arXiv subjects

Shuiwang Ji

Publications and source records attributed to Shuiwang Ji.

At least 19 recordsLinked to original sources

arXiv2026

VerifiedLab: Harnessing Knowns for Unknowns

Across human history, knowledge has undergone several transitions, from orality to writing and then to digital archives. At each transition, humans established new conventions to preserve knowledge for the new era. Nowadays, as research agents are increasingly deployed for laboratory experiments, knowledge is crossing another boundary: from records written for humans to those for machines. In this work, we introduce VerifiedLab, a multi-agent harness framework for this human-to-machine transition of knowledge. VerifiedLab transforms research output from passive artifacts into active systems that accelerate downstream use, adoption and prediction of future trends. In VerifiedLab, a team of AI scientists with distinct roles reasons over records verified field by field: a principal investigator plans, a librarian computes the evidence directly from the records, specialists draft, and a gate and a critic check each claim against the measured reliability of its data before the harness decides whether to release or withhold it. We demonstrate the efficacy of VerifiedLab through extensive experiments on perovskite solar cells: VerifiedLab recovers known physical trends, anticipates devices reported a year later, and lets AI scientists inherit the literature together with a measure of how far it can be trusted. By scaling the inference-time verification compute, VerifiedLab introduces a new pathway for knowledge dissemination and machine harness for AI co-scientists.

cs.AI↗

arXiv2026

FRIGID: Scaling Diffusion-Based Molecular Generation from Mass Spectra at Training and Inference Time

Tandem mass spectrometry is prominent in scientific discovery workflows for identifying unknown small molecules, yet high-throughput structural elucidation remains challenging. While recent autoregressive and graph diffusion models have shown promise in de novo elucidation, performance remains limited by poor scalability during both training and inference time. In this work, we present FRIGID, a framework with a novel diffusion language model that generates molecular structures conditioned on mass spectra via intermediate fingerprint representations and determined chemical formulae, training at the scale of hundreds of millions of unlabeled structures. We then demonstrate how forward fragmentation models enable inference-time scaling by identifying spectrum-inconsistent fragments and refining them through targeted remasking and denoising. While FRIGID already achieves strong performance with its diffusion base, inference-time scaling significantly improves its accuracy, surpassing 18% Top-1 accuracy on the challenging MassSpecGym benchmark and tripling the Top-1 accuracy of the leading methods on NPLIB1. Further empirical analyses show that FRIGID exhibits log-linear performance scaling with increasing inference-time compute, opening a promising new direction for continued improvements in de novo structural elucidation. FRIGID code is publicly available at https://github.com/coleygroup/FRIGID.

cs.LG↗

arXiv2026

AnaDiffusion: Anatomically Compositional Latent Diffusion for Controllable 3D Brain MRI Generation

3D brain MRI generation has made significant advances in medical imaging, simulation, and controllable anatomical analysis. However, existing generative models typically synthesize 3D volumes monolithically, often overlooking regional anatomical structures and limiting local controllability. To address these limitations, we introduce AnaDiffusion, an anatomically compositional latent diffusion framework that factorizes the generation process into distinct, anatomically meaningful regions, followed by part-to-whole assembly and global refinement. Our approach first trains part diffusion models to capture local structural priors. We then inject an assembled anatomical composite of the parts into the whole-brain latent representation and continue denoising. This mechanism enables the model to resolve global context while preserving the injected anatomy. As a result, AnaDiffusion produces both explicit part assets and a globally coherent volume, thereby enabling controllable part editing without requiring subject-specific dense segmentation maps at inference time while maintaining consistent part-to-whole brain structure. On the subject-disjoint ADNI test split, AnaDiffusion achieves the lowest FID across the whole brain, left and right hemispheres, cerebellar-brainstem complex, and seam regions. It also achieves the best cerebellar and second-best ventricular and brainstem absolute Cohen's d values among the evaluated methods. In localized editing experiments, paired MS-SSIM demonstrates high target transfer and off-target preservation, supporting controllable part replacement with minimal unintended anatomical alterations.

