formulation for approximately learning probabilistic EBMs in combinatorially-large discrete spaces, such as sets or permutations. Our key idea is to jointly learn both an energy model and its log-partition, parameterized as a neural network. Our approach not only provides a novel tractable objective criterion to learn EBMs by stochastic gradient descent (without relying on MCMC), but also a novel means to estimate the log-partition function on unseen data points.On the theoretical side, we show that our approach recovers the optimal MLE solution when optimizing in the space of continuous functions.Furthermore, we show that our approach naturally extends to the broader family of Fenchel-Young losses, allowing us to obtainthe first tractable method for optimizing the sparsemax loss in combinatorially-large spaces.We demonstrate our approach on multilabel classification and label ranking.

General Machine Learning · Sequential, Network, and Time Series Modeling

Andrea Testa, Søren Hauberg, Tamim Asfour, Leonel Rozo

Accurately modeling and predicting complex dynamical systems, particularly those involving force exchange and dissipation, is crucial for applications ranging from fluid dynamics to robotics, but presents significant challenges due to the intricate interplay of geometric constraints and energy transfer. This paper introduces Geometric Contact Flows (GFC), a novel framework leveraging Riemannian and Contact geometry as inductive biases to learn such systems. GCF constructs a latent contact Hamiltonian model encoding desirable properties like stability or energy conservation. An ensemble of contactomorphisms then adapts this model to the target dynamics while preserving these properties. This ensemble allows for uncertainty-aware geodesics that attract the system’s behavior toward the data support, enabling robust generalization and adaptation to unseen scenarios. Experiments on learning dynamics for physical systems and for controlling robots on interaction tasks demonstrate the effectiveness of our approach.

Applications · Neuroscience, Cognitive Science

Yufei Guo, Yuhan Zhang, Zhou Jie, Xiaode Liu, Xin Tong, Yuanpei Chen, Weihang Peng, Zhe Ma

The Spiking Neural Network (SNN), a biologically inspired neural network infrastructure, has garnered significant attention recently. SNNs utilize binary spike activations for efficient information transmission, replacing multiplications with additions, thereby enhancing energy efficiency. However, binary spike activation maps often fail to capture sufficient data information, resulting in reduced accuracy.To address this challenge, we advocate reversing the bit of the weight and activation, called \textbf{ReverB}, inspired by recent findings that highlight greater accuracy degradation from quantizing activations compared to weights. Specifically, our method employs real-valued spike activations alongside binary weights in SNNs. This preserves the event-driven and multiplication-free advantages of standard SNNs while enhancing the information capacity of activations.Additionally, we introduce a trainable factor within binary weights to adaptively learn suitable weight amplitudes during training, thereby increasing network capacity. To maintain efficiency akin to vanilla \textbf{ReverB}, our trainable binary weight SNNs are converted back to standard form using a re-parameterization technique during inference.Extensive experiments across various network architectures and datasets, both static and dynamic, demonstrate that our approach consistently outperforms state-of-the-art methods.

Applications · Chemistry, Physics, and Earth Sciences

Yeyun Chen

Predicting the solvation free energy of molecules using graph neural networks holds significant potential for advancing drug discovery and the design of novel materials. While previous methods have demonstrated success on independent and identically distributed (IID) datasets, their performance in out-of-distribution (OOD) scenarios remains largely unexplored. We propose a novel Relational Invariant Learning framework (RILOOD) to enhance OOD generalization in solvation free energy prediction. RILOOD comprises three key components: (i) a mixup-based conditional modeling module that integrates diverse environments, (ii) a novel multi-granularity refinement strategy that extends beyond core substructures to enable context-aware representation learning for capturing multi-level interactions, and (iii) an invariant learning mechanism that identifies robust patterns generalizable to unseen environments. Extensive experiments demonstrate that RILOOD significantly outperforms state-of-the-art methods across various distribution shifts, highlighting its effectiveness in improving solvation free energy prediction under diverse conditions.

