ICLR 2026 Papers

The inverse design of RNA three-dimensional (3D) structures is crucial for engineering functional RNAs in synthetic biology and therapeutics. While recent deep learning approaches have advanced this field, they are typically optimized and evaluated using native sequence recovery, which is a limited surrogate for structural fidelity, since different sequences can fold into similar 3D structures and high recovery does not necessarily indicate correct folding. To address this limitation, we propose RIDER, an RNA Inverse DEsign framework with Reinforcement learning that directly optimizes for 3D structural similarity. First, we develop and pre-train a GNN-based generative diffusion model conditioned on the target 3D structure, achieving a $9\\%$ improvement in native sequence recovery over state-of-the-art methods. Then, we fine-tune the model with an improved policy gradient algorithm using four task-specific reward functions based on 3D self-consistency metrics. Experimental results show that RIDER improves structural similarity by over $100\\%$ across all metrics and discovers designs that are distinct from native sequences.

Modeling single-cell gene expression across diverse biological and technical conditions is essential for understanding cellular states and simulating unobserved scenarios. We present SAVE, a unified generative framework for multi-condition single-cell modeling. SAVE combines a variational autoencode with conditional Transformer, enhanced by gene block attention and a novel conditional mask modeling strategy. This design enables effective modeling of biological structure under multi-condition effects and supports generalization to unseen condition combinations. We evaluate SAVE on a range of benchmarks, including conditional generation, batch effect correction, and perturbation prediction. SAVE consistently outperforms state-of-the-art methods in generation fidelity and extrapolative gener-alization, especially in low-resource or combinatorially held-out settings. Overall, SAVE offers a scalable and generalizable solution for modeling complex single-cell data, with broad utility in virtual cell synthesis and biological discovery.

The orienteering problem with time windows and variable profits (OPTWVP) is common in many real-world applications and involves continuous time variables. Current approaches fail to develop an efficient solver for this orienteering problem variant with discrete and continuous variables. In this paper, we propose a learning-based two-stage DEcoupled discrete-Continuous optimization with Service-time-guided Trajectory (DeCoST), which aims to effectively decouple the discrete and continuous decision variables in the OPTWVP problem, while enabling efficient and learnable coordination between them. In the first stage, a parallel decoding structure is employed to predict the path and the initial service time allocation. The second stage optimizes the service times through a linear programming (LP) formulation and provides a long-horizon learning of structure estimation. We rigorously prove the global optimality of the second-stage solution. Experiments on OPTWVP instances demonstrate that DeCoST outperforms both state-of-the-art constructive solvers and the latest meta-heuristic algorithms in terms of solution quality and computational efficiency, achieving up to 6.6x inference speedup on instances with fewer than 500 nodes. Moreover, the proposed framework is compatible with various constructive solvers and consistently enhances the solution quality for OPTWVP.

Diffusion models offer a powerful means of capturing the manifold of realistic protein structures, enabling rapid design for protein engineering tasks. However, existing approaches observe critical failure modes when precise constraints are necessary for functional design. To this end, we present a constrained diffusion framework for structure-guided protein design, ensuring strict adherence to functional requirements while maintaining precise stereochemical and geometric feasibility. The approach integrates proximal feasibility updates with ADMM decomposition into the generative process, scaling effectively to the complex constraint sets of this domain. We evaluate on challenging protein design tasks, including motif scaffolding and vacancy-constrained pocket design, while introducing a novel curated benchmark dataset for motif scaffolding in the PDZ domain. Our approach achieves state-of-the-art, providing perfect satisfaction of bonding and geometric constraints with no degradation in structural diversity.

We present a framework for fine-tuning flow-matching generative models to enforce physical constraints and solve inverse problems in scientific systems. Starting from a model trained on low-fidelity or observational data, we apply a differentiable post-training procedure that minimizes weak-form residuals of governing partial differential equations (PDEs), promoting physical consistency and adherence to boundary conditions without distorting the underlying learned distribution. To infer unknown physical inputs, such as source terms, material parameters, or boundary data, we augment the generative process with a learnable latent parameter predictor and propose a joint optimization strategy. The resulting model produces physically valid field solutions alongside plausible estimates of hidden parameters, effectively addressing ill-posed inverse problems in a data-driven yet physics-aware manner. We validate our method on canonical PDE problems, demonstrating improved satisfaction of physical constraints and accurate recovery of latent coefficients. Further, we confirm cross-domain utility through fine-tuning of natural-image models. Our approach bridges generative modelling and scientific inference, opening new avenues for simulation-augmented discovery and data-efficient modelling of physical systems.

