ICLR 2025 论文列表

Continuous dynamical systems are cornerstones of many scientific and engineering disciplines. While machine learning offers powerful tools to model these systems from trajectory data, challenges arise when these trajectories are captured as images, resulting in pixel-level observations that are discrete in nature. Consequently, a naive application of a convolutional autoencoder can result in latent coordinates that are discontinuous in time. To resolve this, we propose continuity-preserving convolutional autoencoders (CpAEs) to learn continuous latent states and their corresponding continuous latent dynamical models from discrete image frames. We present a mathematical formulation for learning dynamics from image frames, which illustrates issues with previous approaches and motivates our methodology based on promoting the continuity of convolution filters, thereby preserving the continuity of the latent states. This approach enables CpAEs to produce latent states that evolve continuously with the underlying dynamics, leading to more accurate latent dynamical models. Extensive experiments across various scenarios demonstrate the effectiveness of CpAEs.

While continuous diffusion models excel in modeling continuous distributions, their application to categorical data has been less effective. Recent work has shown that ratio-matching through *score-entropy* within a continuous-time discrete Markov chain (CTMC) framework serves as a competitive alternative to autoregressive models in language modeling. To enhance this framework, we first introduce three new theorems concerning the KL divergence between the data and learned distribution. Our results serve as the discrete counterpart to those established for continuous diffusion models and allow us to derive an improved upper bound of the perplexity. Second, we empirically show that ratio-matching performed by minimizing the *denoising cross-entropy* between the clean and corrupted data enables models to outperform those utilizing score-entropy with up to 10\% lower perplexity/generative-perplexity, and 15\% faster training steps. To further support our findings, we introduce and evaluate a novel CTMC transition-rate matrix that allows prediction refinement, and derive the analytic expression for its matrix exponential which facilitates the computation of conditional ratios thus enabling efficient training and generation.

Brain-inspired Spiking Neural Networks (SNNs) leverage sparse spikes to encode information and operate in an asynchronous event-driven manner, offering a highly energy-efficient paradigm for machine intelligence. However, the current SNN community focuses primarily on performance improvement by developing large-scale models, which limits the applicability of SNNs in resource-limited edge devices. In this paper, we propose a hardware-friendly and lightweight SNN, aimed at effectively deploying high-performance SNN in resource-limited scenarios. Specifically, we first develop a baseline model that integrates uniform quantization and structured pruning, called QP-SNN baseline. While this baseline significantly reduces storage demands and computational costs, it suffers from performance decline. To address this, we conduct an in-depth analysis of the challenges in quantization and pruning that lead to performance degradation and propose solutions to enhance the baseline's performance. For weight quantization, we propose a weight rescaling strategy that utilizes bit width more effectively to enhance the model's representation capability. For structured pruning, we propose a novel pruning criterion using the singular value of spatiotemporal spike activities to enable more accurate removal of redundant kernels. Extensive experiments demonstrate that integrating two proposed methods into the baseline allows QP-SNN to achieve state-of-the-art performance and efficiency, underscoring its potential for enhancing SNN deployment in edge intelligence computing.

We consider the problem of predicting gene expressions from DNA sequences. A key challenge of this task is to find the regulatory elements that control gene expressions. Here, we introduce Seq2Exp, a Sequence to Expression network explicitly designed to discover and extract regulatory elements that drive target gene expression, enhancing the accuracy of the gene expression prediction. Our approach captures the causal relationship between epigenomic signals, DNA sequences and their associated regulatory elements. Specifically, we propose to decompose the epigenomic signals and the DNA sequence conditioned on the causal active regulatory elements, and apply an information bottleneck with the Beta distribution to combine their effects while filtering out non-causal components. Our experiments demonstrate that Seq2Exp outperforms existing baselines in gene expression prediction tasks and discovers influential regions compared to commonly used statistical methods for peak detection such as MACS3. The source code is released as part of the AIRS library (https://github.com/divelab/AIRS/).