cs.CV↗

arXiv2026

Generative AI for Autonomous Driving: Frontiers and Opportunities

Generative Artificial Intelligence (GenAI) constitutes a transformative technological wave that reconfigures industries through its unparalleled capabilities for content creation, reasoning, planning, and multimodal understanding. This revolutionary force offers the most promising path yet toward solving one of engineering's grandest challenges: achieving reliable, fully autonomous driving, particularly the pursuit of Level 5 autonomy. This survey delivers a comprehensive and critical synthesis of the emerging role of GenAI across the autonomous driving stack. We begin by distilling the principles and trade-offs of modern generative modeling, encompassing VAEs, GANs, Diffusion Models, and Large Language Models (LLMs). We then map their frontier applications in image, LiDAR, trajectory, occupancy, video generation as well as LLM-guided reasoning and decision making. We categorize practical applications, such as synthetic data workflows, end-to-end driving strategies, high-fidelity digital twin systems, smart transportation networks, and cross-domain transfer to embodied AI. We identify key obstacles and possibilities such as comprehensive generalization across rare cases, evaluation and safety checks, budget-limited implementation, regulatory compliance, ethical concerns, and environmental effects, while proposing research plans across theoretical assurances, trust metrics, transport integration, and socio-technical influence. By unifying these threads, the survey provides a forward-looking reference for researchers, engineers, and policymakers navigating the convergence of generative AI and advanced autonomous mobility. An actively maintained repository of cited works is available at https://github.com/taco-group/GenAI4AD.

cs.CV↗

arXiv2026

Equivariant Flow Matching for Electron Density Prediction

Machine learning surrogates for density functional theory (DFT) have been increasingly used to reduce the cost of first-principles calculations. In this arena, predicting real-space electron densities offers a scalable and transferable initialization for self-consistent field (SCF) procedures. However, current methods face a clear dilemma. That is, grid-based architectures incur a high computational cost, while basis-set methods fail to capture the structural correlations inherent in the coefficient space. Here, we develop OrbFlow, an $\mathrm{SE}(3)$-equivariant generative model that predicts Gaussian-type orbital (GTO) coefficients via flow matching. OrbFlow retains the efficiency of a compact atom-centered basis while replacing pointwise regression with a learned probability path over the full coefficient space. It is trained through a two-phase trajectory curriculum that mitigates discretization drift during numerical integration. OrbFlow achieves state-of-the-art accuracy on QM9, reducing density error by 13.6% relative to the previous best model, and reduces error by 51% to 63% on every molecule of the MD benchmark relative to the strongest prior method sharing its basis. The predicted density also cuts SCF iterations by up to 68% with zero-shot transfer to unseen exchange-correlation functionals and recovers dipole and quadrupole moments to within a few percent of DFT references without any SCF calculation.

physics.chem-ph↗

arXiv2026

Assay-Aware BindingDB: Curating Experimental Context for Binding Affinity Prediction

Protein--ligand binding affinity prediction is fundamental to computational drug discovery, yet modern AI-driven models are limited by pervasive heterogeneity in their training data: bioactivity values are aggregated across diverse assay types and experimental conditions without accounting for protocol-level differences, introducing systematic noise. Existing harmonization approaches either discard assay-level metadata or collapse it into coarse categorical distinctions, leaving rich contextual signal unused. We address this gap with two contributions. First, we introduce Assay-Aware BindingDB, augmenting 74,425 BindingDB protein--ligand pairs across four assay types (ITC, SPR, RBA, and FPA) with structured metadata extracted from primary literature using a two-stage agentic framework that separates evidence extraction from ontology-conditioned JSON synthesis. Against domain-expert references, the framework achieves presence F1 $\geq 0.947$ and semantic content accuracy $\geq 0.913$ across all assay types. Second, we develop a context-conditioned affinity model that injects an assay-context embedding into the Boltz-2 affinity module. On a paper-level held-out split, the model reduces combined-regime MSE from $1.27$ to $1.19$ and increases Pearson correlation from $0.64$ to $0.67$, with significant gains for SPR and FPA. ITC, the only label- and immobilization-free assay considered, shows no improvement, consistent with its design removing the protocol artifacts the metadata captures. These results support the hypothesis that systematically curated assay metadata provides informative signal for affinity prediction.

q-bio.BM↗

arXiv2026

Toward Greater Autonomy in Materials Discovery Agents: Unifying Planning, Physics, and Scientists

We aim at designing language agents with greater autonomy for crystal materials discovery. While most of existing studies restrict the agents to perform specific tasks within predefined workflows, we aim to automate workflow planning given high-level goals and scientist intuition. To this end, we propose Materials Agent unifying Planning, Physics, and Scientists, known as MAPPS. MAPPS consists of a Workflow Planner, a Tool Code Generator, and a Scientific Mediator. The Workflow Planner uses large language models (LLMs) to generate structured and multi-step workflows. The Tool Code Generator synthesizes executable Python code for various tasks, including invoking a force field foundation model that encodes physics. The Scientific Mediator coordinates communications, facilitates scientist feedback, and ensures robustness through error reflection and recovery. By unifying planning, physics, and scientists, MAPPS enables flexible and reliable materials discovery with greater autonomy, achieving a five-fold improvement in stability, uniqueness, and novelty rates compared with prior generative models when evaluated on the MP-20 data. We provide extensive experiments across diverse tasks to show that MAPPS is a promising framework for autonomous materials discovery.

