ICLR 2025 Papers

Material discovery is a critical research area with profound implications for various industries. In this work, we introduce MatExpert, a novel framework that leverages Large Language Models (LLMs) and contrastive learning to accelerate the discovery and design of new solid-state materials. Inspired by the workflow of human materials design experts, our approach integrates three key stages: retrieval, transition, and generation. First, in the retrieval stage, MatExpert identifies an existing material that closely matches the desired criteria. Second, in the transition stage, MatExpert outlines the necessary modifications to transform this material formulation to meet specific requirements outlined by the initial user query. Third, in the generation state, MatExpert performs detailed computations and structural generation to create a new material based on the provided information. Our experimental results demonstrate that MatExpert outperforms state-of-the-art methods in material generation tasks, achieving superior performance across various metrics including validity, distribution, and stability. As such, MatExpert represents a meaningful advancement in computational material discovery using langauge-based generative models.

While there has been significant progress in evaluating and comparing different representations for learning on protein data, the role of surface-based learning approaches remains not well-understood. In particular, there is a lack of direct and fair benchmark comparison between the best available surface-based learning methods against alternative representations such as graphs. Moreover, the few existing surface-based approaches either use surface information in isolation or, at best, perform global pooling between surface and graph-based architectures. In this work, we fill this gap by first adapting a state-of-the-art surface encoder for protein learning tasks. We then perform a direct and fair comparison of the resulting method against alternative approaches within the Atom3D benchmark, highlighting the limitations of pure surface-based learning. Finally, we propose an integrated approach, which allows learned feature sharing between graphs and surface representations on the level of nodes and vertices \textit{across all layers}. We demonstrate that the resulting architecture achieves state-of-the-art results on all tasks in the Atom3D benchmark, while adhering to the strict benchmark protocol, as well as more broadly on binding site identification and binding pocket classification. Furthermore, we use coarsened surfaces and optimize our approach for efficiency, making our tool competitive in training and inference time with existing techniques. Code can be found online: https://github.com/Vincentx15/atomsurf

The loss functions of many learning problems contain multiple additive terms that can disagree and yield conflicting update directions. For Physics-Informed Neural Networks (PINNs), loss terms on initial/boundary conditions and physics equations are particularly interesting as they are well-established as highly difficult tasks. To improve learning the challenging multi-objective task posed by PINNs, we propose the ConFIG method, which provides conflict-free updates by ensuring a positive dot product between the final update and each loss-specific gradient. It also maintains consistent optimization rates for all loss terms and dynamically adjusts gradient magnitudes based on conflict levels. We additionally leverage momentum to accelerate optimizations by alternating the back-propagation of different loss terms. We provide a mathematical proof showing the convergence of the ConFIG method, and it is evaluated across a range of challenging PINN scenarios. ConFIG consistently shows superior performance and runtime compared to baseline methods. We also test the proposed method in a classic multi-task benchmark, where the ConFIG method likewise exhibits a highly promising performance. Source code is available at https://tum-pbs.github.io/ConFIG

In this paper, we use the Fire Dynamics Simulator (FDS) combined with the {\fontfamily{lmtt}\selectfont \textit{supercomputer}} support to create a \textbf{C}ombustion \textbf{K}inetics (CK) dataset for machine learning and scientific research. This dataset captures the development of fires in industrial parks with high-precision Computational Fluid Dynamics (CFD) simulations. It includes various physical fields such as temperature and pressure, and covers multiple environmental combinations for exploring \underline{multi-physics} field coupling phenomena. Additionally, we evaluate several advanced machine learning architectures across our {\fontfamily{lmtt}\selectfont {Open-CK}} benchmark using a substantial computational setup of 64 NVIDIA A100 GPUs: \ding{182} vision backbone; \ding{183} spatio-temporal predictive models; \ding{184} operator learning frameworks. These architectures uniquely excel at handling complex physical field data. We also introduce three benchmarks to demonstrate their potential in enhancing the exploration of downstream tasks: (a) capturing continuous changes in combustion kinetics; (b) a neural partial differential equation solver for learning temperature fields and turbulence; (c) reconstruction of sparse physical observations. The Open-CK dataset and benchmarks aim to advance research in combustion kinetics driven by machine learning, providing a reliable baseline for developing and comparing cutting-edge technologies and models. We hope to further promote the application of deep learning in earth sciences. Our project is available at \url{https://github.com/whscience/Open-CK}.

