ICML 2026 论文列表

Soil microorganisms control organic matter cycling and largely determine how soil systems can cope with and mitigate climate change and environmental threats. Representing microbial dynamics in process-based soil models is therefore critical to predict carbon cycling in soils, albeit highly challenging to inform from data. One promising approach to improve their parametrisation is the integration of genomic data, yet modelling the complex and unknown relationship between genomes and the processes the microbes are driving is an unsolved problem. In this work, we present the first hybrid modeling framework for deriving biokinetic parameter values of a process-based soil organic matter turnover model from metagenome-inferred functional traits based on DNA sequencing data. Our model predicts biokinetic parameters of the process-based model from genomic trait data with a neural network and integrates constraints from ecological theory and literature to ensure realistic behavior, even of non-observed state variables. We evaluate our method on synthetic genomic trait datasets of varying complexity and on real data, showing that our approach improves performance over multiple baselines and learns the dynamics of unmeasurable components of the process-based model effectively, even for small training datasets.

Continual Learning (CL) requires models to sequentially adapt to new tasks without forgetting old knowledge. Recently, Low-Rank Adaptation (LoRA), a representative Parameter-Efficient Fine-Tuning (PEFT) method, has gained increasing attention in CL. Several LoRA-based CL methods reduce interference across tasks by separating their update spaces, typically building the new space from the estimated null space of past tasks. However, they (i) overlook task-shared directions, which suppresses knowledge transfer, and (ii) fail to capture truly effective task-specific directions since these ``null bases" of old tasks can remain nearly inactive for new task under correlated tasks. To address this, we study LoRA learning capability from a projection energy perspective, and propose Low-rank Decomposition and Adaptation (LoDA). It performs a task-driven decomposition to build general and truly task-specific LoRA subspaces by solving two energy-based objectives, decoupling directions for knowledge sharing and isolation. LoDA fixes LoRA down-projections on two subspaces and learns robust up-projections via a Gradient-Aligned Optimization (GAO) approach. After each task, before integrating the LoRA updates into the backbone, LoDA derives a closed-form recalibration for the general update, approximating a feature-level joint optimum along this task-shared direction. Experiments indicate that LoDA outperforms existing CL methods.

Tokenization is a promising path to multi-modal models capable of jointly understanding protein sequences, structure, and function. Existing protein structure tokenizers create tokens by pooling information from local neighborhoods, an approach that limits their performance on generative and representation tasks. In this work, we present a method for global tokenization of protein structures in which successive tokens contribute increasing levels of detail to a global representation. This change resolves several issues with generative models based on local protein tokenization: it mitigates error accumulation, provides embeddings without sequence-reduction operations, and allows task-specific adaptation of a tokenized sequence's information content. We validate our method on reconstruction, generative, and representation tasks and demonstrate that it matches or outperforms existing models based on local protein structure tokenizers. We show that our adaptive approach enables inference criteria based on the information content of the generated proteins. We validate representations generated from our tokenizer on CATH classification tasks and demonstrate that non-linear probing on our tokenized sequences outperforms equivalent probing on representations from other tokenizers. Finally, we demonstrate how our method supports zero-shot protein shrinking and affinity maturation.

Reliable long-horizon precipitation nowcasting requires preserving fine-scale echo structures while maintaining coherent transport. Although Rectified Flow (RF) can generate detail-preserving future sequences, numerical ODE integration compounds velocity estimation errors and induces progressive off-manifold drift, causing morphological distortions at extended lead times. We propose Physically-guided Data-space Rectified Flow (PDRF), which re-parameterizes the generative ODE in data space: the network predicts the clean future sequence, analytically inducing a coupled vector field with an implicit restoring effect that suppresses drift. We also introduce a soft Semi-Lagrangian teacher based on an advection prior to regularize large-scale transport, while allowing local growth/decay/deformation to be learned from data. Experiments on four public benchmarks demonstrate consistent improvements in event-based skill and better preservation of intense-echo morphology over long horizons.

