arXiv subjects

Hongtu Zhu

Publications and source records attributed to Hongtu Zhu.

At least 55 records · Page 3Linked to original sources

arXiv2025

Challenge Summary U-MedSAM: Uncertainty-aware MedSAM for Medical Image Segmentation

Medical Image Foundation Models have proven to be powerful tools for mask prediction across various datasets. However, accurately assessing the uncertainty of their predictions remains a significant challenge. To address this, we propose a new model, U-MedSAM, which integrates the MedSAM model with an uncertainty-aware loss function and the Sharpness-Aware Minimization (SharpMin) optimizer. The uncertainty-aware loss function automatically combines region-based, distribution-based, and pixel-based loss designs to enhance segmentation accuracy and robustness. SharpMin improves generalization by finding flat minima in the loss landscape, thereby reducing overfitting. Our method was evaluated in the CVPR24 MedSAM on Laptop challenge, where U-MedSAM demonstrated promising performance.

eess.IV↗

arXiv2025

ARMA-Design: Optimal Treatment Allocation Strategies for A/B Testing in Partially Observable Time Series Experiments

Online experiments %in which experimental units receive a sequence of treatments over time are frequently employed in many technological companies to evaluate the performance of a newly developed policy, product, or treatment relative to a baseline control. In many applications, the experimental units receive a sequence of treatments over time. To handle these time-dependent settings, existing A/B testing solutions typically assume a fully observable experimental environment that satisfies the Markov condition. However, this assumption often does not hold in practice. This paper studies the optimal design for A/B testing in partially observable online experiments. We introduce a controlled (vector) autoregressive moving average model to capture partial observability. We introduce a small signal asymptotic framework to simplify the calculation of asymptotic mean squared errors of average treatment effect estimators under various designs. We develop two algorithms to estimate the optimal design: one utilizing constrained optimization and the other employing reinforcement learning. We demonstrate the superior performance of our designs using two dispatch simulators that realistically mimic the behaviors of drivers and passengers to create virtual environments, along with two real datasets from a ride-sharing company. A Python implementation of our proposal is available at https://github.com/datake/ARMADesign.

econ.EM↗

arXiv2025

Large Language Models for Bioinformatics

With the rapid advancements in large language model (LLM) technology and the emergence of bioinformatics-specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications. This survey aims to address this need by providing a thorough review of BioLMs, focusing on their evolution, classification, and distinguishing features, alongside a detailed examination of training methodologies, datasets, and evaluation frameworks. We explore the wide-ranging applications of BioLMs in critical areas such as disease diagnosis, drug discovery, and vaccine development, highlighting their impact and transformative potential in bioinformatics. We identify key challenges and limitations inherent in BioLMs, including data privacy and security concerns, interpretability issues, biases in training data and model outputs, and domain adaptation complexities. Finally, we highlight emerging trends and future directions, offering valuable insights to guide researchers and clinicians toward advancing BioLMs for increasingly sophisticated biological and clinical applications.

q-bio.QM↗

arXiv2024

Optimal Functional Bilinear Regression with Two-way Functional Covariates via Reproducing Kernel Hilbert Space

Traditional functional linear regression usually takes a one-dimensional functional predictor as input and estimates the continuous coefficient function. Modern applications often generate two-dimensional covariates, which become matrices when observed at grid points. To avoid the inefficiency of the classical method involving estimation of a two-dimensional coefficient function, we propose a functional bilinear regression model, and introduce an innovative three-term penalty to impose roughness penalty in the estimation. The proposed estimator exhibits minimax optimal property for prediction under the framework of reproducing kernel Hilbert space. An iterative generalized cross-validation approach is developed to choose tuning parameters, which significantly improves the computational efficiency over the traditional cross-validation approach. The statistical and computational advantages of the proposed method over existing methods are further demonstrated via simulated experiments, the Canadian weather data, and a biochemical long-range infrared light detection and ranging data.

stat.ME↗

arXiv2024

Sampling-guided Heterogeneous Graph Neural Network with Temporal Smoothing for Scalable Longitudinal Data Imputation

In this paper, we propose a novel framework, the Sampling-guided Heterogeneous Graph Neural Network (SHT-GNN), to effectively tackle the challenge of missing data imputation in longitudinal studies. Unlike traditional methods, which often require extensive preprocessing to handle irregular or inconsistent missing data, our approach accommodates arbitrary missing data patterns while maintaining computational efficiency. SHT-GNN models both observations and covariates as distinct node types, connecting observation nodes at successive time points through subject-specific longitudinal subnetworks, while covariate-observation interactions are represented by attributed edges within bipartite graphs. By leveraging subject-wise mini-batch sampling and a multi-layer temporal smoothing mechanism, SHT-GNN efficiently scales to large datasets, while effectively learning node representations and imputing missing data. Extensive experiments on both synthetic and real-world datasets, including the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset, demonstrate that SHT-GNN significantly outperforms existing imputation methods, even with high missing data rates. The empirical results highlight SHT-GNN's robust imputation capabilities and superior performance, particularly in the context of complex, large-scale longitudinal data.