Applications · Chemistry, Physics, and Earth Sciences

Jeet Mohapatra, Nima Dehmamy, Csaba Both, Subhro Das, Tommi Jaakkola

We introduce a novel approach for discovering effective degrees of freedom (DOF) in molecular dynamics simulations by mapping the DOF to approximate symmetries of the energy landscape. Unlike most existing methods, we do not require trajectory data but instead rely on knowledge of the forcefield (energy function) around the initial state. We present a scalable symmetry loss function compatible with existing force-field frameworks and a Hessian-based method efficient for smaller systems. Our approach enables systematic exploration of conformational space by connecting structural dynamics to energy landscape symmetries. We apply our method to two systems, Alanine dipeptide and Chignolin, recovering their known important conformations. Our approach can prove useful for efficient exploration in molecular simulations with potential applications in protein folding and drug discovery.

Applications · Health / Medicine

Piyush Lalitkumar Tiwary, Kinjawl Bhattacharyya, Prathosh AP

Medical image segmentation models often struggle to generalize across different domains due to various reasons. Domain Generalization (DG) methods overcome this either through representation learning or data augmentation (DA). While representation learning methods seek domain-invariant features, they often rely on ad-hoc techniques and lack formal guarantees. DA methods, which enrich model representations through synthetic samples, have shown comparable or superior performance to representation learning approaches. We propose LangDAug, a novel **Lang**evin **D**ata **Aug**mentation for multi-source domain generalization in 2D medical image segmentation. LangDAug leverages Energy-Based Models (EBMs) trained via contrastive divergence to traverse between source domains, generating intermediate samples through Langevin dynamics. Theoretical analysis shows that LangDAug induces a regularization effect, and for GLMs, it upper-bounds the Rademacher complexity by the intrinsic dimensionality of the data manifold. Through extensive experiments on Fundus segmentation and 2D MRI prostate segmentation benchmarks, we show that LangDAug outperforms state-of-the-art domain generalization methods and effectively complements existing domain-randomization approaches. The codebase for our method is available at https://github.com/backpropagator/LangDAug.

Applications · Everything Else

Pratinav Seth, Michelle Lin, BREFO YAW, Jade Boutot, Mary Kang, David Rolnick

Millions of abandoned oil and gas wells are scattered across the world, leaching methane into the atmosphere and toxic compounds into the groundwater. Many of these locations are unknown, preventing the wells from being plugged and their polluting effects averted. Remote sensing is a relatively unexplored tool for pinpointing abandoned wells at scale. We introduce the first large-scale Benchmark dataset for this problem, leveraging high-resolution multi-spectral satellite imagery from Planet Labs. Our curated Dataset comprises over 213,000 wells (abandoned, suspended, and active) from Alberta, a region with especially high well density, sourced from the Alberta Energy Regulator and verified by domain experts. We evaluate baseline algorithms for well detection and segmentation, showing the promise of computer vision approaches but also significant room for improvement.

Matthew Smart, Alberto Bietti, Anirvan Sengupta

We introduce in-context denoising, a task that refines the connection between attention-based architectures and dense associative memory (DAM) networks, also known as modern Hopfield networks. Using a Bayesian framework, we show theoretically and empirically that certain restricted denoising problems can be solved optimally even by a single-layer transformer. We demonstrate that a trained attention layer processes each denoising prompt by performing a single gradient descent update on a context-aware DAM energy landscape, where context tokens serve as associative memories and the query token acts as an initial state. This one-step update yields better solutions than exact retrieval of either a context token or a spurious local minimum, providing a concrete example of DAM networks extending beyond the standard retrieval paradigm. Overall, this work solidifies the link between associative memory and attention mechanisms first identified by Ramsauer et al., and demonstrates the relevance of associative memory models in the study of in-context learning.

