ICLR 2025 Papers

Sequence labeling problems arise in several real-world applications such as healthcare and robotics. In many such applications, sequence data are irregularly sampled and are of varying complexities. Recently, efforts have been made to develop neural ODE-based architectures to model the evolution of hidden states continuously in time, to address irregularly sampled sequence data. However, they assume a fixed architectural depth and limit their flexibility to adapt to data sets with varying complexities. We propose the neural wave equation, a novel deep learning method inspired by the wave equation, to address this through continuous modeling of depth. Neural Wave Equation models the evolution of hidden states continuously across time as well as depth by using a non-homogeneous wave equation parameterized by a neural network. Through d'Alembert's analytical solution of the wave equation, we also show that the neural wave equation provides denser connections across the hidden states, allowing for better modeling capability. We conduct experiments on several sequence labeling problems involving irregularly sampled sequence data and demonstrate the superior performance of the proposed neural wave equation model.

The site conditions that make astronomical observatories in space and on the ground so desirable---cold and dark---demand a physical remoteness that leads to limited data transmission capabilities. Such transmission limitations directly bottleneck the amount of data acquired and in an era of costly modern observatories, any improvements in lossless data compression has the potential scale to billions of dollars worth of additional science that can be accomplished on the same instrument. Traditional lossless methods for compressing astrophysical data are manually designed. Neural data compression, on the other hand, holds the promise of learning compression algorithms end-to-end from data and outperforming classical techniques by leveraging the unique spatial, temporal, and wavelength structures of astronomical images. This paper introduces [AstroCompress](https://huggingface.co/AstroCompress): a neural compression challenge for astrophysics data, featuring four new datasets (and one legacy dataset) with 16-bit unsigned integer imaging data in various modes: space-based, ground-based, multi-wavelength, and time-series imaging. We provide code to easily access the data and benchmark seven lossless compression methods (three neural and four non-neural, including all practical state-of-the-art algorithms). Our results on lossless compression indicate that lossless neural compression techniques can enhance data collection at observatories, and provide guidance on the adoption of neural compression in scientific applications. Though the scope of this paper is restricted to lossless compression, we also comment on the potential exploration of lossy compression methods in future studies.

While backpropagation effectively trains models, it presents challenges related to bio-plausibility, resulting in high memory demands and limited parallelism. Recently, Hinton (2022) proposed the Forward-Forward (FF) algorithm for high-parallel local updates. FF leverages squared sums as the local update target, termed goodness, and decouples goodness by normalizing the vector length to extract new features. However, this design encounters issues with feature scaling and deactivated neurons, limiting its application mainly to shallow networks. This paper proposes a novel goodness design utilizing **layer normalization** and **mean goodness** to overcome these challenges, demonstrating performance improvements even in 17-layer CNNs. Experiments on CIFAR-10, MNIST, and Fashion-MNIST show significant advantages over existing FF-based algorithms, highlighting the potential of FF in deep models. Furthermore, the model parallel strategy is proposed to achieve highly efficient training based on the property of local updates.

Air pollution significantly threatens human health and ecosystems, necessitating effective air quality prediction to inform public policy. Traditional approaches are generally categorized into physics-based and data-driven models. Physics-based models usually struggle with high computational demands and closed-system assumptions, while data-driven models may overlook essential physical dynamics, confusing the capturing of spatiotemporal correlations. Although some physics-guided approaches combine the strengths of both models, they often face a mismatch between explicit physical equations and implicit learned representations. To address these challenges, we propose Air-DualODE, a novel physics-guided approach that integrates dual branches of Neural ODEs for air quality prediction. The first branch applies open-system physical equations to capture spatiotemporal dependencies for learning physics dynamics, while the second branch identifies the dependencies not addressed by the first in a fully data-driven way. These dual representations are temporally aligned and fused to enhance prediction accuracy. Our experimental results demonstrate that Air-DualODE achieves state-of-the-art performance in predicting pollutant concentrations across various spatial scales, thereby offering a promising solution for real-world air quality challenges.