cs.LG↗

arXiv2024

Enhancing Missing Data Imputation through Combined Bipartite Graph and Complete Directed Graph

In this paper, we aim to address a significant challenge in the field of missing data imputation: identifying and leveraging the interdependencies among features to enhance missing data imputation for tabular data. We introduce a novel framework named the Bipartite and Complete Directed Graph Neural Network (BCGNN). Within BCGNN, observations and features are differentiated as two distinct node types, and the values of observed features are converted into attributed edges linking them. The bipartite segment of our framework inductively learns embedding representations for nodes, efficiently utilizing the comprehensive information encapsulated in the attributed edges. In parallel, the complete directed graph segment adeptly outlines and communicates the complex interdependencies among features. When compared to contemporary leading imputation methodologies, BCGNN consistently outperforms them, achieving a noteworthy average reduction of 15% in mean absolute error for feature imputation tasks under different missing mechanisms. Our extensive experimental investigation confirms that an in-depth grasp of the interdependence structure substantially enhances the model's feature embedding ability. We also highlight the model's superior performance in label prediction tasks involving missing data, and its formidable ability to generalize to unseen data points.

cs.LG↗

arXiv2024

CARES: A Comprehensive Benchmark of Trustworthiness in Medical Vision Language Models

Artificial intelligence has significantly impacted medical applications, particularly with the advent of Medical Large Vision Language Models (Med-LVLMs), sparking optimism for the future of automated and personalized healthcare. However, the trustworthiness of Med-LVLMs remains unverified, posing significant risks for future model deployment. In this paper, we introduce CARES and aim to comprehensively evaluate the Trustworthiness of Med-LVLMs across the medical domain. We assess the trustworthiness of Med-LVLMs across five dimensions, including trustfulness, fairness, safety, privacy, and robustness. CARES comprises about 41K question-answer pairs in both closed and open-ended formats, covering 16 medical image modalities and 27 anatomical regions. Our analysis reveals that the models consistently exhibit concerns regarding trustworthiness, often displaying factual inaccuracies and failing to maintain fairness across different demographic groups. Furthermore, they are vulnerable to attacks and demonstrate a lack of privacy awareness. We publicly release our benchmark and code in https://cares-ai.github.io/.

cs.LG↗

arXiv2024

R2Gen-Mamba: A Selective State Space Model for Radiology Report Generation

Radiology report generation is crucial in medical imaging,but the manual annotation process by physicians is time-consuming and labor-intensive, necessitating the develop-ment of automatic report generation methods. Existingresearch predominantly utilizes Transformers to generateradiology reports, which can be computationally intensive,limiting their use in real applications. In this work, we presentR2Gen-Mamba, a novel automatic radiology report genera-tion method that leverages the efficient sequence processingof the Mamba with the contextual benefits of Transformerarchitectures. Due to lower computational complexity ofMamba, R2Gen-Mamba not only enhances training and in-ference efficiency but also produces high-quality reports.Experimental results on two benchmark datasets with morethan 210,000 X-ray image-report pairs demonstrate the ef-fectiveness of R2Gen-Mamba regarding report quality andcomputational efficiency compared with several state-of-the-art methods. The source code can be accessed online.

cs.CL↗

arXiv2024

RULE: Reliable Multimodal RAG for Factuality in Medical Vision Language Models

The recent emergence of Medical Large Vision Language Models (Med-LVLMs) has enhanced medical diagnosis. However, current Med-LVLMs frequently encounter factual issues, often generating responses that do not align with established medical facts. Retrieval-Augmented Generation (RAG), which utilizes external knowledge, can improve the factual accuracy of these models but introduces two major challenges. First, limited retrieved contexts might not cover all necessary information, while excessive retrieval can introduce irrelevant and inaccurate references, interfering with the model's generation. Second, in cases where the model originally responds correctly, applying RAG can lead to an over-reliance on retrieved contexts, resulting in incorrect answers. To address these issues, we propose RULE, which consists of two components. First, we introduce a provably effective strategy for controlling factuality risk through the calibrated selection of the number of retrieved contexts. Second, based on samples where over-reliance on retrieved contexts led to errors, we curate a preference dataset to fine-tune the model, balancing its dependence on inherent knowledge and retrieved contexts for generation. We demonstrate the effectiveness of RULE on medical VQA and report generation tasks across three datasets, achieving an average improvement of 47.4% in factual accuracy. We publicly release our benchmark and code in https://github.com/richard-peng-xia/RULE.

