arXiv subjects

Xueshen Li

Publications and source records attributed to Xueshen Li.

13 recordsLinked to original sources

arXiv2026

MAIL: Memory-driven, Adaptive, Incremental, and Literature-grounded Framework for Hypothesis Generation in Chemistry

The ever-expanding volume of the chemical literature offers unprecedented opportunities to generate novel and impactful hypotheses. However, the bottleneck lies in efficiently navigating this vast knowledge base to formulate high-quality, experimentally meaningful insights. While Large Language Models (LLMs) show promise for this task, existing methods often rely on static inspiration corpora, predefined heuristics, or laborious human-in-the-loop pipelines and decision-support frameworks that limit scalability and novelty. In this work, we propose an automated approach, a Memory-augmented, Adaptive, Incremental, and Literature-grounded (MAIL) framework for hypothesis generation in chemistry. Our MAIL method formulates hypothesis generation as a temporally grounded, memory-driven reasoning process, where hypotheses emerge from an evolving conceptual path that continuously accumulates and reinterprets prior knowledge. We evaluated the MAIL framework on a public TOMATO-Chem dataset and a newly curated and disseminated high-novelty nature/science challenge (HN-NS) dataset. Across both datasets, MAIL generates structurally coherent and mechanistically plausible hypotheses, achieves the highest MIOS and MPOS by more effectively recovering the central ideas and methodological elements of the historical target hypotheses, and obtains the highest overall expert-evaluation scores for scientific quality. These results demonstrate the potential of LLMs to autonomously explore chemical domains and generate hypotheses that are both innovative and chemically plausible.

cs.AI↗

arXiv2026

Adaptive Retrieval Strategies for Biomedical Question Answering

Biomedical question answering (QA) encompasses diverse question types, including yes/no, factoid, list, and summary questions, each requiring distinct forms of evidence and reasoning. However, most retrieval-augmented QA systems rely on a unified retrieval pipeline, regardless of the information needs of different question categories. This one-size-fits-all approach may limit the effectiveness of evidence acquisition and downstream answer generation. In this work, we propose an adaptive retrieval framework that selects retrieval and evidence aggregation strategies according to question type. The system combines query understanding, biomedical document retrieval, reranking, knowledge graph augmentation, document clustering, and large language model-based answer generation. For yes/no questions, it focuses on precise evidence retrieval; for factoid and list questions, it emphasizes entity-oriented retrieval and clustering; and for summary questions, it performs broader evidence collection and synthesis. We evaluate the proposed framework on the BioASQ benchmark and demonstrate that adaptive retrieval strategies improve evidence relevance and answer quality across multiple question types. Our results suggest that aligning retrieval mechanisms with question-specific information needs provides an effective direction for enhancing retrieval-augmented biomedical QA systems.

cs.IR↗

arXiv2025

ProMRVL-CAD: Proactive Dialogue System with Multi-Round Vision-Language Interactions for Computer-Aided Diagnosis

Recent advancements in large language models (LLMs) have demonstrated extraordinary comprehension capabilities with remarkable breakthroughs on various vision-language tasks. However, the application of LLMs in generating reliable medical diagnostic reports remains in the early stages. Currently, medical LLMs typically feature a passive interaction model where doctors respond to patient queries with little or no involvement in analyzing medical images. In contrast, some ChatBots simply respond to predefined queries based on visual inputs, lacking interactive dialogue or consideration of medical history. As such, there is a gap between LLM-generated patient-ChatBot interactions and those occurring in actual patient-doctor consultations. To bridge this gap, we develop an LLM-based dialogue system, namely proactive multi-round vision-language interactions for computer-aided diagnosis (ProMRVL-CAD), to generate patient-friendly disease diagnostic reports. The proposed ProMRVL-CAD system allows proactive dialogue to provide patients with constant and reliable medical access via an integration of knowledge graph into a recommendation system. Specifically, we devise two generators: a Proactive Question Generator (Pro-Q Gen) to generate proactive questions that guide the diagnostic procedure and a Multi-Vision Patient-Text Diagnostic Report Generator (MVP-DR Gen) to produce high-quality diagnostic reports. Evaluating two real-world publicly available datasets, MIMIC-CXR and IU-Xray, our model has better quality in generating medical reports. We further demonstrate the performance of ProMRVL achieves robust under the scenarios with low image quality. Moreover, we have created a synthetic medical dialogue dataset that simulates proactive diagnostic interactions between patients and doctors, serving as a valuable resource for training LLM.

cs.AI↗

arXiv2024

Enhancing Screen Time Identification in Children with a Multi-View Vision Language Model and Screen Time Tracker

