arXiv subjects

Xiaoning Qian

Publications and source records attributed to Xiaoning Qian.

At least 19 recordsLinked to original sources

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

GFlowNet Training by Policy Gradients

Generative Flow Networks (GFlowNets) have been shown effective to generate combinatorial objects with desired properties. We here propose a new GFlowNet training framework, with policy-dependent rewards, that bridges keeping flow balance of GFlowNets to optimizing the expected accumulated reward in traditional Reinforcement-Learning (RL). This enables the derivation of new policy-based GFlowNet training methods, in contrast to existing ones resembling value-based RL. It is known that the design of backward policies in GFlowNet training affects efficiency. We further develop a coupled training strategy that jointly solves GFlowNet forward policy training and backward policy design. Performance analysis is provided with a theoretical guarantee of our policy-based GFlowNet training. Experiments on both simulated and real-world datasets verify that our policy-based strategies provide advanced RL perspectives for robust gradient estimation to improve GFlowNet performance.

cs.LG↗

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

Perron--Frobenius Operator Matching for Generative Modeling

We introduce Perron--Frobenius Operator Matching (PFOM), a generative framework that matches density evolution via the integral PF operator, subsuming flow, diffusion, and jump models. We prove that among Bregman divergences, only Kullback--Leibler divergence preserves equality between density-level and sample-conditioned objectives, yielding a practical loss equivalent to Koopman path matching. We further develop Nesterov-accelerated training and sampling that stabilize discretization and accelerate convergence. %On Gaussian mixtures and two-moons, PFOM achieves faster KL/$W_2$/MMD decrease and improved wall-clock efficiency with empirical validation. PFOM unifies operator-theoretic identification with modern generative modeling and opens paths to adaptive dictionaries and high-dimensional applications.

cs.LG↗

arXiv2026

Goal-driven Bayesian Optimal Experimental Design for Robust Decision-Making Under Model Uncertainty

Bayesian optimal experimental design (BOED) selects experiments to maximize information gain about model parameters. However, in decision-critical settings, reducing parameter uncertainty does not necessarily improve downstream decisions, as only specific parameter directions relevant to the objective truly matter. We propose GoBOED, a goal-driven BOED framework that directly optimizes experimental designs for a specified decision-making objective. GoBOED combines an amortized variational posterior surrogate with a differentiable convex decision layer, enabling gradient-based design optimization that is fully decision-focused. We theoretically show that GoBOED gradients are insensitive to parameter directions irrelevant to the decision objective, providing a formal justification for why goal-driven design achieves equivalent decision quality over a wider set of experimental designs than information-gain maximization. Empirically, across source localization, epidemic management, and pharmacokinetic control, GoBOED identifies designs that better align with downstream decision objectives and reveals that near-optimal design windows are substantially wider than those predicted by goal-agnostic BOED approaches.

cs.LG↗

arXiv2026

Causal Discovery Should Embrace the Wisdom of the Crowd

This paper argues for recognizing an emerging paradigm of causal learning by wisdom of the crowd. Recent developments in government, industry, and research point to the rise of decentralized and crowd-based approaches within causal modeling, where causal knowledge distributed across many contributors can be systematically elicited and integrated with causal learning workflows. In this paradigm, causal learning becomes a distributed decision-making problem: each participant contributes partial and potentially noisy knowledge, while collective contributions help construct a global causal structure. This direction is enabled by advances in crowdsourcing platforms, expert knowledge elicitation, aggregation techniques, and large language model (LLM)-augmented information acquisition. Its promise is increasingly visible in early research and emerging real-world practices. Building on this momentum, we outline a framework for crowd-based causal learning spanning elicitation, modeling, aggregation, and optimization. We further discuss the opportunities and challenges introduced by this paradigm and call for interdisciplinary collaboration across causal learning, collective intelligence, human-AI interaction, and decision science.

cs.LG↗

arXiv2026

Evaluating GFlowNet from partial episodes for stable and flexible policy-based training