cs.AI↗

arXiv2026

When Do Multi-Agent Systems Help? An Information Bottleneck Perspective

LLM powered multi-agent systems (MAS) have emerged as a promising paradigm for complex tasks. However, their advantages over single-agent systems (SAS) remain unclear, with performance varying inconsistently across settings. Here, we provide an information bottleneck perspective on elucidating the differences between MAS and SAS. Specifically, our key observation is that a SAS accumulates its full reasoning trace in one shared context, while a MAS uses isolated local contexts connected by bounded relay messages. We show that, under infinite relay bandwidth, any SAS can be simulated by a MAS that transmits the full upstream context. Thus, the nontrivial advantage of MAS arises under bounded relays, where compression introduces a fundamental trade-off: reducing redundant context can improve efficiency, but may also incur loss of task-relevant information. We formalize this trade-off as an information bottleneck controlled by an effective parameter $β$, which captures how the balance shifts with model capability, and shows that MAS gains arise when context reduction outweighs relay information loss. We conduct 18 controlled experiments across five benchmarks and three model scales to validate our theoretical studies. We observe that MAS consistently helps when relays are near-sufficient, especially for weaker models. In contrast, MAS gains shrink or reverse when relays incur information loss, especially for stronger models that can already extract useful information from redundant context and thus gain little from compression. Our study shows that multi-agent design is fundamentally an information-bottleneck optimization problem. This perspective explains when bounded inter-agent communication helps or hurts.

cs.LG↗

arXiv2026

Spin-Weighted Spherical Harmonics Enable Complete and Scalable $\mathrm{E}(3)$-Equivariant Networks

$\mathrm{E}(3)$-equivariant networks are promising for 3D atomistic system modeling, yet their scalability is limited by the $O(L^6)$ complexity of the Clebsch-Gordan Tensor Product (CGTP). The recently proposed Gaunt Tensor Product (GTP) reduces the complexity but is unable to capture the antisymmetric paths, resulting in incomplete expressivity. In this work, we present SpinGTP, an approach to overcome the GTP incompleteness by generalizing from scalar functions to Spin-Weighted Spherical Harmonics (SWSH). By relying on the algebraic properties of SWSH, SpinGTP recovers the missing antisymmetric interactions while maintaining the asymptotic efficiency of GTP. It also allows for a more expressive equivariant basis that naturally accounts for the parity-odd components of tensor products. We evaluate SpinGTP across diverse benchmarks, including Tetris, 3BPA, SPICE-MACE-OFF, and OC20. Our results show that SpinGTP achieves accuracies comparable to full CGTP. Notably, by explicitly capturing antisymmetric paths, SpinGTP exhibits superior performance in tasks involving chiral materials and non-centrosymmetric geometries. This work provides a complete, scalable, and mathematically rigorous path toward high-order equivariance in large-scale 3D atomistic system simulations.

cs.LG↗

arXiv2026

Data-Efficient Autoregressive-to-Diffusion Language Models via On-Policy Distillation

We study the transformation of autoregressive models (ARLMs) into diffusion language models (DLMs). Rather than pretraining from scratch, prior work replaces the causal attention in ARLMs with bidirectional attention and then trains the resulting model using a DLM objective. However, these approaches incur two distribution shifts. First, transitioning from a next-token prediction objective to a DLM objective can discard knowledge acquired by the ARLM during training. Second, standard DLMs suffer from a train-inference mismatch, as the training loss is defined on randomly masked sequences rather than the trajectories encountered at inference produced by confidence-based decoding. To address both challenges, we introduce an On-Policy Diffusion Language Model (OPDLM) in which On-Policy Distillation (OPD) is employed for ARLM-to-DLM transformation. Specifically, OPDLM is trained via self-OPD, where the student, an ARLM with bidirectional attention, generates its own trajectories, and the teacher, the original frozen ARLM, distills its knowledge by providing target logits on these trajectories. By training directly in an on-policy manner, OPDLM eliminates the train-inference mismatch in DLMs, while distillation from the original model enhances knowledge retention from the ARLM. Empirical results demonstrate that OPDLM requires 15x to 7,000x fewer training tokens with strong performance across a wide variety of tasks. OPDLM avoids the prohibitive cost of DLM pretraining and positions DLM transformation as a form of ARLM post-training.