Accurately predicting protein-ligand binding affinity is a critical challenge in drug discovery, crucial for understanding drug efficacy. While existing models typically rely on atom-level interactions, they often fail to capture the complex, higher-order interactions, resulting in noise and computational inefficiency. Transitioning to modeling these interactions at the cluster level is challenging because it is difficult to determine which atoms form meaningful clusters that drive the protein-ligand interactions. To address this, we propose CheapNet, a novel interaction-based model that integrates atom-level representations with hierarchical cluster-level interactions through a cross-attention mechanism. By employing differentiable pooling of atom-level embeddings, CheapNet efficiently captures essential higher-order molecular representations crucial for accurate binding predictions. Extensive evaluations demonstrate that CheapNet not only achieves state-of-the-art performance across multiple binding affinity prediction tasks but also maintains prediction accuracy with reasonable computational efficiency. The code of CheapNet is available at https://github.com/hyukjunlim/CheapNet.

Do Large Vision Models (LVMs) extract medically and semantically relevant features similar to those identified by human experts? Currently, only biased, qualitative approaches with limited, small-scale expert evaluations are available to answer this question. In this study, we propose the Boltzmann Semantic Score (BSS), a novel method inspired by state space modeling, to evaluate the encoding space of LVMs from medical images using the encoding space of Large Language Models (LLMs) from medical reports. Through extensive experimentation on 32 datasets from The Cancer Genome Atlas collection using five state-of-the-art LLMs, we first establish a baseline of LLMs' performance in digital pathology and show that LLMs' encoding can be linked to patient outcomes. Then, we compared seven LVMs with BSS and showed that LVMs suffer from poor semantic capability when compared with encoded expert knowledge from pathology reports. We also found statistically significant correlations between BSS (as a measure of structural similarity) and performance in two downstream tasks: information retrieval and survival prediction tasks. Our study also investigates the consensus among LLMs in evaluating LVMs using BSS, indicating that LLMs generally reach substantial consensus in rating LVMs, with some variation dependant on the cancer type. We believe the BSS metric proposed here holds significant potential for application in other domains with similar contexts. Data and code can be found in \footnotesize \url{ https://github.com/AIMLab-UBC/Boltzmann}

The dynamic nature of proteins, influenced by ligand interactions, is essential for comprehending protein function and progressing drug discovery. Traditional structure-based drug design (SBDD) approaches typically target binding sites with rigid structures, limiting their practical application in drug development. While molecular dynamics simulation can theoretically capture all the biologically relevant conformations, the transition rate is dictated by the intrinsic energy barrier between them, making the sampling process computationally expensive. To overcome the aforementioned challenges, we propose to use generative modeling for SBDD considering conformational changes of protein pockets. We curate a dataset of apo and multiple holo states of protein-ligand complexes, simulated by molecular dynamics, and propose a full-atom flow model (and a stochastic version), named DynamicFlow, that learns to transform apo pockets and noisy ligands into holo pockets and corresponding 3D ligand molecules. Our method uncovers promising ligand molecules and corresponding holo conformations of pockets. Additionally, the resultant holo-like states provide superior inputs for traditional SBDD approaches, playing a significant role in practical drug discovery.

Self-driving laboratories have begun to replace human experimenters in performing single experimental skills or predetermined experimental protocols. However, as the pace of idea iteration in scientific research has been intensified by Artificial Intelligence, the demand for rapid design of new protocols for new discoveries become evident. Efforts to automate protocol design have been initiated, but the capabilities of knowledge-based machine designers, such as Large Language Models, have not been fully elicited, probably for the absence of a systematic representation of experimental knowledge, as opposed to isolated, flatten pieces of information. To tackle this issue, we propose a multi-faceted, multi-scale representation, where instance actions, generalized operations, and product flow models are hierarchically encapsulated using Domain-Specific Languages. We further develop a data-driven algorithm based on non-parametric modeling that autonomously customizes these representations for specific domains. The proposed representation is equipped with various machine designers to manage protocol design tasks, including planning, modification, and adjustment. The results demonstrate that the proposed method could effectively complement Large Language Models in the protocol design process, serving as an auxiliary module in the realm of machine-assisted scientific exploration.