Large Language Models (LLMs) generating unsafe responses to toxic prompts is a significant issue in their applications. While various efforts aim to address this safety concern, previous approaches often demand substantial human data collection or rely on the less dependable option of using another LLM to generate corrective data. In this paper, we aim to take this problem and overcome limitations of requiring significant high-quality human data. Our method requires only a small set of unsafe responses to toxic prompts, easily obtained from the unsafe LLM itself. By employing a semantic cost combined with a negative Earth Mover Distance (EMD) loss, we guide the LLM away from generating unsafe responses. Additionally, we propose a novel lower bound for EMD loss, enabling more efficient optimization. Our results demonstrate superior performance and data efficiency compared to baselines, and we further examine the nuanced effects of over-alignment and potential degradation of language capabilities when using contrastive data.

We present RelCon, a novel self-supervised Relative Contrastive learning approach for training a motion foundation model from wearable accelerometry sensors. First, a learnable distance measure is trained to capture motif similarity and domain-specific semantic information such as rotation invariance. Then, the learned distance provides a measurement of semantic similarity between a pair of accelerometry time-series, which we use to train our foundation model to model relative relationships across time and across subjects. The foundation model is trained on 1 billion segments from 87,376 participants, and achieves strong performance across multiple downstream tasks, including human activity recognition and gait metric regression. To our knowledge, we are the first to show the generalizability of a foundation model with motion data from wearables across distinct evaluation tasks.

Peptides, short chains of amino acids, interact with target proteins, making them a unique class of protein-based therapeutics for treating human diseases. Recently, deep generative models have shown great promise in peptide generation. However, several challenges remain in designing effective peptide binders. First, not all residues contribute equally to peptide-target interactions. Second, the generated peptides must adopt valid geometries due to the constraints of peptide bonds. Third, realistic tasks for peptide drug development are still lacking. To address these challenges, we introduce PepHAR, a hot-spot-driven autoregressive generative model for designing peptides targeting specific proteins. Building on the observation that certain hot spot residues have higher interaction potentials, we first use an energy-based density model to fit and sample these key residues. Next, to ensure proper peptide geometry, we autoregressively extend peptide fragments by estimating dihedral angles between residue frames. Finally, we apply an optimization process to iteratively refine fragment assembly, ensuring correct peptide structures. By combining hot spot sampling with fragment-based extension, our approach enables \textit{de novo} peptide design tailored to a target protein and allows the incorporation of key hot spot residues into peptide scaffolds. Extensive experiments, including peptide design and peptide scaffold generation, demonstrate the strong potential of PepHAR in computational peptide binder design. The source code will be available at https://github.com/Ced3-han/PepHAR.

Physics-informed deep learning often faces optimization challenges due to the complexity of solving partial differential equations (PDEs), which involve exploring large solution spaces, require numerous iterations, and can lead to unstable training. These challenges arise particularly from the ill-conditioning of the optimization problem, caused by the differential terms in the loss function. To address these issues, we propose learning a solver, i.e., solving PDEs using a physics-informed iterative algorithm trained on data. Our method learns to condition a gradient descent algorithm that automatically adapts to each PDE instance, significantly accelerating and stabilizing the optimization process and enabling faster convergence of physics-aware models. Furthermore, while traditional physics-informed methods solve for a single PDE instance, our approach addresses parametric PDEs. Specifically, our method integrates the physical loss gradient with the PDE parameters to solve over a distribution of PDE parameters, including coefficients, initial conditions, or boundary conditions. We demonstrate the effectiveness of our method through empirical experiments on multiple datasets, comparing training and test-time optimization performance.

Biological language model performance depends heavily on pretraining data quality, diversity, and size. While metagenomic datasets feature enormous biological diversity, their utilization as pretraining data has been limited due to challenges in data accessibility, quality filtering and deduplication. Here, we present the Open MetaGenomic (OMG) corpus, a genomic pretraining dataset totalling 3.1T base pairs and 3.3B protein coding sequences, obtained by combining two largest metagenomic dataset repositories (JGI's IMG and EMBL's MGnify). We first document the composition of the dataset and describe the quality filtering steps taken to remove poor quality data. We make the OMG corpus available as a mixed-modality genomic sequence dataset that represents multi-gene encoding genomic sequences with translated amino acids for protein coding sequences, and nucleic acids for intergenic sequences. We train the first mixed-modality genomic language model (gLM2) that leverages genomic context information to learn robust functional representations, as well as coevolutionary signals in protein-protein interfaces and genomic regulatory syntax. Furthermore, we show that deduplication in embedding space can be used to balance the corpus, demonstrating improved performance on downstream tasks. The OMG dataset is publicly hosted on the Hugging Face Hub at https://huggingface.co/datasets/tattabio/OMG and gLM2 is available at https://huggingface.co/tattabio/gLM2_650M.