Being able to accurately monitor the screen exposure of young children is important for research on phenomena linked to screen use such as childhood obesity, physical activity, and social interaction. Most existing studies rely upon self-report or manual measures from bulky wearable sensors, thus lacking efficiency and accuracy in capturing quantitative screen exposure data. In this work, we developed a novel sensor informatics framework that utilizes egocentric images from a wearable sensor, termed the screen time tracker (STT), and a vision language model (VLM). In particular, we devised a multi-view VLM that takes multiple views from egocentric image sequences and interprets screen exposure dynamically. We validated our approach by using a dataset of children's free-living activities, demonstrating significant improvement over existing methods in plain vision language models and object detection models. Results supported the promise of this monitoring approach, which could optimize behavioral research on screen exposure in children's naturalistic settings.

cs.CV↗

arXiv2024

A Two-Stage Proactive Dialogue Generator for Efficient Clinical Information Collection Using Large Language Model

Efficient patient-doctor interaction is among the key factors for a successful disease diagnosis. During the conversation, the doctor could query complementary diagnostic information, such as the patient's symptoms, previous surgery, and other related information that goes beyond medical evidence data (test results) to enhance disease diagnosis. However, this procedure is usually time-consuming and less-efficient, which can be potentially optimized through computer-assisted systems. As such, we propose a diagnostic dialogue system to automate the patient information collection procedure. By exploiting medical history and conversation logic, our conversation agents, particularly the doctor agent, can pose multi-round clinical queries to effectively collect the most relevant disease diagnostic information. Moreover, benefiting from our two-stage recommendation structure, carefully designed ranking criteria, and interactive patient agent, our model is able to overcome the under-exploration and non-flexible challenges in dialogue generation. Our experimental results on a real-world medical conversation dataset show that our model can generate clinical queries that mimic the conversation style of real doctors, with efficient fluency, professionalism, and safety, while effectively collecting relevant disease diagnostic information.

cs.CL↗

arXiv2023

Push the Boundary of SAM: A Pseudo-label Correction Framework for Medical Segmentation

Segment anything model (SAM) has emerged as the leading approach for zero-shot learning in segmentation tasks, offering the advantage of avoiding pixel-wise annotations. It is particularly appealing in medical image segmentation, where the annotation process is laborious and expertise-demanding. However, the direct application of SAM often yields inferior results compared to conventional fully supervised segmentation networks. An alternative approach is to use SAM as the initial stage to generate pseudo labels for further network training. However, the performance is limited by the quality of pseudo labels. In this paper, we propose a novel label correction framework to push the boundary of SAM-based segmentation. Our model utilizes a label quality evaluation module to distinguish between noisy labels and clean labels. This enables the correction of the noisy labels using an uncertainty-based self-correction module, thereby enriching the clean training set. Finally, we retrain the segmentation network with updated labels to optimize its weights for future predictions. One key advantage of our model is its ability to train deep networks using SAM-generated pseudo labels without relying on a set of expert-level annotations while attaining good segmentation performance. We demonstrate the effectiveness of our proposed model on three public datasets, indicating its ability to improve segmentation accuracy and outperform baseline methods in label correction.

eess.IV↗

arXiv2023

SCPAT-GAN: Structural Constrained and Pathology Aware Convolutional Transformer-GAN for Virtual Histology Staining of Human Coronary OCT images

There is a significant need for the generation of virtual histological information from coronary optical coherence tomography (OCT) images to better guide the treatment of coronary artery disease. However, existing methods either require a large pixel-wisely paired training dataset or have limited capability to map pathological regions. To address these issues, we proposed a structural constrained, pathology aware, transformer generative adversarial network, namely SCPAT-GAN, to generate virtual stained H&E histology from OCT images. The proposed SCPAT-GAN advances existing methods via a novel design to impose pathological guidance on structural layers using transformer-based network.

eess.IV↗

arXiv2023

Frequency-aware optical coherence tomography image super-resolution via conditional generative adversarial neural network

Optical coherence tomography (OCT) has stimulated a wide range of medical image-based diagnosis and treatment in fields such as cardiology and ophthalmology. Such applications can be further facilitated by deep learning-based super-resolution technology, which improves the capability of resolving morphological structures. However, existing deep learning-based method only focuses on spatial distribution and disregard frequency fidelity in image reconstruction, leading to a frequency bias. To overcome this limitation, we propose a frequency-aware super-resolution framework that integrates three critical frequency-based modules (i.e., frequency transformation, frequency skip connection, and frequency alignment) and frequency-based loss function into a conditional generative adversarial network (cGAN). We conducted a large-scale quantitative study from an existing coronary OCT dataset to demonstrate the superiority of our proposed framework over existing deep learning frameworks. In addition, we confirmed the generalizability of our framework by applying it to fish corneal images and rat retinal images, demonstrating its capability to super-resolve morphological details in eye imaging.

physics.med-ph↗

arXiv2023

Detecting and measuring human gastric peristalsis using magnetically controlled capsule endoscope