With the recent development and advancement of Transformer and MLP architectures, significant strides have been made in time series analysis. Conversely, the performance of Convolutional Neural Networks (CNNs) in time series analysis has fallen short of expectations, diminishing their potential for future applications. Our research aims to enhance the representational capacity of Convolutional Neural Networks (CNNs) in time series analysis by introducing novel perspectives and design innovations. To be specific, We introduce a novel time series reshaping technique that considers the inter-patch, intra-patch, and cross-variable dimensions. Consequently, we propose TVNet, a dynamic convolutional network leveraging a 3D perspective to employ time series analysis. TVNet retains the computational efficiency of CNNs and achieves state-of-the-art results in five key time series analysis tasks, offering a superior balance of efficiency and performance over the state-of-the-art Transformer-based and MLP-based models. Additionally, our findings suggest that TVNet exhibits enhanced transferability and robustness. Therefore, it provides a new perspective for applying CNN in advanced time series analysis tasks.

Messenger RNA (mRNA) plays a crucial role in protein synthesis, with its codon structure directly impacting biological properties. While Language Models (LMs) have shown promise in analyzing biological sequences, existing approaches fail to account for the hierarchical nature of mRNA's codon structure. We introduce Hierarchical Encoding for mRNA Language Modeling (HELM), a novel pre-training strategy that incorporates codon-level hierarchical structure into language model training. HELM modulates the loss function based on codon synonymity, aligning the model's learning process with the biological reality of mRNA sequences. We evaluate HELM on diverse mRNA datasets and tasks, demonstrating that HELM outperforms standard language model pre-training as well as existing foundation model baselines on six diverse downstream property prediction tasks and an antibody region annotation tasks on average by around 8%. Additionally, HELM enhances the generative capabilities of language model, producing diverse mRNA sequences that better align with the underlying true data distribution compared to non-hierarchical baselines.

Recent advancements in operator-type neural networks have shown promising results in approximating the solutions of spatiotemporal Partial Differential Equations (PDEs). However, these neural networks often entail considerable training expenses, and may not always achieve the desired accuracy required in many scientific and engineering disciplines. In this paper, we propose a new learning framework to address these issues. A new spatiotemporal adaptation is proposed to generalize any Fourier Neural Operator (FNO) variant to learn maps between Bochner spaces, which can perform an arbitrary-length temporal super-resolution for the first time. To better exploit this capacity, a new paradigm is proposed to refine the commonly adopted end-to-end neural operator training and evaluations with the help from the wisdom from traditional numerical PDE theory and techniques. Specifically, in the learning problems for the turbulent flow modeled by the Navier-Stokes Equations (NSE), the proposed paradigm trains an FNO only for a few epochs. Then, only the newly proposed spatiotemporal spectral convolution layer is fine-tuned without the frequency truncation. The spectral fine-tuning loss function uses a negative Sobolev norm for the first time in operator learning, defined through a reliable functional-type a posteriori error estimator whose evaluation is exact thanks to the Parseval identity. Moreover, unlike the difficult nonconvex optimization problems in the end-to-end training, this fine-tuning loss is convex. Numerical experiments on commonly used NSE benchmarks demonstrate significant improvements in both computational efficiency and accuracy, compared to end-to-end evaluation and traditional numerical PDE solvers under certain conditions. The source code is publicly available at https://github.com/scaomath/torch-cfd.

Large language models (LLMs) are driving substantial advancements in software engineering, with successful applications like Copilot and Cursor transforming real-world development practices. However, current research predominantly focuses on the early stages of development, such as code generation, while overlooking the post-development phases that are crucial to user experience. To explore the potential of LLMs in this direction, we propose OpenRCA, a benchmark dataset and evaluation framework for assessing LLMs’ ability to identify the root cause of software failures. OpenRCA includes 335 failures from three enterprise software systems, along with over 68 GB of telemetry data (logs, metrics, and traces). Given a failure case and its associated telemetry, the LLM is tasked to identify the root cause that triggered the failure, requiring comprehension of software dependencies and reasoning over heterogeneous, long-context telemetry data. Our results show substantial room for improvement, as current models can only handle the simplest cases. Even with the specially designed RCA-agent, the best-performing model, Claude 3.5, solved only 11.34% failure cases. Our work paves the way for future research in this direction.