Discovering atom-level phenomena requires molecular dynamics (MD) simulations with ab initio accuracy. Machine learning interatomic potentials (MLIPs) enable stable, high-accuracy MD simulations, and their models exhibit scaling-law trends similar to large language models. However, the lack of scalable and efficient distributed training systems for conservative MLIPs makes them difficult to scale. This is because conservative MLIPs inherently follow a double-backward execution pattern, which involves computing gradients during the forward pass. This pattern creates a mismatch with existing distributed training systems, especially for pipeline parallelism. Therefore, we present JanusPipe, an efficient 3D-parallel (PP/DP/GP) training system tailored for conservative MLIPs. It integrates SymFold to enable memory-efficient pipeline parallelism for conservative MLIPs, and WaveK to reduce pipeline bubbles by balancing the four-phase compute time. Experimental results on 32 GPUs show that JanusPipe improves throughput by $1.51\times$ and $1.45\times$ on average over 1F1B and Hanayo, respectively.

High-fidelity solubility prediction is fundamental to pharmaceutical development and environmental partitioning, where accurate modeling must couple molecular structure with thermodynamic behavior across diverse chemical environments. However, recent advancements have been dominated by deep learning architectures that often sacrifice physical interpretability for predictive power. We challenge this trend by showing that state-of-the-art performance does not require such non-transparent architectures. To address this, we introduce DISSOLVR, a transparent framework for molecular solubility prediction. In addition, we perform a comprehensive literature review and a benchmarking study against various methods. We show that Dissolvr approaches the aleatoric limit of experimental uncertainty and achieves OOD generalization through structural invariance derived by mapping molecules to physically-grounded descriptors. Then, we present an LLM-assisted post-hoc explanation pipeline that bridges the gap between symbolic model artifacts and chemically grounded narratives. Finally, a comparative benchmark of a survey involving 22 expert chemists reveals that expert evaluators provide deep insights.

Generating long-horizon molecular dynamics (MD) is difficult due to error accumulation in time-domain autoregressive models, which causes drift, and fixed step-size constraints on temporal resolution. We propose **BioDynaSpec**, which reformulates protein dynamics as spatio-spectral generation: **Independent Windowed Fourier Decomposition (IWFD)** decomposes trajectories into window-wise spectral representations, and a generator combines low-to-high frequency autoregression with diffusion denoising to reconstruct continuous motion. This formulation is motivated by **a local near-equilibrium view of protein dynamics**: after per-window alignment, fluctuations around an anchor conformation are better characterized in spectral space, where local mode structure is more explicit than in frame-wise coordinates. To improve cross-residue and cross-frequency consistency, we introduce **Inter-Residue Frequency Coupling (IRFC)**, a learnable Gaussian distance bias in attention that injects a resonance-inspired structural prior. On ATLAS, BioDynaSpec improves 250-frame trajectory generation with $R_{250}=1.509$ Å, where $R_s$ denotes the mean per-frame C$\alpha$-RMSE over the first $s$ frames after alignment, reducing error by 60.4\% versus MDGEN and 57.2\% versus ProAR, while achieving the best PCA-2D displacement-profile correlation and stepwise distribution matching. For equilibrium conformational sampling, it achieves Root Mean $W_2=1.31$, MD PCA $W_2=0.90$, and Joint PCA $W_2=1.19$, improving over the next best method by 50.03\%, 35.25\%, and 47.58\%, respectively. It also improves near-equilibrium local-dynamics and covariance consistency, achieving PCA-PSD-LogCorr $=0.817$ and CFRE $=0.989$, corresponding to a 21.9\% gain and a 36.7\% reduction over the next best method, respectively. The source code is available at https://github.com/Linmj-Judy/BioDynaSpec.git.

We introduce \textsc{Mosaic}, a probabilistic weather forecasting model that addresses two sources of spectral degradation in ML-based weather prediction: training to predict the ensemble mean deterministically and compressive encoding creating an information bottleneck. \textsc{Mosaic} combines learned functional perturbations for ensemble forecasting with block-sparse attention, a hardware-aligned formulation that shares keys and values across spatially adjacent queries, enabling each block to dynamically attend to the most relevant regions. By capturing arbitrarily long-range dependencies at linear cost, \textsc{Mosaic} processes high-resolution weather data without compression. On IFS HRES data, \textsc{Mosaic} at 1.5° resolution matches or outperforms models trained on 0.25° data, with individual ensemble members exhibiting near-perfect spectral alignment across all resolved frequencies.