The massive and large-scale design of foundational semiconductor integrated circuits (ICs) is crucial to sustaining the advancement of many emerging and future technologies, such as generative AI, 5G/6G, and quantum computing. Excitingly, recent studies have shown the great capabilities of foundational models in expediting the design of digital ICs. Yet, applying generative AI techniques to accelerate the design of analog ICs remains a significant challenge due to critical domain-specific issues, such as the lack of a comprehensive dataset and effective representation methods for analog circuits. This paper proposes, $\textbf{AnalogGenie}$, a $\underline{\textbf{Gen}}$erat$\underline{\textbf{i}}$ve $\underline{\textbf{e}}$ngine for automatic design/discovery of $\underline{\textbf{Analog}}$ circuit topologies--the most challenging and creative task in the conventional manual design flow of analog ICs. AnalogGenie addresses two key gaps in the field: building a foundational comprehensive dataset of analog circuit topology and developing a scalable sequence-based graph representation universal to analog circuits. Experimental results show the remarkable generation performance of AnalogGenie in broadening the variety of analog ICs, increasing the number of devices within a single design, and discovering unseen circuit topologies far beyond any prior arts. Our work paves the way to transform the longstanding time-consuming manual design flow of analog ICs to an automatic and massive manner powered by generative AI. Our source code is available at https://github.com/xz-group/AnalogGenie.

The Earth's weather system involves intricate weather data modalities and diverse weather understanding tasks, which hold significant value to human life. Existing data-driven models focus on single weather understanding tasks (e.g., weather forecasting). While these models have achieved promising results, they fail to tackle various complex tasks within a single and unified model. Moreover, the paradigm that relies on limited real observations for a single scenario hinders the model's performance upper bound. Inspired by the in-context learning paradigm from visual foundation models and large language models, in this paper, we introduce the first generalist weather generalist foundation model (WeatherGFM) to address weather understanding tasks in a unified manner. Specifically, we first unify the representation and definition for diverse weather understanding tasks. Subsequently, we design weather prompt formats to handle different weather data modalities, including single, multiple, and temporal modalities. Finally, we adopt a visual prompting question-answering paradigm for the training of unified weather understanding tasks. Extensive experiments indicate that our WeatherGFM can effectively handle up to 12 weather understanding tasks, including weather forecasting, super-resolution, weather image translation, and post-processing. Our method also showcases generalization ability on unseen tasks. The source code is available at https://github.com/xiangyu-mm/WeatherGFM.

Molecular docking that predicts the bound structures of small molecules (ligands) to their protein targets, plays a vital role in drug discovery. However, existing docking methods often face limitations: they either overlook crucial structural changes by assuming protein rigidity or suffer from low computational efficiency due to their reliance on generative models for structure sampling. To address these challenges, we propose FABFlex, a fast and accurate regression-based multi-task learning model designed for realistic blind flexible docking scenarios, where proteins exhibit flexibility and binding pocket sites are unknown (blind). Specifically, FABFlex's architecture comprises three specialized modules working in concert: (1) A pocket prediction module that identifies potential binding sites, addressing the challenges inherent in blind docking scenarios. (2) A ligand docking module that predicts the bound (holo) structures of ligands from their unbound (apo) states. (3) A pocket docking module that forecasts the holo structures of protein pockets from their apo conformations. Notably, FABFlex incorporates an iterative update mechanism that serves as a conduit between the ligand and pocket docking modules, enabling continuous structural refinements. This approach effectively integrates the three subtasks of blind flexible docking—pocket identification, ligand conformation prediction, and protein flexibility modeling—into a unified, coherent framework. Extensive experiments on public benchmark datasets demonstrate that FABFlex not only achieves superior effectiveness in predicting accurate binding modes but also exhibits a significant speed advantage (208$\times$) compared to existing state-of-the-art methods. Our code is released at~\url{https://github.com/tmlr-group/FABFlex}.