Neural activity in the brain is known to encode low-dimensional, time-evolving, behaviour-related variables. A long-standing goal of neural data analysis has been to identify these variables and their mapping to neural activity. A productive and canonical approach has been to simply visualise neural "tuning curves" as a function of behaviour. However, significant discrepancies between behaviour and the true latent variables -- such as an agent thinking of position Y whilst located at position X -- distort and blur the tuning curves, decreasing their interpretability. To address this, latent variable models propose to learn the latent variable from data; these are typically expensive, hard to tune, or scale poorly, complicating their adoption. Here we propose SIMPL (Scalable Iterative Maximization of Population-coded Latents), an EM-style algorithm which iteratively optimises latent variables and tuning curves. SIMPL is fast, scalable and exploits behaviour as an initial condition to further improve convergence and identifiability. It can accurately recover latent variables in spatial and non-spatial tasks. When applied to a large hippocampal dataset SIMPL converges on smaller, more numerous, and more uniformly sized place fields than those based on behaviour, suggesting the brain may encode space with greater resolution than previously thought.

Accurate prediction of RNA properties, such as stability and interactions, is crucial for advancing our understanding of biological processes and developing RNA-based therapeutics. RNA structures can be represented as 1D sequences, 2D topological graphs, or 3D all-atom models, each offering different insights into its function. Existing works predominantly focus on 1D sequence-based models, which overlook the geometric context provided by 2D and 3D geometries. This study presents the first systematic evaluation of incorporating explicit 2D and 3D geometric information into RNA property prediction, considering not only performance but also real-world challenges such as limited data availability, partial labeling, sequencing noise, and computational efficiency. To this end, we introduce a newly curated set of RNA datasets with enhanced 2D and 3D structural annotations, providing a resource for model evaluation on RNA data. Our findings reveal that models with explicit geometry encoding generally outperform sequence-based models, with an average prediction RMSE reduction of around 12% across all various RNA tasks and excelling in low-data and partial labeling regimes, underscoring the value of explicitly incorporating geometric context. On the other hand, geometry-unaware sequence-based models are more robust under sequencing noise but often require around 2-5x training data to match the performance of geometry-aware models. Our study offers further insights into the trade-offs between different RNA representations in practical applications and addresses a significant gap in evaluating deep learning models for RNA tasks.

Zeolites are crystalline porous materials that have been widely utilized in petrochemical industries as well as sustainable chemistry areas. Synthesis of zeolites often requires small molecules termed Organic Structure Directing Agents (OSDAs), which are critical in forming the porous structure. Molecule generation models can aid the design of OSDAs, but they are limited by single functionality and lack of interactivity. Meanwhile, large language models (LLMs) such as GPT-4, as general-purpose artificial intelligence systems, excel in instruction comprehension, logical reasoning, and interactive communication. However, LLMs lack in-depth chemistry knowledge and first-principle computation capabilities, resulting in uncontrollable outcomes even after fine-tuning. In this paper, we propose OSDA Agent, an interactive OSDA design framework that leverages LLMs as the brain, coupled with computational chemistry tools. The OSDA Agent consists of three main components: the Actor, responsible for generating potential OSDA structures; the Evaluator, which assesses and scores the generated OSDAs using computational chemistry tools; and the Self-reflector, which produces reflective summaries based on the Evaluator's feedback to refine the Actor's subsequent outputs. Experiments on representative zeolite frameworks show the generation-evaluation-reflection-refinement workflow can perform de novo design of OSDAs with superior generation quality than the pure LLM model, generating candidates consistent with experimentally validated OSDAs and optimizing known OSDAs.

Modelling the propagation of electromagnetic wireless signals is critical for designing modern communication systems. Wireless ray tracing simulators model signal propagation based on the 3D geometry and other scene parameters, but their accuracy is fundamentally limited by underlying modelling assumptions and correctness of parameters. In this work, we introduce Wi-GATr, a fully-learnable neural simulation surrogate designed to predict the channel observations based on scene primitives (e. g., surface mesh, antenna position and orientation). Recognizing the inherently geometric nature of these primitives, Wi-GATr leverages an equivariant Geometric Algebra Transformer that operates on a tokenizer specifically tailored for wireless simulation. We evaluate our approach on a range of tasks (i. e., signal strength and delay spread prediction, receiver localization, and geometry reconstruction) and find that Wi-GATr is accurate, fast, sample-efficient, and robust to symmetry-induced transformations. Remarkably, we find our results also translate well to the real world: Wi-GATr demonstrates more than 35% lower error than hybrid techniques, and 70% lower error than a calibrated wireless tracer.