ML attacks on Learning with Errors (LWE) with binary or small secrets only succeed on LWE settings with very simple secrets. For example, they can recover secrets with up to three non-zero bits when models are trained on not-reduced LWE data, and three non-zero bits in the ''cruel region'' [9] when BKZ pre-processing is applied. We show that larger training sets and the use of repeated examples in the training data allow the recovery of denser secrets. We empirically observe a power-law relationship between model based attempts to recover the secrets, dataset size and repeated examples. We introduce a stepwise regression technique to recover the ``cool bits'' of the secret. Overall, these techniques allow for the recovery of denser binary secrets: up to Hamming weight $70$ (and $8$ cruel bits) for dimension $256$ $\log_2 q=20$ and $75$ (and $7$ cruel bits) for dimension $512$ $\log_2 q=41$ (vs $33$ and $63$ Hamming weight and $3$ cruel bits in previous works). We also demonstrate our methods' effectiveness on denser ternary secrets, showing a substantial improvement over prior work.

Learning fluid PDE dynamics has increasingly benefited from neural operators and Transformer-based models, but their latent states often remain opaque, and sample-wise attention can be costly at high resolutions. We propose the \emph{Gaussian Particle Operator} (GPO), a basis-to-basis neural operator that represents fields with a learned \emph{Gaussian basis}. Each atom carries explicit geometric parameters, including centers, anisotropic scales, and weights, yielding a compact, mesh-agnostic, and directly visualizable intermediate representation. GPO operates in modal space: learned Gaussian modal windows perform Petrov--Galerkin measurements, and a PG Gaussian Attention module couples the resulting modes globally before scattering them back to the spatial domain. This design is resolution-agnostic, scales near-linearly with the number of samples for a fixed modal budget, and naturally applies to irregular geometries and 3D domains. We separately evaluate Gaussian-basis reconstruction and operator prediction. Across standard PDE benchmarks and real reanalysis datasets, GPO achieves competitive accuracy against neural-operator and Transformer baselines, ranking best on most tasks and close to the best on the remainder. The learned particles and modal couplings further provide representation-level interpretability, positioning GPO as a useful intermediate representation rather than a one-to-one decomposition of physical structures. The code is available at \url{https://github.com/lizhihao2022/GPO}.

We introduce Flower, a neural architecture for learning PDE solution operators built entirely from multihead warps. Aside from pointwise channel mixing and a multiscale scaffold, Flowers use no Fourier multipliers, no dot-product attention, and no convolutional mixing. Each head predicts a displacement field and warps the mixed input features. Motivated by physics and computational efficiency, displacements are predicted pointwise, without any spatial aggregation, and nonlocality enters *only* through sparse sampling at source coordinates, *one* per head. Stacking warps in multiscale residual blocks yields Flowers, which implement adaptive, global interactions at linear cost. We theoretically motivate this design through three complementary lenses: flow maps for conservation laws, waves in inhomogeneous media, and a kinetic-theoretic continuum limit. Flowers achieve excellent performance on a broad suite of 2D and 3D time-dependent PDE benchmarks, particularly flows and waves. A compact 17M-parameter model consistently outperforms Fourier, convolution, and attention-based baselines of similar size, while a 150M-parameter variant improves over recent transformer-based foundation models with much more parameters, data, and training compute.