Advancements in Large Language Models (LLMs) drive interest in scientific applications, necessitating specialized benchmarks such as Earth science. Existing benchmarks either present a general science focus devoid of Earth science specificity or cover isolated subdomains, lacking holistic evaluation. Furthermore, current benchmarks typically neglect the assessment of LLMs' capabilities in open-ended scientific exploration. In this paper, we present a comprehensive and professional benchmark for the Earth sciences, designed to evaluate the capabilities of LLMs in scientific exploration within this domain, spanning from fundamental to advanced levels. Leveraging a corpus of 100,000 research papers, we first construct two Question Answering (QA) datasets: Earth-Iron, which offers extensive question coverage for broad assessment, and Earth-Silver, which features a higher level of difficulty to evaluate professional depth. These datasets encompass five Earth spheres, 114 disciplines, and 11 task categories, assessing foundational knowledge crucial for scientific exploration. Most notably, we introduce Earth-Gold with new metrics, a dataset comprising open-ended multi-turn dialogues specifically designed to evaluate the depth and diversity of LLMs in scientific exploration, including methodology induction, limitation analysis, and concept proposal. Extensive experiments reveal limitations in 11 leading LLMs across different domains and tasks, highlighting considerable room for improvement in their scientific exploration capabilities.

Cancer treatment efficacy exhibits high inter-patient heterogeneity due to genomic variations. While large-scale in vitro drug response data from cancer cell lines exist, predicting patient drug responses remains challenging due to genomic distribution shifts and the scarcity of clinical response data. Existing transfer learning methods primarily align global genomic features between cell lines and patients. However, they often ignore two critical aspects. First, drug response depends on specific drug substructures and genomic pathways. Second, drug response mechanisms differ in vitro and in vivo settings due to factors such as the immune system and tumor microenvironment. To address these limitations, we propose DeepSADR, a novel deep transfer learning framework for enhanced drug response prediction based on subsequence interaction and adaptive readout. In particular, DeepSADR models drug responses as interpretable bipartite interaction graphs between drug substructures and enriched genomic pathways. Subsequently, a supervised graph autoencoder was designed to capture latent interactions between drugs and gene subsequences within these interaction graphs. In addition, DeepSADR treats the drug response process as a transferable domain. A Set Transformer-based adaptive readout (AR) function learns domain-invariant response representations, enabling effective knowledge transfer from abundant cell line data to scarce patient data. Extensive experiments on clinical patient cohorts demonstrate that DeepSADR significantly outperforms state-of-the-art methods, and ablation experiments have validated the effectiveness of each module.

Deep learning methods for material property prediction have been widely explored to advance materials discovery. However, the prevailing pre-train paradigm often fails to address the inherent diversity and disparity of material tasks. To overcome these challenges, we introduce MoMa, a simple Modular framework for Materials that first trains specialized modules across a wide range of tasks and then adaptively composes synergistic modules tailored to each downstream scenario. Evaluation across 17 datasets demonstrates the superiority of MoMa, with a substantial 14% average improvement over the strongest baseline. Few-shot and module scaling experiments further highlight MoMa's potential for real-world applications. Pioneering a new paradigm of modular material learning, MoMa will be open-sourced to foster broader community collaboration.

Molecular Dynamics (MD) is a powerful computational microscope for probing protein functions. However, the need for fine-grained integration and the long timescales of biomolecular events make MD computationally expensive. To address this, several generative models have been proposed to generate surrogate trajectories at lower cost. Yet, these models typically learn a fixed-lag transition density, causing the training signal to be dominated by frequent but uninformative transitions. We introduce a new class of generative models, **MSM Emulators**, which instead learn to sample transitions across discrete states defined by an underlying Markov State Model (MSM). We instantiate this class with Markov Space Flow Matching (MarS-FM), whose sampling offers more than two orders of magnitude speedup compared to implicit- or explicit-solvent MD simulations. We benchmark Mars-FM ability to reproduce MD statistics through structural observables such as RMSD, radius of gyration, and secondary structure content. Our evaluation spans protein domains (up to 500 residues) with significant chemical and structural diversity, including unfolding events, and enforces strict sequence dissimilarity between training and test sets to assess generalization. Across all metrics, MarS-FM outperforms existing methods, often by a substantial margin.

Multimodal learning is of continued interest in artificial intelligence-based applications, motivated by the potential information gain from combining different types of data. However, modalities observed in the source environment may differ from the modalities observed in the target environment due to multiple factors, including cost, hardware failure, or the perceived *informativeness* of a given modality. This shift in missingness between the source and target environment has not been carefully studied. Naive estimation of the information gain associated with including an additional modality without accounting for missingness may result in improper estimates of that modality's value in the target environment. We formalize the problem of missingness, demonstrate its ubiquity, and show that the subsequent distribution shift results in bias when the missingness process is not explicitly accounted for. To address this issue, we introduce ICYM2I (In Case You Multimodal Missed It), a framework for the evaluation of predictive performance and information gain under missingness through inverse probability weighting-based correction. We demonstrate the importance of the proposed adjustment to estimate information gain under missingness on synthetic, semi-synthetic, and real-world datasets.