The emergence of in-context learning (ICL) is potentially attributed to two major abilities: task recognition (TR) for recognizing the task from demonstrations and utilizing pre-trained priors, and task learning (TL) for learning from demonstrations. However, relationships between the two abilities and how such relationships affect the emergence of ICL is unclear. In this paper, we take the first step by examining the pre-training dynamics of the emergence of ICL. With carefully designed metrics, we find that these two abilities are, in fact, competitive during pre-training. Moreover, we observe a negative correlation between the competition and the performance of ICL. Further analysis of common pre-training factors (i.e., model size, dataset size, and data curriculum) demonstrates possible ways to regulate the competition. Based on these insights, we propose a simple yet effective method to better integrate these two abilities for ICL at inference time. Through adaptive ensemble learning, the performance of ICL can be significantly boosted, enabling two small models to outperform a larger one with more than twice the parameters.

Recent years have witnessed significant advancements in graph machine learning (GML), with its applications spanning numerous domains. However, the focus of GML has predominantly been on developing powerful models, often overlooking a crucial initial step: constructing suitable graphs from common data formats, such as tabular data. This construction process is fundamental to applying graph-based models, yet it remains largely understudied and lacks formalization. Our research aims to address this gap by formalizing the graph construction problem and proposing an effective solution. We identify two critical challenges to achieve this goal: 1. The absence of dedicated datasets to formalize and evaluate the effectiveness of graph construction methods, and 2. Existing automatic construction methods can only be applied to some specific cases, while tedious human engineering is required to generate high-quality graphs. To tackle these challenges, we present a two-fold contribution. First, we introduce a set of datasets to formalize and evaluate graph construction methods. Second, we propose an LLM-based solution, AutoG, automatically generating high-quality graph schemas without human intervention. The experimental results demonstrate that the quality of constructed graphs is critical to downstream task performance, and AutoG can generate high-quality graphs that rival those produced by human experts. Our code can be accessible from https://github.com/amazon-science/Automatic-Table-to-Graph-Generation.

Prevalent in biomedical applications (e.g., human phenotype research), multimodal datasets can provide valuable insights into the underlying physiological mechanisms. However, current machine learning (ML) models designed to analyze these datasets often lack interpretability and identifiability guarantees, which are essential for biomedical research. Recent advances in causal representation learning have shown promise in identifying interpretable latent causal variables with formal theoretical guarantees. Unfortunately, most current work on multimodal distributions either relies on restrictive parametric assumptions or yields only coarse identification results, limiting their applicability to biomedical research that favors a detailed understanding of the mechanisms. In this work, we aim to develop flexible identification conditions for multimodal data and principled methods to facilitate the understanding of biomedical datasets. Theoretically, we consider a nonparametric latent distribution (c.f., parametric assumptions in previous work) that allows for causal relationships across potentially different modalities. We establish identifiability guarantees for each latent component, extending the subspace identification results from previous work. Our key theoretical contribution is the structural sparsity of causal connections between modalities, which, as we will discuss, is natural for a large collection of biomedical systems. Empirically, we present a practical framework to instantiate our theoretical insights. We demonstrate the effectiveness of our approach through extensive experiments on both numerical and synthetic datasets. Results on a real-world human phenotype dataset are consistent with established biomedical research, validating our theoretical and methodological framework.

Immunogenicity prediction is a central topic in reverse vaccinology for finding candidate vaccines that can trigger protective immune responses. Existing approaches typically rely on highly compressed features and simple model architectures, leading to limited prediction accuracy and poor generalizability. To address these challenges, we introduce VenusVaccine, a novel deep learning solution with a dual attention mechanism that integrates pre-trained latent vector representations of protein sequences and structures. We also compile the most comprehensive immunogenicity dataset to date, encompassing over 7000 antigen sequences, structures, and immunogenicity labels from bacteria, viruses, and tumors. Extensive experiments demonstrate that VenusVaccine outperforms existing methods across a wide range of evaluation metrics. Furthermore, we establish a post-hoc validation protocol to assess the practical significance of deep learning models in tackling vaccine design challenges. Our work provides an effective tool for vaccine design and sets valuable benchmarks for future research. The implementation is at \url{https://github.com/songleee/VenusVaccine}.