Generative Flow Networks (GFlowNets) were developed to learn policies for efficiently sampling combinatorial candidates by interpreting their generative processes as trajectories in directed acyclic graphs. In the value-based training workflow, the objective is to enforce the balance over partial episodes between the flows of the learned policy and the estimated flows of the desired policy, implicitly encouraging policy divergence minimization. The policy-based strategy alternates between estimating the policy divergence and updating the policy, but reliable estimation of the divergence under directed acyclic graphs remains a major challenge. This work bridges the two perspectives by showing that flow balance also yields a principled policy evaluator that measures the divergence, and an evaluation balance objective over partial episodes is proposed for learning the evaluator. As demonstrated on both synthetic and real-world tasks, evaluation balance not only strengthens the reliability of policy-based training but also broadens its flexibility by seamlessly supporting parameterized backward policies and enabling the integration of offline data-collection techniques.

cs.LG↗

arXiv2026

Causal Bayesian Optimization via Exogenous Distribution Learning

Maximizing a target variable as an operational objective within a structural causal model is a fundamental problem. Causal Bayesian Optimization (CBO) approaches typically achieve this either by performing interventions that modify the causal structure to increase the reward or by introducing action nodes to endogenous variables, thereby adjusting the data-generating mechanisms to meet the objective. In this paper, we propose a novel method that learns the distribution of exogenous variables-an aspect often ignored or marginalized through expectation in existing CBO frameworks. By modeling the exogenous distribution, we enhance the approximation fidelity of the data-generating structural causal models (SCMs) used in surrogate models, which are commonly trained on limited observational data. Furthermore, the ability to recover exogenous variables enables the application of our approach to more general causal structures beyond the confines of Additive Noise Models (ANMs) and single-mode Gaussian, allowing the use of more expressive priors for context noise. We incorporate the learned exogenous distribution into a new CBO method, demonstrating its advantages across diverse datasets and application scenarios.

cs.LG↗

arXiv2025

C-LoRA: Contextual Low-Rank Adaptation for Uncertainty Estimation in Large Language Models

Low-Rank Adaptation (LoRA) offers a cost-effective solution for fine-tuning large language models (LLMs), but it often produces overconfident predictions in data-scarce few-shot settings. To address this issue, several classical statistical learning approaches have been repurposed for scalable uncertainty-aware LoRA fine-tuning. However, these approaches neglect how input characteristics affect the predictive uncertainty estimates. To address this limitation, we propose Contextual Low-Rank Adaptation (C-LoRA) as a novel uncertainty-aware and parameter efficient fine-tuning approach, by developing new lightweight LoRA modules contextualized to each input data sample to dynamically adapt uncertainty estimates. Incorporating data-driven contexts into the parameter posteriors, C-LoRA mitigates overfitting, achieves well-calibrated uncertainties, and yields robust predictions. Extensive experiments on LLaMA2-7B models demonstrate that C-LoRA consistently outperforms the state-of-the-art uncertainty-aware LoRA methods in both uncertainty quantification and model generalization. Ablation studies further confirm the critical role of our contextual modules in capturing sample-specific uncertainties. C-LoRA sets a new standard for robust, uncertainty-aware LLM fine-tuning in few-shot regimes. Although our experiments are limited to 7B models, our method is architecture-agnostic and, in principle, applies beyond this scale; studying its scaling to larger models remains an open problem. Our code is available at https://github.com/ahra99/c_lora.

cs.LG↗

arXiv2025

InvarGC: Invariant Granger Causality for Heterogeneous Interventional Time Series under Latent Confounding

Granger causality is widely used for causal structure discovery in complex systems from multivariate time series data. Traditional Granger causality tests based on linear models often fail to detect even mild non-linear causal relationships. Therefore, numerous recent studies have investigated non-linear Granger causality methods, achieving improved performance. However, these methods often rely on two key assumptions: causal sufficiency and known interventional targets. Causal sufficiency assumes the absence of latent confounders, yet their presence can introduce spurious correlations. Moreover, real-world time series data usually come from heterogeneous environments, without prior knowledge of interventions. Therefore, in practice, it is difficult to distinguish intervened environments from non-intervened ones, and even harder to identify which variables or timesteps are affected. To address these challenges, we propose Invariant Granger Causality (InvarGC), which leverages cross-environment heterogeneity to mitigate the effects of latent confounding and to distinguish intervened from non-intervened environments with edge-level granularity, thereby recovering invariant causal relations. In addition, we establish the identifiability under these conditions. Extensive experiments on both synthetic and real-world datasets demonstrate the competitive performance of our approach compared to state-of-the-art methods.