Magnetically controlled capsule endoscope (MCCE) is an emerging tool for the diagnosis of gastric diseases with the advantages of comfort, safety, and no anesthesia. In this paper, we develop algorithms to detect and measure human gastric peristalsis (contraction wave) using video sequences acquired by MCCE. We develop a spatial-temporal deep learning algorithm to detect gastric contraction waves and measure human gastric peristalsis periods. The quality of MCCE video sequences is prone to camera motion. We design a camera motion detector (CMD) to process the MCCE video sequences, mitigating the camera movement during MCCE examination. To the best of our knowledge, we are the first to propose computer vision-based solutions to detect and measure human gastric peristalsis. Our methods have great potential in assisting the diagnosis of gastric diseases by evaluating gastric motility.

eess.IV↗

arXiv2022

Structural constrained virtual histology staining for human coronary imaging using deep learning

Histopathological analysis is crucial in artery characterization for coronary artery disease (CAD). However, histology requires an invasive and time-consuming process. In this paper, we propose to generate virtual histology staining using Optical Coherence Tomography (OCT) images to enable real-time histological visualization. We develop a deep learning network, namely Coronary-GAN, to transfer coronary OCT images to virtual histology images. With a special consideration on the structural constraints in coronary OCT images, our method achieves better image generation performance than the conventional GAN-based method. The experimental results indicate that Coronary-GAN generates virtual histology images that are similar to real histology images, revealing the human coronary layers.

eess.IV↗

arXiv2022

Towards reliable calcification detection: calibration of uncertainty in coronary optical coherence tomography images

Optical coherence tomography (OCT) has become increasingly essential in assisting the treatment of coronary artery disease (CAD). Image-guided solutions such as Percutaneous Coronary Intervention (PCI) are extensively used during the treatment of CAD. However, unidentified calcified regions within a narrowed artery could impair the outcome of the PCI. Prior to treatments, object detection is paramount to automatically procure accurate readings on the location and thickness of calcifications within the artery. Deep learning-based object detection methods have been explored in a variety of applications. The quality of object detection predictions could lead to uncertain results, which are not desirable in safety-critical scenarios. In this work, we implement an object detection model, You-Only-Look-Once v5 (YOLO), on a calcification detection framework within coronary OCT images. We evaluate the uncertainty of predictions based on the expected calibration errors, thus assessing the certainty level of detection results. To calibrate confidence scores of predictions, we implement dependent logistic calibration using each detection result's confidence and center coordinates. With the calibrated confidence score of each prediction, we lower the uncertainty of predictions in calcification detection. Our results show that the YOLO achieves higher precision and recall in comparison with the other object detection model, meanwhile producing more reliable results. The calibrated confidence of prediction results in a confidence error of approximately 0.13, suggesting that the confidence calibration on calcification detection could provide a more trustworthy result, indicating a great potential to assist clinical evaluation of treating the CAD during the imaging-guided procedure.

eess.IV↗

arXiv2022

Automated player identification and indexing using two-stage deep learning network

American football games attract significant worldwide attention every year. Identifying players from videos in each play is also essential for the indexing of player participation. Processing football game video presents great challenges such as crowded settings, distorted objects, and imbalanced data for identifying players, especially jersey numbers. In this work, we propose a deep learning-based player tracking system to automatically track players and index their participation per play in American football games. It is a two-stage network design to highlight areas of interest and identify jersey number information with high accuracy. First, we utilize an object detection network, a detection transformer, to tackle the player detection problem in a crowded context. Second, we identify players using jersey number recognition with a secondary convolutional neural network, then synchronize it with a game clock subsystem. Finally, the system outputs a complete log in a database for play indexing. We demonstrate the effectiveness and reliability of player tracking system by analyzing the qualitative and quantitative results on football videos. The proposed system shows great potential for implementation in and analysis of football broadcast video.

cs.CV↗

arXiv2022

Multi-scale reconstruction of undersampled spectral-spatial OCT data for coronary imaging using deep learning

Coronary artery disease (CAD) is a cardiovascular condition with high morbidity and mortality. Intravascular optical coherence tomography (IVOCT) has been considered as an optimal imagining system for the diagnosis and treatment of CAD. Constrained by Nyquist theorem, dense sampling in IVOCT attains high resolving power to delineate cellular structures/ features. There is a trade-off between high spatial resolution and fast scanning rate for coronary imaging. In this paper, we propose a viable spectral-spatial acquisition method that down-scales the sampling process in both spectral and spatial domain while maintaining high quality in image reconstruction. The down-scaling schedule boosts data acquisition speed without any hardware modifications. Additionally, we propose a unified multi-scale reconstruction framework, namely Multiscale- Spectral-Spatial-Magnification Network (MSSMN), to resolve highly down-scaled (compressed) OCT images with flexible magnification factors. We incorporate the proposed methods into Spectral Domain OCT (SD-OCT) imaging of human coronary samples with clinical features such as stent and calcified lesions. Our experimental results demonstrate that spectral-spatial downscaled data can be better reconstructed than data that is downscaled solely in either spectral or spatial domain. Moreover, we observe better reconstruction performance using MSSMN than using existing reconstruction methods. Our acquisition method and multi-scale reconstruction framework, in combination, may allow faster SD-OCT inspection with high resolution during coronary intervention.

eess.IV↗