Deep Learning · Attention Mechanisms

Matthew Smart, Alberto Bietti, Anirvan Sengupta

We introduce in-context denoising, a task that refines the connection between attention-based architectures and dense associative memory (DAM) networks, also known as modern Hopfield networks. Using a Bayesian framework, we show theoretically and empirically that certain restricted denoising problems can be solved optimally even by a single-layer transformer. We demonstrate that a trained attention layer processes each denoising prompt by performing a single gradient descent update on a context-aware DAM energy landscape, where context tokens serve as associative memories and the query token acts as an initial state. This one-step update yields better solutions than exact retrieval of either a context token or a spurious local minimum, providing a concrete example of DAM networks extending beyond the standard retrieval paradigm. Overall, this work solidifies the link between associative memory and attention mechanisms first identified by Ramsauer et al., and demonstrates the relevance of associative memory models in the study of in-context learning.

Deep Learning · Generative Models and Autoencoders

RISHI JINKA, Venkata Sai Mothish Gonugunta, Deepak N. Subramani

Time-series forecasting finds application across domains such as finance, climate science, and energy systems. We introduce the Conditional Diffusion with Nonlinear Data Transformation Model (CN-Diff), a generative framework that employs novel nonlinear transformations and learnable conditions in the forward process for time series forecasting. A new loss formulation for training is proposed, along with a detailed derivation of both forward and reverse process. The new additions improve the diffusion model's capacity to capture complex time series patterns, thus simplifying the reverse process. Our novel condition facilitates learning an efficient prior distribution. This also reduces the gap between the true negative log-likelihood and its variational approximation. CN-Diff is shown to perform better than other leading time series models on nine real-world datasets. Ablation studies are conducted to elucidate the role of each component of CN-Diff.

Milong Ren, ZaiKai He, Haicang Zhang

Antibody design is crucial for developing therapies against diseases such as cancer and viral infections. Recent deep generative models have significantly advanced computational antibody design, particularly in enhancing binding affinity to target antigens. However, beyond binding affinity, antibodies should exhibit other favorable biophysical properties such as non-antigen binding specificity and low self-association, which are important for antibody developability and clinical safety. To address this challenge, we propose AbNovo, a framework that leverages constrained preference optimization for multi-objective antibody design. First, we pre-train an antigen-conditioned generative model for antibody structure and sequence co-design. Then, we fine-tune the model using binding affinity as a reward while enforcing explicit constraints on other biophysical properties. Specifically, we model the physical binding energy with continuous rewards rather than pairwise preferences and explore a primal-and-dual approach for constrained optimization. Additionally, we incorporate a structure-aware protein language model to mitigate the issue of limited training data. Evaluated on independent test sets, AbNovo outperforms existing methods in metrics of binding affinity such as Rosetta binding energy and evolutionary plausibility, as well as in metrics for other biophysical properties like stability and specificity.

Applications · Neuroscience, Cognitive Science

Vladimir Fanaskov, Ivan Oseledets

In ``Large Associative Memory Problem in Neurobiology and Machine Learning,'' Dmitry Krotov and John Hopfield introduced a general technique for the systematic construction of neural ordinary differential equations with non-increasing energy or Lyapunov function. We study this energy function and identify that it is vulnerable to the problem of dead neurons. Each point in the state space where the neuron dies is contained in a non-compact region with constant energy. In these flat regions, energy function alone does not completely determine all degrees of freedom and, as a consequence, can not be used to analyze stability or find steady states or basins of attraction. We perform a direct analysis of the dynamical system and show how to resolve problems caused by flat directions corresponding to dead neurons: (i) all information about the state vector at a fixed point can be extracted from the energy and Hessian matrix (of Lagrange function), (ii) it is enough to analyze stability in the range of Hessian matrix, (iii) if steady state touching flat region is stable the whole flat region is the basin of attraction. The analysis of the Hessian matrix can be complicated for realistic architectures, so we show that for a slightly altered dynamical system (with the same structure of steady states), one can derive a diverse family of Lyapunov functions that do not have flat regions corresponding to dead neurons. In addition, these energy functions allow one to use Lagrange functions with Hessian matrices that are not necessarily positive definite and even consider architectures with non-symmetric feedforward and feedback connections.