Numerous biological and physical processes can be modeled as systems of interacting entities evolving continuously over time, e.g. the dynamics of communicating cells or physical particles. Learning the dynamics of such systems is essential for predicting the temporal evolution of populations across novel samples and unseen environments. Flow-based models allow for learning these dynamics at the population level - they model the evolution of the entire distribution of samples. However, current flow-based models are limited to a single initial population and a set of predefined conditions which describe different dynamics. We argue that multiple processes in natural sciences have to be represented as vector fields on the Wasserstein manifold of probability densities. That is, the change of the population at any moment in time depends on the population itself due to the interactions between samples. In particular, this is crucial for personalized medicine where the development of diseases and their respective treatment response depend on the microenvironment of cells specific to each patient. We propose *Meta Flow Matching* (MFM), a practical approach to integrate along these vector fields on the Wasserstein manifold by amortizing the flow model over the initial populations. Namely, we embed the population of samples using a Graph Neural Network (GNN) and use these embeddings to train a Flow Matching model. This gives MFM the ability to generalize over the initial distributions, unlike previously proposed methods. We demonstrate the ability of MFM to improve the prediction of individual treatment responses on a large-scale multi-patient single-cell drug screen dataset.

Spiking Neural Networks (SNNs), models inspired by neural mechanisms in the brain, allow for energy-efficient implementation on neuromorphic hardware. However, SNNs trained with current direct training approaches are constrained to a specific time step. This "temporal inflexibility" 1) hinders SNNs' deployment on time-step-free fully event-driven chips and 2) prevents energy-performance balance based on dynamic inference time steps. In this study, we first explore the feasibility of training SNNs that generalize across different time steps. We then introduce Mixed Time-step Training (MTT), a novel method that improves the temporal flexibility of SNNs, making SNNs adaptive to diverse temporal structures. During each iteration of MTT, random time steps are assigned to different SNN stages, with spikes transmitted between stages via communication modules. After training, the weights are deployed and evaluated on both time-stepped and fully event-driven platforms. Experimental results show that models trained by MTT gain remarkable temporal flexibility, friendliness for both event-driven and clock-driven deployment (nearly lossless on N-MNIST and 10.1\% higher than standard methods on CIFAR10-DVS), enhanced network generalization, and near SOTA performance. To the best of our knowledge, this is the first work to report the results of large-scale SNN deployment on fully event-driven scenarios.

The physics solvers employed for neural network training are primarily iterative, and hence, differentiating through them introduces a severe computational burden as iterations grow large. Inspired by works in bilevel optimization, we show that full accuracy of the network is achievable through physics significantly coarser than fully converged solvers. We propose *progressively refined differentiable physics* (PRDP), an approach that identifies the level of physics refinement sufficient for full training accuracy. By beginning with coarse physics, adaptively refining it during training, and stopping refinement at the level adequate for training, it enables significant compute savings without sacrificing network accuracy. Our focus is on differentiating iterative linear solvers for sparsely discretized differential operators, which are fundamental to scientific computing. PRDP is applicable to both unrolled and implicit differentiation. We validate its performance on a variety of learning scenarios involving differentiable physics solvers such as inverse problems, autoregressive neural emulators, and correction-based neural-hybrid solvers. In the challenging example of emulating the Navier-Stokes equations, we reduce training time by 62%.

Neural Ordinary Differential Equations (NODEs) often struggle to adapt to new dynamic behaviors caused by parameter changes in the underlying physical system, even when these dynamics are similar to previously observed behaviors. This problem becomes more challenging when the changing parameters are unobserved, meaning their value or influence cannot be directly measured when collecting data. To address this issue, we introduce Neural Context Flow (NCF), a robust and interpretable Meta-Learning framework that includes uncertainty estimation. NCF uses Taylor expansion to enable contextual self-modulation, allowing context vectors to influence dynamics from other domains while also modulating themselves. After establishing theoretical guarantees, we empirically test NCF and compare it to related adaptation methods. Our results show that NCF achieves state-of-the-art Out-of-Distribution performance on 5 out of 6 linear and non-linear benchmark problems. Through extensive experiments, we explore the flexible model architecture of NCF and the encoded representations within the learned context vectors. Our findings highlight the potential implications of NCF for foundational models in the physical sciences, offering a promising approach to improving the adaptability and generalization of NODEs in various scientific applications.