SMILES, a crucial textual representation of molecular structures, has garnered significant attention as a foundation for pre-trained language models (LMs). However, most existing pre-trained SMILES LMs focus solely on the single-token level supervision during pre-training, failing to fully leverage the substructural information of molecules. This limitation makes the pre-training task overly simplistic, preventing the models from capturing richer molecular semantic information. Moreover, during pre-training, these SMILES LMs only process corrupted SMILES inputs, never encountering any valid SMILES, which leads to a train-inference mismatch. To address these challenges, we propose SMI-Editor, a novel edit-based pre-trained SMILES LM. SMI-Editor disrupts substructures within a molecule at random and feeds the resulting SMILES back into the model, which then attempts to restore the original SMILES through an editing process. This approach not only introduces fragment-level training signals, but also enables the use of valid SMILES as inputs, allowing the model to learn how to reconstruct complete molecules from these incomplete structures. As a result, the model demonstrates improved scalability and an enhanced ability to capture fragment-level molecular information. Experimental results show that SMI-Editor achieves state-of-the-art performance across multiple downstream molecular tasks, and even outperforming several 3D molecular representation models.

Generative modeling of crystal data distribution is an important yet challenging task due to the unique periodic physical symmetry of crystals. Diffusion-based methods have shown early promise in modeling crystal distribution. More recently, Bayesian Flow Networks were introduced to aggregate noisy latent variables, resulting in a variance-reduced parameter space that has been shown to be advantageous for modeling Euclidean data distributions with structural constraints (Song, et al.,2023). Inspired by this, we seek to unlock its potential for modeling variables located in non-Euclidean manifolds e.g. those within crystal structures, by overcoming challenging theoretical issues. We introduce CrysBFN, a novel crystal generation method by proposing a periodic Bayesian flow, which essentially differs from the original Gaussian-based BFN by exhibiting non-monotonic entropy dynamics. To successfully realize the concept of periodic Bayesian flow, CrysBFN integrates a new entropy conditioning mechanism and empirically demonstrates its significance compared to time-conditioning. Extensive experiments over both crystal ab initio generation and crystal structure prediction tasks demonstrate the superiority of CrysBFN, which consistently achieves new state-of-the-art on all benchmarks. Surprisingly, we found that CrysBFN enjoys a significant improvement in sampling efficiency, e.g., 200x speedup (10 v.s. 2000 steps network forwards) compared with previous Diffusion-based methods on MP-20 dataset.

Analyzing volumetric data with rotational invariance or equivariance is currently an active research topic. Existing deep-learning approaches utilize either group convolutional networks limited to discrete rotations or steerable convolutional networks with constrained filter structures. This work proposes a novel equivariant neural network architecture that achieves analytical Equivariance to Local Pattern Orientation on the continuous SO(3) group while allowing unconstrained trainable filters - EquiLoPO Network. Our key innovations are a group convolutional operation leveraging irreducible representations as the Fourier basis and a local activation function in the SO(3) space that provides a well-defined mapping from input to output functions, preserving equivariance. By integrating these operations into a ResNet-style architecture, we propose a model that overcomes the limitations of prior methods. A comprehensive evaluation on diverse 3D medical imaging datasets from MedMNIST3D demonstrates the effectiveness of our approach, which consistently outperforms state of the art. This work suggests the benefits of true rotational equivariance on SO(3) and flexible unconstrained filters enabled by the local activation function, providing a flexible framework for equivariant deep learning on volumetric data with potential applications across domains. Our code is publicly available at https://gricad-gitlab.univ-grenoble-alpes.fr/GruLab/ILPO/-/tree/main/EquiLoPO.