As a central component in formal verification, statement autoformalization has been widely studied including the recent efforts from machine learning community, but still remains a widely-recognized difficult and open problem. In this paper, we delve into two critical yet under-explored gaps: 1) absence of faithful and universal automated evaluation for autoformalization results; 2) agnosia of contextual information, inducing severe hallucination of formal definitions and theorems. To address the first issue, we propose **BEq** (_**B**idirectional **E**xtended Definitional E**q**uivalence_), an automated neuro-symbolic method to determine the equivalence between two formal statements, which is formal-grounded and well-aligned with human intuition. For the second, we propose **RAutoformalizer** (_**R**etrieval-augmented **Autoformalizer**_), augmenting statement autoformalization by _Dependency Retrieval_, retrieving potentially dependent objects from formal libraries. We parse the dependencies of libraries and propose to _structurally informalise_ formal objects by the topological order of dependencies. To evaluate OOD generalization and research-level capabilities, we build a novel benchmark, _Con-NF_, consisting of 961 informal-formal statement pairs from frontier mathematical researches. Experiments validate the effectiveness of our approaches: BEq is evaluated on 200 diverse formal statement pairs with expert-annotated equivalence label, exhibiting significantly improved accuracy ($82.50\\% \mapsto 90.50\\%$) and precision ($70.59\\% \mapsto 100.0\\%$). For dependency retrieval, a strong baseline is devised. Our RAutoformalizer substantially outperforms SOTA baselines in both in-distribution ProofNet benchmark ($12.83\\% \mapsto 18.18\\%$, BEq@8) and OOD Con-NF scenario ($4.58\\%\mapsto 16.86\\%$, BEq@8).

Implicit neural representations (INRs) exhibit growing promise in addressing Earth representation challenges, ranging from emissions monitoring to climate modeling. However, existing methods disproportionately prioritize global average performance, whereas practitioners require fine-grained insights to understand biases and variations in these models. To bridge this gap, we introduce FAIR-Earth: a first-of-its-kind dataset explicitly crafted to challenge and examine inequities in Earth representations. FAIR-Earth comprises various high-resolution Earth signals, and uniquely aggregates extensive metadata along stratifications like landmass size and population density to assess the fairness of models. Evaluating state-of-the-art INRs across the various modalities of FAIR-Earth, we uncover striking performance disparities. Certain subgroups, especially those associated with high-frequency signals (e.g., islands, coastlines), are consistently poorly modeled by existing methods. In response, we propose spherical wavelet encodings, building on previous spatial encoding research for INRs. Leveraging the multi-resolution analysis capabilities of wavelets, our encodings yield more consistent performance over various scales and locations, offering more accurate and robust representations of the biased subgroups. These open-source contributions represent a crucial step towards facilitating the equitable assessment and deployment of implicit Earth representations.

Phosphorylation site prediction based on kinase-substrate interaction plays a vital role in understanding cellular signaling pathways and disease mechanisms. Computational methods for this task can be categorized into kinase-family-focused and individual kinase-targeted approaches. Individual kinase-targeted methods have gained prominence for their ability to explore a broader protein space and provide more precise target information for kinase inhibitors. However, most existing individual kinase-based approaches focus solely on sequence inputs, neglecting crucial structural information. To address this limitation, we introduce SAGEPhos (Structure-aware kinAse-substrate bio-coupled and bio-auGmented nEtwork for Phosphorylation site prediction), a novel framework that modifies the semantic space of main protein inputs using auxiliary inputs at two distinct modality levels. At the inter-modality level, SAGEPhos introduces a Bio-Coupled Modal Fusion method, distilling essential kinase sequence information to refine task-oriented local substrate feature space, creating a shared semantic space that captures crucial kinase-substrate interaction patterns. Within the substrate's intra-modality domain, it focuses on Bio-Augmented Fusion, emphasizing 2D local sequence information while selectively incorporating 3D spatial information from predicted structures to complement the sequence space. Moreover, to address the lack of structural information in current datasets, we contribute a new, refined phosphorylation site prediction dataset, which incorporates crucial structural elements and will serve as a new benchmark for the field. Experimental results demonstrate that SAGEPhos significantly outperforms baseline methods, notably achieving almost 10\% and 12\% improvements in prediction accuracy and AUC-ROC, respectively. We further demonstrate our algorithm's robustness and generalization through stable results across varied data partitions and significant improvements in zero-shot scenarios. These results underscore the effectiveness of constructing a larger and more precise protein space in advancing the state-of-the-art in phosphorylation site prediction. We release the SAGEPhos models and code at https://github.com/ZhangJJ26/SAGEPhos.