Large language models (LLMs) have demonstrated significant potential in clinical decision support. Yet LLMs still suffer from hallucinations and lack fine-grained contextual medical knowledge, limiting their high-stake healthcare applications such as clinical diagnosis. Traditional retrieval-augmented generation (RAG) methods attempt to address these limitations but frequently retrieve sparse or irrelevant information, undermining prediction accuracy. We introduce KARE, a novel framework that integrates knowledge graph (KG) community-level retrieval with LLM reasoning to enhance healthcare predictions. KARE constructs a comprehensive multi-source KG by integrating biomedical databases, clinical literature, and LLM-generated insights, and organizes it using hierarchical graph community detection and summarization for precise and contextually relevant information retrieval. Our key innovations include: (1) a dense medical knowledge structuring approach enabling accurate retrieval of relevant information; (2) a dynamic knowledge retrieval mechanism that enriches patient contexts with focused, multi-faceted medical insights; and (3) a reasoning-enhanced prediction framework that leverages these enriched contexts to produce both accurate and interpretable clinical predictions. Extensive experiments demonstrate that KARE outperforms leading models by up to 10.8-15.0\% on MIMIC-III and 12.6-12.7\% on MIMIC-IV for mortality and readmission predictions. In addition to its impressive prediction accuracy, our framework leverages the reasoning capabilities of LLMs, enhancing the trustworthiness of clinical predictions.

Scientific literature understanding is crucial for extracting targeted information and garnering insights, thereby significantly advancing scientific discovery. Despite the remarkable success of Large Language Models (LLMs), they face challenges in scientific literature understanding, primarily due to (1) a lack of scientific knowledge and (2) unfamiliarity with specialized scientific tasks. To develop an LLM specialized in scientific literature understanding, we propose a hybrid strategy that integrates continual pre-training (CPT) and supervised fine-tuning (SFT), to simultaneously infuse scientific domain knowledge and enhance instruction-following capabilities for domain-specific tasks. In this process, we identify two key challenges: (1) constructing high-quality CPT corpora, and (2) generating diverse SFT instructions. We address these challenges through a meticulous pipeline, including PDF text extraction, parsing content error correction, quality filtering, and synthetic instruction creation. Applying this strategy, we present a suite of LLMs: SciLitLLM, specialized in scientific literature understanding. These models demonstrate promising performance on scientific literature understanding benchmarks. (1) We present an effective framework that integrates CPT and SFT to adapt LLMs to scientific literature understanding, which can also be easily adapted to other domains. (2) We propose an LLM-based synthesis method to generate diverse and high-quality scientific instructions, resulting in a new instruction set -- SciLitIns -- for less-represented scientific domains. (3) SciLitLLM achieves promising performance in scientific literature understanding benchmarks.

Perception is a crucial component of autonomous driving systems. However, single-agent setups often face limitations due to sensor constraints, especially under challenging conditions like severe occlusion, adverse weather, and long-range object detection. Multi-agent collaborative perception (CP) offers a promising solution that enables communication and information sharing between connected vehicles. Yet, the heterogeneity among agents—in terms of sensors, models, and tasks—significantly hinders effective and efficient cross-agent collaboration. To address these challenges, we propose STAMP, a scalable task- and model-agnostic collaborative perception framework tailored for heterogeneous agents. STAMP utilizes lightweight adapter-reverter pairs to transform Bird's Eye View (BEV) features between agent-specific domains and a shared protocol domain, facilitating efficient feature sharing and fusion while minimizing computational overhead. Moreover, our approach enhances scalability, preserves model security, and accommodates a diverse range of agents. Extensive experiments on both simulated (OPV2V) and real-world (V2V4Real) datasets demonstrate that STAMP achieves comparable or superior accuracy to state-of-the-art models with significantly reduced computational costs. As the first-of-its-kind task- and model-agnostic collaborative perception framework, STAMP aims to advance research in scalable and secure mobility systems, bringing us closer to Level 5 autonomy. Our project page is at https://xiangbogaobarry.github.io/STAMP and the code is available at https://github.com/taco-group/STAMP.