cs.CL↗

arXiv2026

Efficient Prediction of SO(3)-Equivariant Hamiltonian Matrices via SO(2) Local Frames

We consider the task of predicting Hamiltonian matrices to accelerate electronic structure calculations, which plays an important role in physics, chemistry, and materials science. Motivated by the inherent relationship between the off-diagonal blocks of the Hamiltonian matrix and the SO(2) local frame, we propose a novel and efficient network, called QHNetV2, that achieves global SO(3) equivariance without the costly SO(3) Clebsch-Gordan tensor products. This is achieved by introducing a set of new efficient and powerful SO(2)-equivariant operations and performing all off-diagonal feature updates and message passing within SO(2) local frames, thereby eliminating the need of SO(3) tensor products. Moreover, a continuous SO(2) tensor product is performed within the SO(2) local frame at each node to fuse node features, mimicking the symmetric contraction operation. Extensive experiments on the large QH9 and MD17 datasets demonstrate that our model achieves superior performance across a wide range of molecular structures and trajectories, highlighting its strong generalization capability. The proposed SO(2) operations on SO(2) local frames offer a promising direction for scalable and symmetry-aware learning of electronic structures. Our code will be released as part of the AIRS library https://github.com/divelab/AIRS.

cs.LG↗

arXiv2026

Learnability-Informed Fine-Tuning of Diffusion Language Models

We aim to improve the reasoning capabilities of diffusion language models (DLMs). While SFT is a popular post-training recipe for autoregressive models, its use in DLMs faces challenges and can even hurt performance, though the underlying causes remain understudied. Our analysis reveals that vanilla SFT overlooks learnability, namely what and when tokens are learned. Specifically, rare tokens are difficult to learn when most of the input is masked, whereas it is straightforward and thus of little value to learn common tokens when most of the input is unmasked. Motivated by our analysis, we propose LIFT, an efficient SFT-based post-training algorithm for DLMs. LIFT learns easy tokens when most of the input is masked and hard tokens when more context is available, thus aligning the training with the information available at different diffusion time steps. Our results show that LIFT outperforms existing SFT baselines across six reasoning benchmarks, achieving up to a 3x relative gain on AIME'24 and AIME'25. Our code is publicly available at https://github.com/divelab/LIFT.

cs.CL↗

arXiv2026

Orbital Transformers for Predicting Wavefunctions in Time-Dependent Density Functional Theory

We aim to learn wavefunctions simulated by time-dependent density functional theory (TDDFT), which can be efficiently represented as linear combination coefficients of atomic orbitals. In real-time TDDFT, the electronic wavefunctions of a molecule evolve over time in response to an external excitation, enabling first-principles predictions of physical properties such as optical absorption, electron dynamics, and high-order response. However, conventional real-time TDDFT relies on time-consuming propagation of all occupied states with fine time steps. In this work, we propose OrbEvo, which is based on an equivariant graph transformer architecture and learns to evolve the full electronic wavefunction coefficients across time steps. First, to account for external field, we design an equivariant conditioning to encode both strength and direction of external electric field and break the symmetry from SO(3) to SO(2). Furthermore, we design two OrbEvo models, OrbEvo-WF and OrbEvo-DM, using wavefunction pooling and density matrix as interaction method, respectively. Motivated by the central role of the density functional in TDDFT, OrbEvo-DM encodes the density matrix aggregated from all occupied electronic states into feature vectors via tensor contraction, providing a more intuitive approach to learn the time evolution operator. We adopt a training strategy specifically tailored to limit the error accumulation of time-dependent wavefunctions over autoregressive rollout. To evaluate our approach, we generate TDDFT datasets consisting of 5,000 different molecules in the QM9 dataset and 1,500 molecular configurations of the malonaldehyde molecule in the MD17 dataset. Results show that our OrbEvo model accurately captures quantum dynamics of excited states under external field, including time-dependent wavefunctions, time-dependent dipole moment, and optical absorption spectra.

cs.LG↗

arXiv2026

A Two-Phase Deep Learning Framework for Adaptive Time-Stepping in High-Speed Flow Modeling

We consider the problem of modeling high-speed flows using machine learning methods. While most prior studies focus on low-speed fluid flows in which uniform time-stepping is practical, flows approaching and exceeding the speed of sound exhibit sudden changes such as shock waves. In such cases, it is essential to use adaptive time-stepping methods to allow a temporal resolution sufficient to resolve these phenomena while simultaneously balancing computational costs. Here, we propose a two-phase machine learning method, known as ShockCast, to model high-speed flows with adaptive time-stepping. In the first phase, we propose to employ a machine learning model to predict the timestep size. In the second phase, the predicted timestep is used as an input along with the current fluid fields to advance the system state by the predicted timestep. We explore several physically-motivated components for timestep prediction and introduce timestep conditioning strategies inspired by neural ODE and Mixture of Experts. We evaluate our methods by generating three supersonic flow datasets, available at https://huggingface.co/divelab. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

cs.LG↗

arXiv2026

ReviewGrounder: Improving Review Substantiveness with Rubric-Guided, Tool-Integrated Agents