cs.LG↗

arXiv2025

Data-Augmented Few-Shot Neural Emulator for Computer-Model System Identification

Partial differential equations (PDEs) underpin the modeling of many natural and engineered systems. It can be convenient to express such models as neural PDEs rather than using traditional numerical PDE solvers by replacing part or all of the PDE's governing equations with a neural network representation. Neural PDEs are often easier to differentiate, linearize, reduce, or use for uncertainty quantification than the original numerical solver. They are usually trained on solution trajectories obtained by long-horizon rollout of the PDE solver. Here we propose a more sample-efficient data-augmentation strategy for generating neural PDE training data from a computer model by space-filling sampling of local "stencil" states. This approach removes a large degree of spatiotemporal redundancy present in trajectory data and oversamples states that may be rarely visited but help the neural PDE generalize across the state space. We demonstrate that accurate neural PDE stencil operators can be learned from synthetic training data generated by the computational equivalent of 10 timesteps' worth of numerical simulation. Accuracy is further improved if we assume access to a single full-trajectory simulation from the computer model, which is typically available in practice. Across several PDE systems, we show that our data-augmented stencil data yield better trained neural stencil operators, with clear performance gains compared with naively sampled stencil data from simulation trajectories. Finally, with only 10 solver steps' worth of augmented stencil data, our approach outperforms traditional ML emulators trained on thousands of trajectories in long-horizon rollout accuracy and stability.

cs.LG↗

arXiv2025

Uncertainty-Aware Adaptation of Large Language Models for Protein-Protein Interaction Analysis

Identification of protein-protein interactions (PPIs) helps derive cellular mechanistic understanding, particularly in the context of complex conditions such as neurodegenerative disorders, metabolic syndromes, and cancer. Large Language Models (LLMs) have demonstrated remarkable potential in predicting protein structures and interactions via automated mining of vast biomedical literature; yet their inherent uncertainty remains a key challenge for deriving reproducible findings, critical for biomedical applications. In this study, we present an uncertainty-aware adaptation of LLMs for PPI analysis, leveraging fine-tuned LLaMA-3 and BioMedGPT models. To enhance prediction reliability, we integrate LoRA ensembles and Bayesian LoRA models for uncertainty quantification (UQ), ensuring confidence-calibrated insights into protein behavior. Our approach achieves competitive performance in PPI identification across diverse disease contexts while addressing model uncertainty, thereby enhancing trustworthiness and reproducibility in computational biology. These findings underscore the potential of uncertainty-aware LLM adaptation for advancing precision medicine and biomedical research.

cs.LG↗

arXiv2025

Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems

Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural sciences. Today, AI has started to advance natural sciences by improving, accelerating, and enabling our understanding of natural phenomena at a wide range of spatial and temporal scales, giving rise to a new area of research known as AI for science (AI4Science). Being an emerging research paradigm, AI4Science is unique in that it is an enormous and highly interdisciplinary area. Thus, a unified and technical treatment of this field is needed yet challenging. This work aims to provide a technically thorough account of a subarea of AI4Science; namely, AI for quantum, atomistic, and continuum systems. These areas aim at understanding the physical world from the subatomic (wavefunctions and electron density), atomic (molecules, proteins, materials, and interactions), to macro (fluids, climate, and subsurface) scales and form an important subarea of AI4Science. A unique advantage of focusing on these areas is that they largely share a common set of challenges, thereby allowing a unified and foundational treatment. A key common challenge is how to capture physics first principles, especially symmetries, in natural systems by deep learning methods. We provide an in-depth yet intuitive account of techniques to achieve equivariance to symmetry transformations. We also discuss other common technical challenges, including explainability, out-of-distribution generalization, knowledge transfer with foundation and large language models, and uncertainty quantification. To facilitate learning and education, we provide categorized lists of resources that we found to be useful. We strive to be thorough and unified and hope this initial effort may trigger more community interests and efforts to further advance AI4Science.

cs.LG↗

arXiv2025

A Benchmark for Quantum Chemistry Relaxations via Machine Learning Interatomic Potentials

