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Dongxia Wu

Publications and source records attributed to Dongxia Wu.

At least 19 recordsLinked to original sources
arXiv2026

PerturbCellRL: Verifier-Guided Reinforcement Learning for Single-Cell Perturbation Prediction

Single-cell perturbation models can reduce costly wet-lab screening by predicting how cells respond transcriptionally to interventions. While recent generative models improve population-level prediction, individual generated cells are not explicitly checked for biological consistency. We introduce PerturbCellRL, a reinforcement learning (RL) framework that post-trains a pretrained single-cell transcriptomic generator using a suite of cell-level verifiers as rewards. These verifiers define four rewards: Pearson top-k similarity, RMSE top-k proximity, DE Spearman, and Pathway activity. The Pathway activity verifier rewards cells whose pathway responses match known perturbation biology. We evaluate PerturbCellRL on multiple genetic and chemical perturbation benchmarks. Across these benchmarks, PerturbCellRL improves over the pretrained flow-matching generator on reward-aligned evaluation metrics and a held-out evaluation metric. Moreover, PerturbCellRL remains competitive with state-of-the-art methods on population-level metrics. Together, these results frame trustworthy single-cell prediction as verifier-guided generative alignment, moving beyond matching expression distributions toward predictions whose single-cell perturbation effects are explicitly checked for biological consistency.

cs.LG↗
arXiv2026

Calibrating LLMs with Semantic-level Reward

As large language models (LLMs) are deployed in consequential settings such as medical question answering and legal reasoning, the ability to estimate when their outputs are likely to be correct is essential for safe and reliable use, requiring well-calibrated uncertainty. Standard reinforcement learning with verifiable rewards (RLVR) trains models with a binary correctness reward that is indifferent to confidence, providing no penalty for confident but wrong predictions and thereby degrading calibration. Recent work addresses this by training models to produce verbalized confidence scores alongside answers and rewarding agreement with correctness. However, verbalized confidence is calibrated at the token level and thus exhibits inconsistency across textual variations with same semantic meaning. We propose \textbf{Calibration with Semantic Reward (CSR)}, a framework that calibrates language models directly in semantic space without a verbalized confidence interface. CSR combines the correctness reward with a novel semantic calibration reward that encourages exploitation among correct rollouts by promoting semantic agreement, and exploration among incorrect ones by discouraging spurious consistency. Experiments across three model families on HotpotQA (in-distribution) and TriviaQA, MSMARCO, and NQ-Open (out-of-distribution) show that CSR consistently achieves lower ECE and higher AUROC than verbalized-confidence baselines across nearly all settings, reducing ECE by up to $40\%$ and improving AUROC by up to $31\%$ over verbalized-confidence baselines, with calibration behavior generalizing robustly across all four evaluation settings.

cs.CL↗
arXiv2026

BALAR : A Bayesian Agentic Loop for Active Reasoning

Large language models increasingly operate in interactive settings where solving a task requires multiple rounds of information exchange with a user. However, most current systems treat dialogue reactively and lack a principled mechanism to reason about what information is missing and which question should be asked next. We propose BALAR (Bayesian Agentic Loop for Active Reasoning), a task-agnostic outer-loop algorithm that requires no fine-tuning and enables structured multi-turn interaction between an LLM agent and a user. BALAR maintains a structured belief over latent states, selects clarifying questions by maximizing expected mutual information, and dynamically expands its state representation when the current one proves insufficient. We evaluate BALAR on three diverse benchmarks: AR-Bench-DC (detective cases), AR-Bench-SP (thinking puzzles), and iCraft-MD (clinical diagnosis). BALAR significantly outperforms all baselines across all three benchmarks, with $14.6\%$ higher accuracy on AR-Bench-DC, $38.5\%$ on AR-Bench-SP, and $30.5\%$ on iCraft-MD.

cs.AI↗
arXiv2026

Uncertainty-Aware Distribution-to-Distribution Flow Matching for Scientific Imaging