Canonicalization is a widely used strategy in equivariant machine learning, enforcing symmetry in neural networks by mapping each input to a standard form. Yet, it often introduces discontinuities that can affect stability during training, limit generalization, and complicate universal approximation theorems. In this paper, we address this by introducing *adaptive canonicalization*, a general framework in which the canonicalization depends both on the input and the network. Specifically, we present the adaptive canonicalization based on prior maximization, where the standard form of the input is chosen to maximize the predictive confidence of the network. We prove that this construction yields continuous and symmetry-respecting models that admit universal approximation properties. We propose two applications of our setting: (i) resolving eigenbasis ambiguities in spectral graph neural networks, and (ii) handling rotational symmetries in point clouds. We empirically validate our methods on molecular and protein classification, as well as point cloud classification tasks. Our adaptive canonicalization outperforms the three other common solutions to equivariant machine learning: data augmentation, standard canonicalization, and equivariant architectures.

Transformer-based PDE surrogates achieve remarkable performance but face two key challenges: fixed patch sizes cause systematic error accumulation at harmonic frequencies, and computational costs remain inflexible regardless of problem complexity or available resources. We introduce Overtone, a unified solution through dynamic patch size control at inference. Overtone's key insight is that cyclically modulating patch sizes during autoregressive rollouts distributes errors across the frequency spectrum, preventing the systematic harmonic artifacts that plague fixed-patch models. We implement this through two architecture-agnostic modules—CSM (Cyclic Stride Modulator, using dynamic stride modulation) and CKM (Cyclic Kernel Modulator, using dynamic kernel resizing)—that together provide both harmonic mitigation and compute-adaptive deployment. The harmonic mitigation alone yields up to 40% error reduction in long rollouts, while the flexible tokenization allows users to trade accuracy for speed dynamically based on computational constraints. Applied to challenging 2D and 3D PDE benchmarks, a single Overtone model matches or exceeds multiple fixed-patch baselines across all compute budgets.

To address the global health threat of antimicrobial resistance, antimicrobial peptides (AMP) are being explored for their potent and promising ability to fight resistant pathogens. While artificial intelligence (AI) is being employed to advance AMP discovery and design, most AMP design models struggle to balance key goals like activity, toxicity, and novelty, using rigid or unclear scoring methods that make results hard to interpret and optimize. As the capabilities of Large Language Models (LLM) advance and evolve swiftly, we turn to AI multi-agent collaboration based on such models (multi-agent LLMs), which show rapidly rising potential in complex scientific design scenarios. Based on this, we introduce $\textbf{MAC-AMP}$, a closed-loop multi-agent collaboration (MAC) system for multi-objective AMP design. The system implements a fully autonomous simulated peer review-adaptive reinforcement learning framework that requires only a task description and example dataset to design novel AMPs. The novelty of our work lies in introducing a closed-loop multi-agent system for AMP design, with cross-domain transferability, that supports multi-objective optimization while remaining explainable rather than a 'black box'. Experiments show that MAC-AMP outperforms other AMP generative models by effectively optimizing AMP generation for multiple key molecular properties, demonstrating exceptional results in antibacterial activity, AMP likeliness, toxicity compliance, and structural reliability.

Wearable sensors provide abundant physiological time series observations, yet the resolution at which we should extract features for downstream tasks remain unclear. We hypothesize that temporal resolution is a fundamental axis of representation learning, with different clinical and behavioral outcomes relying on features at distinct scales. To test this resolution hypothesis, we introduce HiMAE (Hierarchical Masked Autoencoder), a self-supervised framework that combines masked autoencoding with a hierarchical convolutional encoder–decoder. HiMAE produces multi-resolution embeddings across its intermediate layers that enable systematic evaluation of which temporal scales carry predictive signal, transforming resolution from a hyperparameter into a probe for interpretability. Across classification and generative benchmarks, HiMAE consistently outperforms state-of-the-art foundation models that collapse scale, while being orders of magnitude smaller. Due to the convolution based design choices behind HiMAE, the model is also compact enough to run entirely on-device, achieving sub-millisecond inference on smartwatch-class CPUs for true edge inference. Together, these contributions position HiMAE as both an efficient self supervised learning method and a discovery tool for understanding how time resolution contributes to downstream task alignment.