Articulated object manipulation is a critical capability for robots to perform various tasks in real-world scenarios. Composed of multiple parts connected by joints, articulated objects are endowed with diverse functional mechanisms through complex relative motions. For example, a safe consists of a door, a handle, and a lock, where the door can only be opened when the latch is unlocked. The internal structure, such as the state of a lock or joint angle constraints, cannot be directly observed from visual observation. Consequently, successful manipulation of these objects requires adaptive adjustment based on trial and error rather than a one-time visual inference. However, previous datasets and simulation environments for articulated objects have primarily focused on simple manipulation mechanisms where the complete manipulation process can be inferred from the object's appearance. To enhance the diversity and complexity of adaptive manipulation mechanisms, we build a novel articulated object manipulation environment and equip it with 9 categories of objects. Based on the environment and objects, we further propose an adaptive demonstration collection and 3D visual diffusion-based imitation learning pipeline that learns the adaptive manipulation policy. The effectiveness of our designs and proposed method is validated through both simulation and real-world experiments.

We present Hybrid-Autoregressive INference TrANsducers (HAINAN), a novel architecture for speech recognition that extends the Token-and-Duration Transducer (TDT) model. Trained with randomly masked predictor network outputs, HAINAN supports both autoregressive inference with all network components and non-autoregressive inference without the predictor. Additionally, we propose a novel semi-autoregressive inference method that first generates an initial hypothesis using non-autoregressive inference, followed by refinement steps where each token prediction is regenerated using parallelized autoregression on the initial hypothesis. Experiments on multiple datasets across different languages demonstrate that HAINAN achieves efficiency parity with CTC in non-autoregressive mode and with TDT in autoregressive mode. In terms of accuracy, autoregressive HAINAN achieves parity with TDT and RNN-T, while non-autoregressive HAINAN significantly outperforms CTC. Semi-autoregressive inference further enhances the model's accuracy with minimal computational overhead, and even outperforms TDT results in some cases. These results highlight HAINAN's flexibility in balancing accuracy and speed, positioning it as a strong candidate for real-world speech recognition applications.

Cognition arises from the coordinated interaction of brain regions with distinct computational roles. Despite improvements in our ability to extract the dynamics underlying circuit computation from population activity recorded in individual areas, understanding how multiple areas jointly support distributed computation remains a challenge. As part of this effort, we propose a multi-region neural dynamics model composed of two building blocks: _i)_ within-region (potentially driven) nonlinear dynamics and _ii)_ communication channels between regions, parameterized through their impulse response. Together, these choices make it possible to learn nonlinear neural population dynamics and understand the flow of information between regions by drawing from the rich literature of linear systems theory. We develop a state noise inversion free variational filtering and learning algorithm for our model and show, through neuroscientifically inspired numerical experiments, how the proposed model can reveal interpretable characterizations of the local computations within and the flow of information between neural populations. We further validate the efficacy of our approach using simultaneous population recordings from areas V1 and V2.

Deep neural networks have achieved remarkable accomplishments in practice. The success of these networks hinges on effective initialization methods, which are vital for ensuring stable and rapid convergence during training. Recently, initialization methods that maintain identity transition within layers have shown good efficiency in network training. These techniques (e.g., Fixup) set specific weights to zero to achieve identity control. However, settings of remaining weight (e.g., Fixup uses random values to initialize non-zero weights) will affect the inductive bias that is achieved only by a zero weight, which may be harmful to training. Addressing this concern, we introduce fully identical initialization (IDInit), a novel method that preserves identity in both the main and sub-stem layers of residual networks. IDInit employs a padded identity-like matrix to overcome rank constraints in non-square weight matrices. Furthermore, we show the convergence problem of an identity matrix can be solved by stochastic gradient descent. Additionally, we enhance the universality of IDInit by processing higher-order weights and addressing dead neuron problems. IDInit is a straightforward yet effective initialization method, with improved convergence, stability, and performance across various settings, including large-scale datasets and deep models.

Generative machine learning models are increasingly being used to design novel proteins. However, their major limitation is the inability to account for protein flexibility, a property crucial for protein function. Learning to engineer flexibility is difficult because the relevant data is scarce, heterogeneous, and costly to obtain using computational and experimental methods. Our contributions are three-fold. First, we perform a comprehensive comparison of methods for evaluating protein flexibility and identify relevant data for learning. Second, we overcome the data scarcity issue by leveraging a pre-trained protein language model. We design and train flexibility predictors utilizing either only sequential or both sequential and structural information on the input. Third, we introduce a method for fine-tuning a protein inverse folding model to make it steerable toward desired flexibility at specified regions. We demonstrate that our method Flexpert enables guidance of inverse folding models toward increased flexibility. This opens up a transformative possibility of engineering protein flexibility.