Distribution-to-distribution generative models support scientific imaging tasks ranging from modeling cellular perturbation responses to translating medical images across conditions. Trustworthy generation requires reliability, or generalization across labs, devices, and experimental conditions, and accountability, or detecting out-of-distribution cases where predictions may be unreliable. We leverage Stochastic Flow Matching (SFM), a marginal-preserving stochastic extension of flow matching for improved generalization under distribution shift. SFM augments deterministic flows with a diffusion term together with a learned score-based drift correction, retaining the learned transport marginals while modeling conditional variability. Building on this SFM framework, we introduce Bayesian Stochastic Flow Matching (BSFM) as a companion uncertainty quantification mechanism and develop AVUQ (Antithetic Variance-reduction Uncertainty Quantification) to approximately estimate epistemic and aleatoric uncertainty via sample-efficient antithetic sampling with approximate posterior inference. We further use AVUQ to yield anomaly scores for unreliable generation detection. Experiments on cellular imaging (BBBC021, JUMP) and brain fMRI (Theory of Mind) across diverse unseen scenarios show that SFM improves generalization while AVUQ provides effective uncertainty-based anomaly scores under practical sampling budgets.

cs.LG↗
arXiv2026

CellFluxRL: Biologically-Constrained Virtual Cell Modeling via Reinforcement Learning

Building virtual cells with generative models to simulate cellular behavior in silico is emerging as a promising paradigm for accelerating drug discovery. However, prior image-based generative approaches can produce implausible cell images that violate basic physical and biological constraints. To address this, we propose to post-train virtual cell models with reinforcement learning (RL), leveraging biologically meaningful evaluators as reward functions. We design seven rewards spanning three categories-biological function, structural validity, and morphological correctness-and optimize the state-of-the-art CellFlux model to yield CellFluxRL. CellFluxRL consistently improves over CellFlux across all rewards, with further performance boosts from test-time scaling. Overall, our results present a virtual cell modeling framework that enforces physically-based constraints through RL, advancing beyond "visually realistic" generations towards "biologically meaningful" ones.

cs.LG↗
arXiv2026

Divide and Learn: Multi-Objective Combinatorial Optimization at Scale

Multi-objective combinatorial optimization seeks Pareto-optimal solutions over exponentially large discrete spaces, yet existing methods sacrifice generality, scalability, or theoretical guarantees. We reformulate it as an online learning problem over a decomposed decision space, solving position-wise bandit subproblems via adaptive expert-guided sequential construction. This formulation admits regret bounds of $O(d\sqrt{T \log T})$ depending on subproblem dimensionality \(d\) rather than combinatorial space size. On standard benchmarks, our method achieves 80--98\% of specialized solvers performance while achieving two to three orders of magnitude improvement in sample and computational efficiency over Bayesian optimization methods. On real-world hardware-software co-design for AI accelerators with expensive simulations, we outperform competing methods under fixed evaluation budgets. The advantage grows with problem scale and objective count, establishing bandit optimization over decomposed decision spaces as a principled alternative to surrogate modeling or offline training for multi-objective optimization.

cs.LG↗
arXiv2025

SimulRAG: Simulator-based RAG for Grounding LLMs in Long-form Scientific QA

Large Language Models (LLMs) show promise in generating long-form scientific explanations that synthesize evidence and connect multiple factors. However, in long-form scientific question answering, LLMs often hallucinate, producing unsupported or inconsistent claims. Retrieval-Augmented Generation (RAG) improves trustworthiness by grounding generation in external sources; scientific simulators are valuable because they can validate quantitative hypotheses and capture evolving dynamics. Yet simulation-based RAG is non-trivial due to two challenges: how to retrieve from scientific simulators, and how to efficiently verify and update long-form answers. To overcome these challenges, we propose SimulRAG, a simulator-based RAG framework with a generalized retrieval interface that translates between text and simulator parameters/outputs. SimulRAG further introduces claim-level generation with uncertainty estimation and simulator boundary assessment (UE+SBA) to selectively verify and update claims. Unlike tool-first or holistic answer revision, it first elicits diverse answers without retrieval and then grounds uncertain, simulator-verifiable atomic claims with simulator evidence. We also release a long-form scientific QA benchmark spanning climate science, epidemiology, and urban planning, with ground truth verified by simulations and human annotators. Experiments show SimulRAG improves informativeness by 30.4% and factuality by 16.3% over the strongest adapted RAG baselines, while UE+SBA enhances claim-level efficiency and quality.