Reconstructing atomistic crystal structures from a single noisy STEM projection is an ill-posed inverse problem: multiple lattices can explain similar contrast, and purely feed-forward models cannot verify physical validity. We present **AutoMat**, a failure-aware agentic *controller* that performs inference-time hypothesis search with *closed-loop verification* to convert Scanning Transmission Electron Microscopy (STEM) images into simulation-ready crystal structures and downstream properties. AutoMat composes perception and physics modules—pattern-adaptive denoising, physics-guided template retrieval *as a state-dependent auxiliary branch*, symmetry-constrained atomic reconstruction, and MLIP-based relaxation/validation—and triggers rollback-and-retry when verification fails. For systematic evaluation, we introduce **STEM2Mat-Bench**, a benchmark dataset containing 450+ annotated samples. Performance is assessed using lattice root-mean-square deviation (RMSD), formation energy mean absolute error (MAE), and structure matching accuracy. Results demonstrate that AutoMat outperforms existing approaches including SOTA models, specialized domain tools, and closed-source multimodal large models. This work establishes a direct pathway from microscopic characterization to atomic-scale modeling, addressing a fundamental challenge in materials science.

Accurate prediction of nuclear magnetic resonance (NMR) chemical shifts is fundamental to spectral analysis and molecular structure elucidation, yet existing machine learning methods rely on limited, labor-intensive atom-assigned datasets. We propose a semi-supervised framework that learns NMR chemical shifts from millions of literature-extracted spectra without explicit atom-level assignments, integrating a small amount of labeled data with large-scale unassigned spectra. We formulate chemical shift prediction from literature spectra as a permutation-invariant set supervision problem, and show that under commonly satisfied conditions on the loss function, optimal bipartite matching reduces to a sorting-based loss, enabling stable large-scale semi-supervised training beyond traditional curated datasets. Our models achieve substantially improved accuracy and robustness over state-of-the-art methods and exhibit stronger generalization on significantly larger and more diverse molecular datasets. Moreover, by incorporating solvent information at scale, our approach captures systematic solvent effects across common NMR solvents for the first time. Overall, our results demonstrate that large-scale unlabeled spectra mined from the literature can serve as a practical and effective data source for training NMR shift models, suggesting a broader role of literature-derived, weakly structured data in data-centric AI for science.

Poisson-distributed latent variable models are widely used in computational neuroscience, but differentiating through discrete stochastic samples remains challenging. Two approaches address this: *Exponential Arrival Time* (EAT) simulation and *Gumbel-SoftMax* (GSM) relaxation. We provide the first systematic comparison of these methods, along with practical guidance for practitioners. Our main technical contribution is a modification to the EAT method that theoretically guarantees an unbiased first moment (exactly matching the firing rate), and reduces second-moment bias. We evaluate these methods on their distributional fidelity, gradient quality, and performance on two tasks: (1) variational autoencoders with Poisson latents, and (2) partially observable generalized linear models, where latent neural connectivity must be inferred from observed spike trains. Across all metrics, our modified EAT method exhibits better overall performance (often comparable to exact gradients), and substantially higher robustness to hyperparameter choices. These results extend to over-dispersed Negative Binomial latents, where modified EAT again performs best. However, only GSM generalizes to arbitrary non-Poisson distributions, including the under-dispersed regime. Together, our results clarify the trade-offs between these methods and offer concrete recommendations for practitioners working with Poisson latent variable models.

Many physical AI tasks require sequential implicit computation: at each step, boundary controls are applied, and the resulting configuration is obtained by solving an equilibrium problem. This setting arises naturally in deformable object manipulation, where even bending a deformable linear object (DLO) to a target shape can be nonlinear and multistable: identical boundary conditions may produce different configurations depending on actuation history. Unlike explicit transition models, the control-to-configuration relation is implicit and history-dependent, making long-horizon learning and control brittle; backpropagating through iterative solves is also memory- and compute-intensive. We propose Neural Control, a boundary-control framework that propagates gradients through branch-dependent sequences of equilibrium solves rather than a single fixed point. Neural Control computes trajectory-dependent proxy gradients by differentiating equilibrium conditions with an adjoint formulation, avoiding solver unrolling while keeping forward rollouts on converged equilibria. Combined with receding-horizon continuation, Neural Control re-anchors optimization to realized equilibria and mitigates basin switching. We validate Neural Control on simulated and real DLO manipulation, compare against SPSA and iCEM, and demonstrate applicability to a learned DEQ-style implicit equilibrium model.