cs.LG↗

arXiv2024

UU-Mamba: Uncertainty-aware U-Mamba for Cardiac Image Segmentation

Biomedical image segmentation is critical for accurate identification and analysis of anatomical structures in medical imaging, particularly in cardiac MRI. Manual segmentation is labor-intensive, time-consuming, and prone to errors, highlighting the need for automated methods. However, current machine learning approaches face challenges like overfitting and data demands. To tackle these issues, we propose a new UU-Mamba model, integrating the U-Mamba model with the Sharpness-Aware Minimization (SAM) optimizer and an uncertainty-aware loss function. SAM enhances generalization by locating flat minima in the loss landscape, thus reducing overfitting. The uncertainty-aware loss combines region-based, distribution-based, and pixel-based loss designs to improve segmentation accuracy and robustness. Evaluation of our method is performed on the ACDC cardiac dataset, outperforming state-of-the-art models including TransUNet, Swin-Unet, nnUNet, and nnFormer. Our approach achieves Dice Similarity Coefficient (DSC) and Mean Squared Error (MSE) scores, demonstrating its effectiveness in cardiac MRI segmentation.

eess.IV↗

arXiv2024

Causal Deepsets for Off-policy Evaluation under Spatial or Spatio-temporal Interferences

Off-policy evaluation (OPE) is widely applied in sectors such as pharmaceuticals and e-commerce to evaluate the efficacy of novel products or policies from offline datasets. This paper introduces a causal deepset framework that relaxes several key structural assumptions, primarily the mean-field assumption, prevalent in existing OPE methodologies that handle spatio-temporal interference. These traditional assumptions frequently prove inadequate in real-world settings, thereby restricting the capability of current OPE methods to effectively address complex interference effects. In response, we advocate for the implementation of the permutation invariance (PI) assumption. This innovative approach enables the data-driven, adaptive learning of the mean-field function, offering a more flexible estimation method beyond conventional averaging. Furthermore, we present novel algorithms that incorporate the PI assumption into OPE and thoroughly examine their theoretical foundations. Our numerical analyses demonstrate that this novel approach yields significantly more precise estimations than existing baseline algorithms, thereby substantially improving the practical applicability and effectiveness of OPE methodologies. A Python implementation of our proposed method is available at https://github.com/BIG-S2/Causal-Deepsets.

stat.ML↗

arXiv2024

Nodewise Loreg: Nodewise $L_0$-penalized Regression for High-dimensional Sparse Precision Matrix Estimation

We propose Nodewise Loreg, a nodewise $L_0$-penalized regression method for estimating high-dimensional sparse precision matrices. We establish its asymptotic properties, including convergence rates, support recovery, and asymptotic normality under high-dimensional sub-Gaussian settings. Notably, the Nodewise Loreg estimator is asymptotically unbiased and normally distributed, eliminating the need for debiasing required by Nodewise Lasso. We also develop a desparsified version of Nodewise Loreg, similar to the desparsified Nodewise Lasso estimator. The asymptotic variances of the undesparsified Nodewise Loreg estimator are upper bounded by those of both desparsified Nodewise Loreg and Lasso estimators for Gaussian data, potentially offering more powerful statistical inference. Extensive simulations show that the undesparsified Nodewise Loreg estimator generally outperforms the two desparsified estimators in asymptotic normal behavior. Moreover, Nodewise Loreg surpasses Nodewise Lasso, CLIME, and GLasso in most simulations in terms of matrix norm losses, support recovery, and timing performance. Application to a breast cancer gene expression dataset further demonstrates Nodewise Loreg's superiority over the three $L_1$-norm based methods.

math.ST↗

arXiv2024

Combining Experimental and Historical Data for Policy Evaluation

This paper studies policy evaluation with multiple data sources, especially in scenarios that involve one experimental dataset with two arms, complemented by a historical dataset generated under a single control arm. We propose novel data integration methods that linearly integrate base policy value estimators constructed based on the experimental and historical data, with weights optimized to minimize the mean square error (MSE) of the resulting combined estimator. We further apply the pessimistic principle to obtain more robust estimators, and extend these developments to sequential decision making. Theoretically, we establish non-asymptotic error bounds for the MSEs of our proposed estimators, and derive their oracle, efficiency and robustness properties across a broad spectrum of reward shift scenarios. Numerical experiments and real-data-based analyses from a ridesharing company demonstrate the superior performance of the proposed estimators.

stat.ML↗

arXiv2024

Disentangled Latent Energy-Based Style Translation: An Image-Level Structural MRI Harmonization Framework