cs.CL↗
arXiv2024

MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning

Current generative models for drug discovery primarily use molecular docking as an oracle to guide the generation of active compounds. However, such models are often not useful in practice because even compounds with high docking scores do not consistently show real-world experimental activity. More accurate methods for activity prediction exist, such as molecular dynamics based binding free energy calculations, but they are too computationally expensive to use in a generative model. To address this challenge, we propose Multi-Fidelity Latent space Active Learning (MF-LAL), a generative modeling framework that integrates a set of oracles with varying cost-accuracy tradeoffs. Using active learning, we train a surrogate model for each oracle and use these surrogates to guide generation of compounds with high predicted activity. Unlike previous approaches that separately learn the surrogate model and generative model, MF-LAL combines the generative and multi-fidelity surrogate models into a single framework, allowing for more accurate activity prediction and higher quality samples. Our experiments on two disease-relevant proteins show that MF-LAL produces compounds with significantly better binding free energy scores than other single and multi-fidelity approaches (~50% improvement in mean binding free energy score). The code is available at https://github.com/Rose-STL-Lab/MF-LAL.

cs.LG↗
arXiv2024

Functional-level Uncertainty Quantification for Calibrated Fine-tuning on LLMs

Accurate uncertainty quantification in large language models (LLMs) is essential for reliable confidence estimation, yet fine-tuned LLMs often become overconfident under limited adaptation data. Existing uncertainty methods for PEFT-based LLMs are largely post hoc, estimating uncertainty after fine-tuning rather than improving how adapters specialize to task-specific input-output relationships. We propose Functional-Level Uncertainty Quantification for Calibrated Fine-Tuning (UQ4CT), which calibrates uncertainty over the functional space induced by prompt-dependent mixtures of LoRA experts. UQ4CT implements this perspective through a mixture-of-experts fine-tuning framework, where a calibration loss aligns functional-level confidence with predictive correctness during training. Across four multiple-choice benchmarks and two open-ended generative QA tasks, UQ4CT reduces Expected Calibration Error (ECE) by over $25\%$ while preserving high accuracy. Under distribution shift, UQ4CT maintains superior calibration and competitive accuracy, demonstrating improved reliability and generalization for fine-tuned LLMs.

cs.LG↗
arXiv2024

Diffusion-BBO: Diffusion-Based Inverse Modeling for Online Black-Box Optimization

Online black-box optimization (BBO) aims to optimize an objective function by iteratively querying a black-box oracle in a sample-efficient way. While prior studies focus on forward approaches such as Gaussian Processes (GPs) to learn a surrogate model for the unknown objective function, they struggle with steering clear of out-of-distribution and invalid designs in scientific discovery tasks. Recently, inverse modeling approaches that map the objective space to the design space with conditional diffusion models have demonstrated impressive capability in learning the data manifold. However, these approaches proceed in an offline fashion with pre-collected data. How to design inverse approaches for online BBO to actively query new data and improve the sample efficiency remains an open question. In this work, we propose Diffusion-BBO, a sample-efficient online BBO framework leveraging the conditional diffusion model as the inverse surrogate model. Diffusion-BBO employs a novel acquisition function Uncertainty-aware Exploration (UaE) to propose scores in the objective space for conditional sampling. We theoretically prove that Diffusion-BBO with UaE achieves a near-optimal solution for online BBO. We also empirically demonstrate that Diffusion-BBO with UaE outperforms existing online BBO baselines across 6 scientific discovery tasks.

cs.LG↗
arXiv2024

Multi-Fidelity Residual Neural Processes for Scalable Surrogate Modeling

Multi-fidelity surrogate modeling aims to learn an accurate surrogate at the highest fidelity level by combining data from multiple sources. Traditional methods relying on Gaussian processes can hardly scale to high-dimensional data. Deep learning approaches utilize neural network based encoders and decoders to improve scalability. These approaches share encoded representations across fidelities without including corresponding decoder parameters. This hinders inference performance, especially in out-of-distribution scenarios when the highest fidelity data has limited domain coverage. To address these limitations, we propose Multi-fidelity Residual Neural Processes (MFRNP), a novel multi-fidelity surrogate modeling framework. MFRNP explicitly models the residual between the aggregated output from lower fidelities and ground truth at the highest fidelity. The aggregation introduces decoders into the information sharing step and optimizes lower fidelity decoders to accurately capture both in-fidelity and cross-fidelity information. We show that MFRNP significantly outperforms state-of-the-art in learning partial differential equations and a real-world climate modeling task. Our code is published at: https://github.com/Rose-STL-Lab/MFRNP

cs.LG↗
arXiv2024

Diffusion Models as Constrained Samplers for Optimization with Unknown Constraints