Advances in machine learning research drive progress in real-world applications. To ensure this progress, it is important to understand the potential pitfalls on the way from a novel method's success on academic benchmarks to its practical deployment. In this work, we analyze existing tabular deep learning benchmarks and find two common characteristics of tabular data in typical industrial applications that are underrepresented in the datasets usually used for evaluation in the literature. First, in real-world deployment scenarios, distribution of data often changes over time. To account for this distribution drift, time-based train/test splits should be used in evaluation. However, existing academic tabular datasets often lack timestamp metadata to enable such evaluation. Second, a considerable portion of datasets in production settings stem from extensive data acquisition and feature engineering pipelines. This can have an impact on the absolute and relative number of predictive, uninformative, and correlated features compared to academic datasets. In this work, we aim to understand how recent research advances in tabular deep learning transfer to these underrepresented conditions. To this end, we introduce TabReD -- a collection of eight industry-grade tabular datasets. We reassess a large number of tabular ML models and techniques on TabReD. We demonstrate that evaluation on both time-based data splits and richer feature sets leads to different methods ranking, compared to evaluation on random splits and smaller number of features, which are common in academic benchmarks. Furthermore, simple MLP-like architectures and GBDT show the best results on the TabReD datasets, while other methods are less effective in the new setting.

Prior work has offered evidence for functional localization in the brain; different anatomical regions preferentially activate for certain types of visual input. For example, the fusiform face area preferentially activates for visual stimuli that include a face. However, the spectrum of visual semantics is extensive, and only a few semantically-tuned patches of cortex have so far been identified in the human brain. Using a multimodal (natural language and image) neural network architecture (CLIP, \cite{CLIP}, we train a highly accurate contrastive model that maps brain responses during naturalistic image viewing to CLIP embeddings. We then use a novel adaptation of the DBSCAN clustering algorithm to cluster the parameters of these participant-specific contrastive models. This reveals what we call Shared Decodable Concepts (SDCs): clusters in CLIP space that are decodable from common sets of voxels across multiple participants. Examining the images most and least associated with each SDC cluster gives us additional insight into the semantic properties of each SDC. We note SDCs for previously reported visual features (e.g. orientation tuning in early visual cortex) as well as visual semantic concepts such as faces, places and bodies. In cases where our method finds multiple clusters for a visuo-semantic concept, the least associated images allow us to dissociate between confounding factors. For example, we discovered two clusters of food images, one driven by color, the other by shape. We also uncover previously unreported areas with visuo-semantic sensitivity such as regions of extrastriate body area (EBA) tuned for legs/hands and sensitivity to numerosity in right intraparietal sulcus, sensitivity associated with visual perspective (close/far) and more. Thus, our contrastive-learning methodology better characterizes new and existing visuo-semantic representations in the brain by leveraging multimodal neural network representations and a novel adaptation of clustering algorithms.

In this paper, we investigate the latent geometry of generative diffusion models under the manifold hypothesis. For this purpose, we analyze the spectrum of eigenvalues (and singular values) of the Jacobian of the score function, whose discontinuities (gaps) reveal the presence and dimensionality of distinct sub-manifolds. Using a statistical physics approach, we derive the spectral distributions and formulas for the spectral gaps under several distributional assumptions, and we compare these theoretical predictions with the spectra estimated from trained networks. Our analysis reveals the existence of three distinct qualitative phases during the generative process: a trivial phase; a manifold coverage phase where the diffusion process fits the distribution internal to the manifold; a consolidation phase where the score becomes orthogonal to the manifold and all particles are projected on the support of the data. This `division of labor' between different timescales provides an elegant explanation of why generative diffusion models are not affected by the manifold overfitting phenomenon that plagues likelihood-based models, since the internal distribution and the manifold geometry are produced at different time points during generation.