The rapid rise in AI conference submissions has driven increasing exploration of large language models (LLMs) for peer review support. However, LLM-based reviewers often generate superficial, formulaic comments lacking substantive, evidence-grounded feedback. We attribute this to the underutilization of two key components of human reviewing: explicit rubrics and contextual grounding in existing work. To address this, we introduce REVIEWBENCH, a benchmark evaluating review text according to paper-specific rubrics derived from official guidelines, the paper's content, and human-written reviews. We further propose REVIEWGROUNDER, a rubric-guided, tool-integrated multi-agent framework that decomposes reviewing into drafting and grounding stages, enriching shallow drafts via targeted evidence consolidation. Experiments on REVIEWBENCH show that REVIEWGROUNDER, using a Phi-4-14B-based drafter and a GPT-OSS-120B-based grounding stage, consistently outperforms baselines with substantially stronger/larger backbones (e.g., GPT-4.1 and DeepSeek-R1-670B) in both alignment with human judgments and rubric-based review quality across 8 dimensions. The code is available \href{https://github.com/EigenTom/ReviewGrounder}{here}.

cs.CL↗

arXiv2026

Autonomous Agents for Scientific Discovery: Orchestrating Scientists, Language, Code, and Physics

Computing has long served as a cornerstone of scientific discovery. Recently, a paradigm shift has emerged with the rise of large language models (LLMs), introducing autonomous systems, referred to as agents, that accelerate discovery across varying levels of autonomy. These language agents provide a flexible and versatile framework that orchestrates interactions with human scientists, natural language, computer language and code, and physics. This paper presents our view and vision of LLM-based scientific agents and their growing role in transforming the scientific discovery lifecycle, from hypothesis discovery, experimental design and execution, to result analysis and refinement. We critically examine current methodologies, emphasizing key innovations, practical achievements, and outstanding limitations. Additionally, we identify open research challenges and outline promising directions for building more robust, generalizable, and adaptive scientific agents. Our analysis highlights the transformative potential of autonomous agents to accelerate scientific discovery across diverse domains.

cs.AI↗

arXiv2026

Equivariance via Minimal Frame Averaging for More Symmetries and Efficiency

We consider achieving equivariance in machine learning systems via frame averaging. Current frame averaging methods involve a costly sum over large frames or rely on sampling-based approaches that only yield approximate equivariance. Here, we propose Minimal Frame Averaging (MFA), a mathematical framework for constructing provably minimal frames that are exactly equivariant. The general foundations of MFA also allow us to extend frame averaging to more groups than previously considered, including the Lorentz group for describing symmetries in space-time, and the unitary group for complex-valued domains. Results demonstrate the efficiency and effectiveness of encoding symmetries via MFA across a diverse range of tasks, including $n$-body simulation, top tagging in collider physics, and relaxed energy prediction. Our code is available at https://github.com/divelab/MFA.

cs.LG↗

arXiv2026

Curriculum Reinforcement Learning from Easy to Hard Tasks Improves LLM Reasoning

We aim to improve the reasoning capabilities of language models via reinforcement learning (RL). Recent RL post-trained models like DeepSeek-R1 have demonstrated reasoning abilities on mathematical and coding tasks. However, prior studies suggest that using RL alone to improve reasoning on inherently difficult tasks is less effective. Here, we draw inspiration from curriculum learning and propose to schedule tasks from easy to hard (E2H), allowing LLMs to build reasoning skills gradually. Our method is termed E2H Reasoner. Empirically, we observe that, although easy tasks are important initially, fading them out through appropriate scheduling is essential in preventing overfitting. Theoretically, we establish convergence guarantees for E2H Reasoner within an approximate policy iteration framework. We derive finite-sample complexity bounds and show that when tasks are appropriately decomposed and conditioned, learning through curriculum stages requires fewer total samples than direct learning. Experiments across multiple domains show that E2H Reasoner significantly improves the reasoning ability of small LLMs (1.5B to 3B), which otherwise struggle when trained with vanilla RL alone, highlighting the effectiveness of our method. Our code can be found on https://github.com/divelab/E2H-Reasoning.

cs.LG↗