Addressing real-world optimization problems becomes particularly challenging when analytic objective functions or constraints are unavailable. While numerous studies have addressed the issue of unknown objectives, limited research has focused on scenarios where feasibility constraints are not given explicitly. Overlooking these constraints can lead to spurious solutions that are unrealistic in practice. To deal with such unknown constraints, we propose to perform optimization within the data manifold using diffusion models. To constrain the optimization process to the data manifold, we reformulate the original optimization problem as a sampling problem from the product of the Boltzmann distribution defined by the objective function and the data distribution learned by the diffusion model. Depending on the differentiability of the objective function, we propose two different sampling methods. For differentiable objectives, we propose a two-stage framework that begins with a guided diffusion process for warm-up, followed by a Langevin dynamics stage for further correction. For non-differentiable objectives, we propose an iterative importance sampling strategy using the diffusion model as the proposal distribution. Comprehensive experiments on a synthetic dataset, six real-world black-box optimization datasets, and a multi-objective molecule optimization dataset show that our method achieves better or comparable performance with previous state-of-the-art baselines.

cs.LG↗
arXiv2024

MFBind: a Multi-Fidelity Approach for Evaluating Drug Compounds in Practical Generative Modeling

Current generative models for drug discovery primarily use molecular docking to evaluate the quality of generated compounds. However, such models are often not useful in practice because even compounds with high docking scores do not consistently show experimental activity. More accurate methods for activity prediction exist, such as molecular dynamics based binding free energy calculations, but they are too computationally expensive to use in a generative model. We propose a multi-fidelity approach, Multi-Fidelity Bind (MFBind), to achieve the optimal trade-off between accuracy and computational cost. MFBind integrates docking and binding free energy simulators to train a multi-fidelity deep surrogate model with active learning. Our deep surrogate model utilizes a pretraining technique and linear prediction heads to efficiently fit small amounts of high-fidelity data. We perform extensive experiments and show that MFBind (1) outperforms other state-of-the-art single and multi-fidelity baselines in surrogate modeling, and (2) boosts the performance of generative models with markedly higher quality compounds.

q-bio.BM↗
arXiv2024

Learning Granger Causality from Instance-wise Self-attentive Hawkes Processes

We address the problem of learning Granger causality from asynchronous, interdependent, multi-type event sequences. In particular, we are interested in discovering instance-level causal structures in an unsupervised manner. Instance-level causality identifies causal relationships among individual events, providing more fine-grained information for decision-making. Existing work in the literature either requires strong assumptions, such as linearity in the intensity function, or heuristically defined model parameters that do not necessarily meet the requirements of Granger causality. We propose Instance-wise Self-Attentive Hawkes Processes (ISAHP), a novel deep learning framework that can directly infer the Granger causality at the event instance level. ISAHP is the first neural point process model that meets the requirements of Granger causality. It leverages the self-attention mechanism of the transformer to align with the principles of Granger causality. We empirically demonstrate that ISAHP is capable of discovering complex instance-level causal structures that cannot be handled by classical models. We also show that ISAHP achieves state-of-the-art performance in proxy tasks involving type-level causal discovery and instance-level event type prediction.

cs.LG↗
arXiv2023

Deep Bayesian Active Learning for Accelerating Stochastic Simulation

Stochastic simulations such as large-scale, spatiotemporal, age-structured epidemic models are computationally expensive at fine-grained resolution. While deep surrogate models can speed up the simulations, doing so for stochastic simulations and with active learning approaches is an underexplored area. We propose Interactive Neural Process (INP), a deep Bayesian active learning framework for learning deep surrogate models to accelerate stochastic simulations. INP consists of two components, a spatiotemporal surrogate model built upon Neural Process (NP) family and an acquisition function for active learning. For surrogate modeling, we develop Spatiotemporal Neural Process (STNP) to mimic the simulator dynamics. For active learning, we propose a novel acquisition function, Latent Information Gain (LIG), calculated in the latent space of NP based models. We perform a theoretical analysis and demonstrate that LIG reduces sample complexity compared with random sampling in high dimensions. We also conduct empirical studies on three complex spatiotemporal simulators for reaction diffusion, heat flow, and infectious disease. The results demonstrate that STNP outperforms the baselines in the offline learning setting and LIG achieves the state-of-the-art for Bayesian active learning.

