arXiv subjects

Fusheng Wang

Publications and source records attributed to Fusheng Wang.

At least 19 recordsLinked to original sources

arXiv2026

When More Is Not Better: Component Anti-Synergy in a P300 Speller

P300 brain-computer interface (BCI) spellers can provide hands-free communication for people with severe motor impairments. Modern pipelines combine multiple individually promising components, often assuming that 'more-is-better'. We tested this assumption using a four-component full-factorial experiment varying the inclusion of Euclidean Alignment (EA), xDAWN spatial filtering, subject calibration, and language model priors on a public P300 dataset. Performance was evaluated using accuracy, repetitions, and information transfer rate (ITR) with mixed-effects models. Results show that the value of components is conditional rather than additive. Calibration was the strongest singular contributor, while EA compensated for its absence in zero-calibration settings. Adding independently useful components could also reduce performance, revealing component anti-synergy. Contrary to conventional wisdom, LM support was not universally beneficial: its effect depends strongly on the strength of the underlying EEG pipeline, while results from a larger LM showed a similar pattern. Together, these findings challenge maximal 'all-on' pipeline design and highlight the value of selecting spatial and language-support components according to the quality of available EEG evidence.

cs.LG↗

arXiv2026

Streaming P300 Acquisition and Statistical Signal Validation Across Five EEG Platforms: A Hardware-Agnostic BrainFlow/LSL Pipeline

P300 spellers offer people with severe motor impairment, such as ALS, an effective communication channel and remain one of the most established surgery-free alternatives to intracortical interfaces. Advanced language models have made spellers faster and more robust, yet the hardware beneath them is under-studied. We present a hardware-agnostic, real-time P300 acquisition pipeline built on BrainFlow and Lab Streaming Layer (LSL) that runs unchanged across consumer- and research-grade EEG headsets, with permutation tests of signal separability. Using a standard 6 x 6 row/column paradigm, we piloted five configurations: a custom dry system, a custom wet/gel system, Emotiv Flex, Emotiv EPOC X, and Muse 2. The custom systems and EPOC X showed weak or inconsistent signal separability, Muse 2 had the highest acquisition reliability despite limited centro-parietal coverage, and Flex showed the most promising signal. In 20 further Flex sessions varying subject, timing, and phrase length (131 target characters), a peak-amplitude permutation test and a cross-validated xDAWN decoder both detected a significant target response under two channel-exclusion policies, with decoder AUC reaching about 0.72 after 15 repetitions. Character accuracy depended heavily on evaluation methodology: in-sample majority voting reached 94.7%, whereas character-held-out accuracy was 31.3% with evidence accumulated across repetitions, about three times that of held-out majority voting. These analyses indicate that Flex captured a detectable, if still weak, P300 under the studied conditions, while broader participant-level validation and improved decoding remain necessary.

cs.HC↗

arXiv2026

A Comparative Study of Feature Selection Methods for EHR Diagnosis Codes in Opioid Use Disorder Prediction

Feature selection is a critical step in electronic health record (EHR)-based predictive modeling, where input variables are often high-dimensional, sparse, noisy, and redundant. Large feature sets not only increase computational burden and overfitting risk, but also make model interpretation difficult, leading to limited usefulness in clinical settings. In this study, we focus on diagnosis-related features and compare five feature selection paradigms for opioid use disorder (OUD) prediction: recurrence enrichment, NTK-motivated early gradient sensitivity, LightGBM-SHAP, Elastic Net, and large language model (LLM)-guided semantic selection. We use a unified preprocessing and evaluation framework and assess each method by downstream predictive performance, resampling stability, and representation of infrequent diagnosis codes. Our results demonstrate that performance improves with larger feature budgets with diminishing returns beyond a moderate size. NTK sensitivity provides the best overall balance of accuracy and stability, and LLM-guided selection contributes complementary clinically meaningful signals despite lower standalone performance.