Hazard and survival functions are natural, interpretable targets in time-to-event prediction tasks such as patient survival and disease progression modeling, but their inherent non-additivity fundamentally limits standard additive explanation methods. We introduce Survival Functional Decomposition (SurvFD), a principled approach for analyzing feature interactions in machine learning survival models. By decomposing higher-order effects into time-dependent and time-independent components, SurvFD offers a previously unrecognized perspective on survival explanations, explicitly characterizing when and why additive explanations fail. Building on this theoretical decomposition, we propose SurvSHAP-IQ, which extends Shapley interactions to time-indexed functions, providing a practical estimator for higher-order, time-dependent interactions. We validate the framework on simulated data and demonstrate its utility through cancer survival applications, including multi-modal breast cancer prognosis combining histopathology with clinical features. Together, SurvFD and SurvSHAP-IQ establish an interaction- and time-aware interpretability approach for survival modeling, with broad applicability across medicine, healthcare and other time-to-event prediction tasks.

Biomolecules such as proteins and small-molecule ligands play a central role in biological systems, arising from the tight interplay between sequence and three-dimensional structure. Recent generative models for biomolecular co-design aim to capture this interplay by jointly modeling coupled modalities. However, existing approaches largely adopt a parallel execution of marginal generative processes, implicitly enforcing fixed synchronous coupling. We argue that a critical but overlooked degree of freedom lies in how these marginal processes are \emph{temporally coupled} during training and generation, where inappropriate coupling can introduce high-variance supervision and inconsistent intermediate states, affecting modality consistency. To address this, we introduce GeoCoupling, a systematic framework that optimizes for temporal couplings between heterogeneous modalities. Empirical results across structure-based drug design and unconditional protein design demonstrate the learned couplings consistently outperform synchronous and randomly coupled baselines, yielding biomolecules with improved physical validity and diversity.

Credit assignment, the process of determining how changes in individual neurons and synapses influence a network’s output, is central to learning in brains and machines. Noise correlation-based methods, which estimate gradients by correlating perturbations of activity with changes in output, provide a biologically plausible solution to credit assignment but scales poorly as accurately estimating the Jacobian requires that the number of perturbations scale with network size. Moreover, isotropic noise conflicts with neurobiological observations that neural activity lies on a low-dimensional manifold. To address these drawbacks, we propose *neural manifold noise correlation* (NMNC), which performs credit assignment using perturbations restricted to the neural manifold. We show theoretically and empirically that the Jacobian row space aligns with the neural manifold in trained networks, and that manifold dimensionality scales slowly with network size. NMNC substantially improves performance and sample efficiency over vanilla noise correlation in convolutional networks trained on CIFAR-10, ImageNet-scale models, and recurrent networks. NMNC also yields representations more similar to the primate visual system than vanilla noise correlation. These findings offer a mechanistic hypothesis for how biological circuits could support credit assignment, and suggest that biologically inspired constraints may enable, rather than limit, effective learning at scale.

We aim to develop physics foundation models for science and engineering that provide real-time solutions to Partial Differential Equations (PDEs) which preserve structure and accuracy under adaptation to unseen geometries. To this end, we introduce General-Geometry Neural Whitney Forms (Geo-NeWF): a data-driven finite element method. We jointly learn a differential operator and compatible reduced finite element spaces defined on the underlying geometry. The resulting model is solved to generate predictions, while exactly preserving physical conservation laws through Finite Element Exterior Calculus. Geometry enters the model as a discretized mesh both through a transformer-based encoding and as the basis for the learned finite element spaces. This explicitly connects the underlying geometry and imposed boundary conditions to the solution, providing a powerful inductive bias for learning neural PDEs which we demonstrate improves generalization to unseen domains. We provide a novel parameterization of the constitutive model ensuring existence and uniqueness of the solution. Our approach demonstrates state-of-the-art performance on several steady-state PDE benchmarks and provides a significant improvement over conventional baselines on out-of-distribution geometries.