cs.LG↗
arXiv2023

Disentangled Multi-Fidelity Deep Bayesian Active Learning

To balance quality and cost, various domain areas of science and engineering run simulations at multiple levels of sophistication. Multi-fidelity active learning aims to learn a direct mapping from input parameters to simulation outputs at the highest fidelity by actively acquiring data from multiple fidelity levels. However, existing approaches based on Gaussian processes are hardly scalable to high-dimensional data. Deep learning-based methods often impose a hierarchical structure in hidden representations, which only supports passing information from low-fidelity to high-fidelity. These approaches can lead to the undesirable propagation of errors from low-fidelity representations to high-fidelity ones. We propose a novel framework called Disentangled Multi-fidelity Deep Bayesian Active Learning (D-MFDAL), which learns the surrogate models conditioned on the distribution of functions at multiple fidelities. On benchmark tasks of learning deep surrogates of partial differential equations including heat equation, Poisson's equation and fluid simulations, our approach significantly outperforms state-of-the-art in prediction accuracy and sample efficiency.

cs.LG↗
arXiv2022

Multi-fidelity Hierarchical Neural Processes

Science and engineering fields use computer simulation extensively. These simulations are often run at multiple levels of sophistication to balance accuracy and efficiency. Multi-fidelity surrogate modeling reduces the computational cost by fusing different simulation outputs. Cheap data generated from low-fidelity simulators can be combined with limited high-quality data generated by an expensive high-fidelity simulator. Existing methods based on Gaussian processes rely on strong assumptions of the kernel functions and can hardly scale to high-dimensional settings. We propose Multi-fidelity Hierarchical Neural Processes (MF-HNP), a unified neural latent variable model for multi-fidelity surrogate modeling. MF-HNP inherits the flexibility and scalability of Neural Processes. The latent variables transform the correlations among different fidelity levels from observations to latent space. The predictions across fidelities are conditionally independent given the latent states. It helps alleviate the error propagation issue in existing methods. MF-HNP is flexible enough to handle non-nested high dimensional data at different fidelity levels with varying input and output dimensions. We evaluate MF-HNP on epidemiology and climate modeling tasks, achieving competitive performance in terms of accuracy and uncertainty estimation. In contrast to deep Gaussian Processes with only low-dimensional (< 10) tasks, our method shows great promise for speeding up high-dimensional complex simulations (over 7000 for epidemiology modeling and 45000 for climate modeling).

cs.LG↗
arXiv2021

A Deep Learning Based Automatic Defect Analysis Framework for In-situ TEM Ion Irradiations

Videos captured using Transmission Electron Microscopy (TEM) can encode details regarding the morphological and temporal evolution of a material by taking snapshots of the microstructure sequentially. However, manual analysis of such video is tedious, error-prone, unreliable, and prohibitively time-consuming if one wishes to analyze a significant fraction of frames for even videos of modest length. In this work, we developed an automated TEM video analysis system for microstructural features based on the advanced object detection model called YOLO and tested the system on an in-situ ion irradiation TEM video of dislocation loops formed in a FeCrAl alloy. The system provides analysis of features observed in TEM including both static and dynamic properties using the YOLO-based defect detection module coupled to a geometry analysis module and a dynamic tracking module. Results show that the system can achieve human comparable performance with an F1 score of 0.89 for fast, consistent, and scalable frame-level defect analysis. This result is obtained on a real but exceptionally clean and stable data set and more challenging data sets may not achieve this performance. The dynamic tracking also enabled evaluation of individual defect evolution like per defect growth rate at a fidelity never before achieved using common human analysis methods. Our work shows that automatically detecting and tracking interesting microstructures and properties contained in TEM videos is viable and opens new doors for evaluating materials dynamics.

cs.CV↗