The global dimensionality of a neural representation manifold provides rich insight into the computational process underlying both artificial and biological neural networks. However, all existing measures of global dimensionality are sensitive to the number of samples, i.e., the number of rows and columns of the sample matrix. We show that, in particular, the participation ratio of eigenvalues, a popular measure of global dimensionality, is highly biased with small sample sizes, and propose a bias-corrected estimator that is more accurate with finite samples and with noise. On synthetic data examples, we demonstrate that our estimator can recover the true known dimensionality. We apply our estimator to neural brain recordings, including calcium imaging, electrophysiological recordings, and fMRI data, and to the neural activations in a large language model and show our estimator is invariant to the sample size. Finally, our estimators can additionally be used to measure the local dimensionalities of curved neural manifolds by weighting the finite samples appropriately.

We introduce PAT3D, the first physics-augmented text-to-3D scene generation framework that integrates vision–language models with physics-based simulation to produce physically plausible, simulation-ready, and intersection-free 3D scenes. Given a text prompt, PAT3D generates 3D objects, infers their spatial relations, and organizes them into a hierarchical scene tree, which is then converted into initial simulation conditions. A rigid-body simulator ensures realistic object interactions under gravity, driving the scene toward static equilibrium without interpenetrations. To further enhance scene quality, we introduce a simulation-in-the-loop optimization procedure that guarantees physical stability and non-intersection, while improving semantic consistency with the input prompt. Experiments demonstrate that PAT3D substantially outperforms prior approaches in physical plausibility, semantic accuracy, and visual quality. Beyond high-quality generation, PAT3D uniquely enables simulation-ready 3D scenes for downstream tasks such as scene editing and robotic manipulation. Code and data will be released upon acceptance.

Sheaf Neural Networks (SNNs) are a powerful algebraic-topology generalization of Graph Neural Networks (GNNs), and have been shown to significantly improve our ability to model complex relational data. While the GNN literature proved that incorporating directionality can substantially boost performance in many real-world applications, no SNNs approaches are known with such a capability. To address this limitation, we introduce the Directed Cellular Sheaf, a generalized cellular sheaf designed to explicitly account for edge orientations. Building on it, we define a corresponding sheaf Laplacian, the Directed Sheaf Laplacian $L^{\widetilde{\mathcal{F}}}$, which exploits the sheaf's structure to capture both the graph’s topology and its directions. $L^{\widetilde{\mathcal{F}}}$ serves as the backbone of the Directed Sheaf Neural Network (DSNN), the first SNN model to embed a directional bias into its architecture. Extensive experiments on twelve real-world benchmarks show that DSNN consistently outperforms many baseline methods.

Industrial design evaluation often relies on high-fidelity simulations of governing partial differential equations (PDEs). While accurate, these simulations are computationally expensive, making dense exploration of design spaces impractical. Operator learning has emerged as a promising approach to accelerate PDE solution prediction; however, its effectiveness is often limited by the scarcity of labeled physics-based data. At the same time, large numbers of geometry-only candidate designs are readily available but remain largely untapped. We propose a two-stage framework to better exploit this abundant, physics-agnostic resource and improve supervised operator learning under limited labeled data. In Stage 1, we pretrain an autoencoder on a geometry reconstruction task to learn an expressive latent representation without PDE labels. In Stage 2, the neural operator is trained in a standard supervised manner to predict PDE solutions, using the pretrained latent embeddings as inputs instead of raw point clouds. Transformer-based architectures are adopted for both the autoencoder and the neural operator to handle point cloud data and integrate both stages seamlessly. Across four PDE datasets and three state-of-the-art transformer-based neural operators, our approach consistently improves prediction accuracy compared to models trained directly on raw point cloud inputs. These results demonstrate that representations from physics-agnostic pretraining provide a powerful foundation for data-efficient operator learning.

A core challenge in scientific machine learning, and scientific computing more generally, is modeling continuous phenomena which (in practice) are represented discretely. Machine-learned operators (MLO) have been introduced as a means to achieve this modeling goal, as this class of architecture can perform inference at arbitrary resolution. In this work, we evaluate whether this architectural innovation is sufficient to perform “zero-shot super-resolution,” namely to enable a model to serve inference on higher-resolution data than that on which it was originally trained. We comprehensively evaluate both zero-shot sub-resolution and super-resolution (i.e., multi-resolution) inference in MLOs. We decouple multi-resolution inference into two key behaviors: 1) extrapolation to varying frequency information; and 2) interpolating across varying resolutions. We empirically demonstrate that MLOs fail to do both of these tasks in a zero-shot manner. Consequently, we find MLOs are not able to perform accurate inference at resolutions different from those on which they were trained, and instead they are brittle and susceptible to aliasing. To address these failure modes, we propose a simple, computationally-efficient, and data-driven multi-resolution training protocol that overcomes aliasing and that provides robust multi-resolution generalization.