cs.LG↗

arXiv2026

Spectra-Guided Neural Tucker Factorization

This paper proposes Spectra-Guided Neural Tucker Factorization (SG-NTF) for High-Dimensional and Incomplete (HDI) tensor completion. Circumventing discrete representational limits, SG-NTF maps scalar timestamps into a continuous spectral space to abstract temporal periodicities. Concurrently, a Spatio-Temporal Co-Gating (STCG) mechanism explicitly filters latent interactions via multiplicative modulation on spatiotemporal contexts. Evaluations on real-world HDI tensors verify that SG-NTF maintains competitive completion accuracy with parameter efficiency.

stat.ML↗

arXiv2026

3DPipe: A Pipelined GPU Framework for Scalable Generalized Spatial Join over Polyhedral Objects

Spatial join is a fundamental operation in spatial databases. With the rapid growth of 3D data in applications such as LiDAR-based object detection and 3D digital pathology, there is an increasing need to support spatial join over 3D datasets. However, existing techniques are largely designed for 2D data, leaving 3D spatial join underexplored and computationally expensive. We present 3DPipe, a pipelined GPU framework for scalable spatial join over polyhedral objects. 3DPipe exploits GPU parallelism across both filtering and refinement stages, incorporates a multi-level pruning strategy for efficient candidate reduction, and employs chunked streaming to handle datasets exceeding GPU memory. Its pipelined execution overlaps CPU data preparation, host-device data transfer, and GPU computation to improve throughput. Experiments show that 3DPipe achieves up to 9.0$\times$ speedup over the state-of-the-art GPU solution, TDBase, while maintaining excellent scalability. 3DPipe is open-sourced at https://github.com/lyuheng/3dpipe.

cs.DB↗

arXiv2025

A Versatile Three Dimensional Traction Force Microscopy Framework for Uncovering the Mechanics of Bio-Adhesion

This study presents a novel, versatile traction force microscopy framework for quantifying three-dimensional (3D) interfacial forces during bio-adhesion by integrating in situ stereo digital image correlation with finite element (FE) simulation. The method enables accurate measurement of microscale displacements and force distributions at the interfaces in both dry and wet environments, addressing limitations of conventional microscopy techniques related to limited measurement scales, restricted fields of view, and surface disturbance from contact or fluorescence. An analytical model was developed to guide the design of a deformable substrate, supporting selection of substrate material and thickness of the substrate. System accuracy was examined through steel ball compression experiments, which were validated against FE simulations. The framework was applied to marine mussel plaque adhesion under 15 directional tension to characterize interfacial traction force distributions. Sensitivity analyses examined the effects of Poisson's ratio, Young's modulus, and constitutive models on the results. This approach offers a versatile platform for investigating interfacial mechanics in adhesives, with broad relevance to bioengineering applications.

physics.ins-det↗

arXiv2024

BadCLM: Backdoor Attack in Clinical Language Models for Electronic Health Records

The advent of clinical language models integrated into electronic health records (EHR) for clinical decision support has marked a significant advancement, leveraging the depth of clinical notes for improved decision-making. Despite their success, the potential vulnerabilities of these models remain largely unexplored. This paper delves into the realm of backdoor attacks on clinical language models, introducing an innovative attention-based backdoor attack method, BadCLM (Bad Clinical Language Models). This technique clandestinely embeds a backdoor within the models, causing them to produce incorrect predictions when a pre-defined trigger is present in inputs, while functioning accurately otherwise. We demonstrate the efficacy of BadCLM through an in-hospital mortality prediction task with MIMIC III dataset, showcasing its potential to compromise model integrity. Our findings illuminate a significant security risk in clinical decision support systems and pave the way for future endeavors in fortifying clinical language models against such vulnerabilities.

cs.CL↗

arXiv2024

Integrative Graph-Transformer Framework for Histopathology Whole Slide Image Representation and Classification