Brain magnetic resonance imaging (MRI) has been extensively employed across clinical and research fields, but often exhibits sensitivity to site effects arising from non-biological variations such as differences in field strength and scanner vendors. Numerous retrospective MRI harmonization techniques have demonstrated encouraging outcomes in reducing the site effects at the image level. However, existing methods generally suffer from high computational requirements and limited generalizability, restricting their applicability to unseen MRIs. In this paper, we design a novel disentangled latent energy-based style translation (DLEST) framework for unpaired image-level MRI harmonization, consisting of (a) site-invariant image generation (SIG), (b) site-specific style translation (SST), and (c) site-specific MRI synthesis (SMS). Specifically, the SIG employs a latent autoencoder to encode MRIs into a low-dimensional latent space and reconstruct MRIs from latent codes. The SST utilizes an energy-based model to comprehend the global latent distribution of a target domain and translate source latent codes toward the target domain, while SMS enables MRI synthesis with a target-specific style. By disentangling image generation and style translation in latent space, the DLEST can achieve efficient style translation. Our model was trained on T1-weighted MRIs from a public dataset (with 3,984 subjects across 58 acquisition sites/settings) and validated on an independent dataset (with 9 traveling subjects scanned in 11 sites/settings) in four tasks: histogram and feature visualization, site classification, brain tissue segmentation, and site-specific structural MRI synthesis. Qualitative and quantitative results demonstrate the superiority of our method over several state-of-the-arts.

eess.IV↗

arXiv2023

Policy Evaluation for Temporal and/or Spatial Dependent Experiments

The aim of this paper is to establish a causal link between the policies implemented by technology companies and the outcomes they yield within intricate temporal and/or spatial dependent experiments. We propose a novel temporal/spatio-temporal Varying Coefficient Decision Process (VCDP) model, capable of effectively capturing the evolving treatment effects in situations characterized by temporal and/or spatial dependence. Our methodology encompasses the decomposition of the Average Treatment Effect (ATE) into the Direct Effect (DE) and the Indirect Effect (IE). We subsequently devise comprehensive procedures for estimating and making inferences about both DE and IE. Additionally, we provide a rigorous analysis of the statistical properties of these procedures, such as asymptotic power. To substantiate the effectiveness of our approach, we carry out extensive simulations and real data analyses.

stat.ME↗

arXiv2023

Optimal Treatment Allocation for Efficient Policy Evaluation in Sequential Decision Making

A/B testing is critical for modern technological companies to evaluate the effectiveness of newly developed products against standard baselines. This paper studies optimal designs that aim to maximize the amount of information obtained from online experiments to estimate treatment effects accurately. We propose three optimal allocation strategies in a dynamic setting where treatments are sequentially assigned over time. These strategies are designed to minimize the variance of the treatment effect estimator when data follow a non-Markov decision process or a (time-varying) Markov decision process. We further develop estimation procedures based on existing off-policy evaluation (OPE) methods and conduct extensive experiments in various environments to demonstrate the effectiveness of the proposed methodologies. In theory, we prove the optimality of the proposed treatment allocation design and establish upper bounds for the mean squared errors of the resulting treatment effect estimators.

stat.ME↗

arXiv2023

Evaluating the Potential of Leading Large Language Models in Reasoning Biology Questions

Recent advances in Large Language Models (LLMs) have presented new opportunities for integrating Artificial General Intelligence (AGI) into biological research and education. This study evaluated the capabilities of leading LLMs, including GPT-4, GPT-3.5, PaLM2, Claude2, and SenseNova, in answering conceptual biology questions. The models were tested on a 108-question multiple-choice exam covering biology topics in molecular biology, biological techniques, metabolic engineering, and synthetic biology. Among the models, GPT-4 achieved the highest average score of 90 and demonstrated the greatest consistency across trials with different prompts. The results indicated GPT-4's proficiency in logical reasoning and its potential to aid biology research through capabilities like data analysis, hypothesis generation, and knowledge integration. However, further development and validation are still required before the promise of LLMs in accelerating biological discovery can be realized.

cs.CL↗

arXiv2023

Controlling Neural Style Transfer with Deep Reinforcement Learning

Controlling the degree of stylization in the Neural Style Transfer (NST) is a little tricky since it usually needs hand-engineering on hyper-parameters. In this paper, we propose the first deep Reinforcement Learning (RL) based architecture that splits one-step style transfer into a step-wise process for the NST task. Our RL-based method tends to preserve more details and structures of the content image in early steps, and synthesize more style patterns in later steps. It is a user-easily-controlled style-transfer method. Additionally, as our RL-based model performs the stylization progressively, it is lightweight and has lower computational complexity than existing one-step Deep Learning (DL) based models. Experimental results demonstrate the effectiveness and robustness of our method.

cs.CV↗