Computational quantum chemistry plays a critical role in drug discovery, chemical synthesis, and materials science. While first-principles methods, such as density functional theory (DFT), provide high accuracy in modeling electronic structures and predicting molecular properties, they are computationally expensive. Machine learning interatomic potentials (MLIPs) have emerged as promising surrogate models that aim to achieve DFT-level accuracy while enabling efficient large-scale atomistic simulations. The development of accurate and transferable MLIPs requires large-scale, high-quality datasets with both energy and force labels. Critically, MLIPs must generalize not only to stable geometries but also to intermediate, non-equilibrium conformations encountered during atomistic simulations. In this work, we introduce PubChemQCR, a large-scale dataset of molecular relaxation trajectories curated from the raw geometry optimization outputs of the PubChemQC project. PubChemQCR is the largest publicly available dataset of DFT-based relaxation trajectories for small organic molecules, comprising approximately 3.5 million trajectories and over 300 million molecular conformations computed at various levels of theory. Each conformation is labeled with both total energy and atomic forces, making the dataset suitable for training and evaluating MLIPs. To provide baselines for future developments, we benchmark nine representative MLIP models on the dataset. Our resources are publicly available at https://huggingface.co/divelab

q-bio.QM↗

arXiv2025

Cost-effective Reduced-Order Modeling via Bayesian Active Learning

Machine Learning surrogates have been developed to accelerate solving systems dynamics of complex processes in different science and engineering applications. To faithfully capture governing systems dynamics, these methods rely on large training datasets, hence restricting their applicability in real-world problems. In this work, we propose BayPOD-AL, an active learning framework based on an uncertainty-aware Bayesian proper orthogonal decomposition (POD) approach, which aims to effectively learn reduced-order models from high-fidelity full-order models representing complex systems. Experimental results on predicting the temperature evolution over a rod demonstrate BayPOD-AL's effectiveness in suggesting the informative data and reducing computational cost related to constructing a training dataset compared to other uncertainty-guided active learning strategies. Furthermore, we demonstrate BayPOD-AL's generalizability and efficiency by evaluating its performance on a dataset of higher temporal resolution than the training dataset.

cs.LG↗

arXiv2025

A Materials Foundation Model via Hybrid Invariant-Equivariant Architectures

Machine learning interatomic potentials (MLIPs) can predict energy, force, and stress of materials and enable a wide range of downstream discovery tasks. A key design choice in MLIPs involves the trade-off between invariant and equivariant architectures. Invariant models offer computational efficiency but may not perform as well, especially when predicting high-order outputs. In contrast, equivariant models can capture high-order symmetries, but are computationally expensive. In this work, we propose HIENet, a hybrid invariant-equivariant materials interatomic potential model that integrates both invariant and equivariant message passing layers, while provably satisfying key physical constraints. HIENet achieves state-of-the-art performance with considerable computational speedups over prior models. Experimental results on both common benchmarks and downstream materials discovery tasks demonstrate the efficiency and effectiveness of HIENet.

cs.LG↗

arXiv2025

Invariant Tokenization of Crystalline Materials for Language Model Enabled Generation

We consider the problem of crystal materials generation using language models (LMs). A key step is to convert 3D crystal structures into 1D sequences to be processed by LMs. Prior studies used the crystallographic information framework (CIF) file stream, which fails to ensure SE(3) and periodic invariance and may not lead to unique sequence representations for a given crystal structure. Here, we propose a novel method, known as Mat2Seq, to tackle this challenge. Mat2Seq converts 3D crystal structures into 1D sequences and ensures that different mathematical descriptions of the same crystal are represented in a single unique sequence, thereby provably achieving SE(3) and periodic invariance. Experimental results show that, with language models, Mat2Seq achieves promising performance in crystal structure generation as compared with prior methods.

cs.LG↗

arXiv2024

Dynamic Incremental Optimization for Best Subset Selection

Best subset selection is considered the `gold standard' for many sparse learning problems. A variety of optimization techniques have been proposed to attack this non-smooth non-convex problem. In this paper, we investigate the dual forms of a family of $\ell_0$-regularized problems. An efficient primal-dual algorithm is developed based on the primal and dual problem structures. By leveraging the dual range estimation along with the incremental strategy, our algorithm potentially reduces redundant computation and improves the solutions of best subset selection. Theoretical analysis and experiments on synthetic and real-world datasets validate the efficiency and statistical properties of the proposed solutions.

cs.LG↗