In digital pathology, the multiple instance learning (MIL) strategy is widely used in the weakly supervised histopathology whole slide image (WSI) classification task where giga-pixel WSIs are only labeled at the slide level. However, existing attention-based MIL approaches often overlook contextual information and intrinsic spatial relationships between neighboring tissue tiles, while graph-based MIL frameworks have limited power to recognize the long-range dependencies. In this paper, we introduce the integrative graph-transformer framework that simultaneously captures the context-aware relational features and global WSI representations through a novel Graph Transformer Integration (GTI) block. Specifically, each GTI block consists of a Graph Convolutional Network (GCN) layer modeling neighboring relations at the local instance level and an efficient global attention model capturing comprehensive global information from extensive feature embeddings. Extensive experiments on three publicly available WSI datasets: TCGA-NSCLC, TCGA-RCC and BRIGHT, demonstrate the superiority of our approach over current state-of-the-art MIL methods, achieving an improvement of 1.0% to 2.6% in accuracy and 0.7%-1.6% in AUROC.

eess.IV↗

arXiv2023

Unraveling Key Elements Underlying Molecular Property Prediction: A Systematic Study

Artificial intelligence (AI) has been widely applied in drug discovery with a major task as molecular property prediction. Despite booming techniques in molecular representation learning, key elements underlying molecular property prediction remain largely unexplored, which impedes further advancements in this field. Herein, we conduct an extensive evaluation of representative models using various representations on the MoleculeNet datasets, a suite of opioids-related datasets and two additional activity datasets from the literature. To investigate the predictive power in low-data and high-data space, a series of descriptors datasets of varying sizes are also assembled to evaluate the models. In total, we have trained 62,820 models, including 50,220 models on fixed representations, 4,200 models on SMILES sequences and 8,400 models on molecular graphs. Based on extensive experimentation and rigorous comparison, we show that representation learning models exhibit limited performance in molecular property prediction in most datasets. Besides, multiple key elements underlying molecular property prediction can affect the evaluation results. Furthermore, we show that activity cliffs can significantly impact model prediction. Finally, we explore into potential causes why representation learning models can fail and show that dataset size is essential for representation learning models to excel.

q-bio.QM↗

arXiv2023

A Multimodal Transformer: Fusing Clinical Notes with Structured EHR Data for Interpretable In-Hospital Mortality Prediction

Deep-learning-based clinical decision support using structured electronic health records (EHR) has been an active research area for predicting risks of mortality and diseases. Meanwhile, large amounts of narrative clinical notes provide complementary information, but are often not integrated into predictive models. In this paper, we provide a novel multimodal transformer to fuse clinical notes and structured EHR data for better prediction of in-hospital mortality. To improve interpretability, we propose an integrated gradients (IG) method to select important words in clinical notes and discover the critical structured EHR features with Shapley values. These important words and clinical features are visualized to assist with interpretation of the prediction outcomes. We also investigate the significance of domain adaptive pretraining and task adaptive fine-tuning on the Clinical BERT, which is used to learn the representations of clinical notes. Experiments demonstrated that our model outperforms other methods (AUCPR: 0.538, AUCROC: 0.877, F1:0.490).

cs.CL↗

arXiv2023

Enhancing Clinical Predictive Modeling through Model Complexity-Driven Class Proportion Tuning for Class Imbalanced Data: An Empirical Study on Opioid Overdose Prediction

Class imbalance problems widely exist in the medical field and heavily deteriorates performance of clinical predictive models. Most techniques to alleviate the problem rebalance class proportions and they predominantly assume the rebalanced proportions should be a function of the original data and oblivious to the model one uses. This work challenges this prevailing assumption and proposes that links the optimal class proportions to the model complexity, thereby tuning the class proportions per model. Our experiments on the opioid overdose prediction problem highlight the performance gain of tuning class proportions. Rigorous regression analysis also confirms the advantages of the theoretical framework proposed and the statistically significant correlation between the hyperparameters controlling the model complexity and the optimal class proportions.

cs.LG↗

arXiv2021

Artificial Intelligence in Drug Discovery: Applications and Techniques

Artificial intelligence (AI) has been transforming the practice of drug discovery in the past decade. Various AI techniques have been used in a wide range of applications, such as virtual screening and drug design. In this survey, we first give an overview on drug discovery and discuss related applications, which can be reduced to two major tasks, i.e., molecular property prediction and molecule generation. We then discuss common data resources, molecule representations and benchmark platforms. Furthermore, to summarize the progress of AI in drug discovery, we present the relevant AI techniques including model architectures and learning paradigms in the papers surveyed. We expect that this survey will serve as a guide for researchers who are interested in working at the interface of artificial intelligence and drug discovery. We also provide a GitHub repository (https://github.com/dengjianyuan/Survey_AI_Drug_Discovery) with the collection of papers and codes, if applicable, as a learning resource, which is regularly updated.

cs.LG↗

arXiv2021

Selective Knowledge Distillation for Neural Machine Translation

Neural Machine Translation (NMT) models achieve state-of-the-art performance on many translation benchmarks. As an active research field in NMT, knowledge distillation is widely applied to enhance the model's performance by transferring teacher model's knowledge on each training sample. However, previous work rarely discusses the different impacts and connections among these samples, which serve as the medium for transferring teacher knowledge. In this paper, we design a novel protocol that can effectively analyze the different impacts of samples by comparing various samples' partitions. Based on above protocol, we conduct extensive experiments and find that the teacher's knowledge is not the more, the better. Knowledge over specific samples may even hurt the whole performance of knowledge distillation. Finally, to address these issues, we propose two simple yet effective strategies, i.e., batch-level and global-level selections, to pick suitable samples for distillation. We evaluate our approaches on two large-scale machine translation tasks, WMT'14 English->German and WMT'19 Chinese->English. Experimental results show that our approaches yield up to +1.28 and +0.89 BLEU points improvements over the Transformer baseline, respectively.

cs.CL↗

arXiv2020

TRACE: Early Detection of Chronic Kidney Disease Onset with Transformer-Enhanced Feature Embedding

Chronic kidney disease (CKD) has a poor prognosis due to excessive risk factors and comorbidities associated with it. The early detection of CKD faces challenges of insufficient medical histories of positive patients and complicated risk factors. In this paper, we propose the TRACE (Transformer-RNN Autoencoder-enhanced CKD Detector) framework, an end-to-end prediction model using patients' medical history data, to deal with these challenges. TRACE presents a comprehensive medical history representation with a novel key component: a Transformer-RNN autoencoder. The autoencoder jointly learns a medical concept embedding via Transformer for each hospital visit, and a latent representation which summarizes a patient's medical history across all the visits. We compared TRACE with multiple state-of-the-art methods on a dataset derived from real-world medical records. Our model has achieved 0.5708 AUPRC with a 2.31% relative improvement over the best-performing method. We also validated the clinical meaning of the learned embeddings through visualizations and a case study, showing the potential of TRACE to serve as a general disease prediction model.

cs.LG↗

arXiv2020

Identifying Risk of Opioid Use Disorder for Patients Taking Opioid Medications with Deep Learning

The United States is experiencing an opioid epidemic, and there were more than 10 million opioid misusers aged 12 or older each year. Identifying patients at high risk of Opioid Use Disorder (OUD) can help to make early clinical interventions to reduce the risk of OUD. Our goal is to predict OUD patients among opioid prescription users through analyzing electronic health records with machine learning and deep learning methods. This will help us to better understand the diagnoses of OUD, providing new insights on opioid epidemic. Electronic health records of patients who have been prescribed with medications containing active opioid ingredients were extracted from Cerner Health Facts database between January 1, 2008 and December 31, 2017. Long Short-Term Memory (LSTM) models were applied to predict opioid use disorder risk in the future based on recent five encounters, and compared to Logistic Regression, Random Forest, Decision Tree and Dense Neural Network. Prediction performance was assessed using F-1 score, precision, recall, and AUROC. Our temporal deep learning model provided promising prediction results which outperformed other methods, with a F1 score of 0.8023 and AUCROC of 0.9369. The model can identify OUD related medications and vital signs as important features for the prediction. LSTM based temporal deep learning model is effective on predicting opioid use disorder using a patient past history of electronic health records, with minimal domain knowledge. It has potential to improve clinical decision support for early intervention and prevention to combat the opioid epidemic.

cs.LG↗

arXiv2020

Towards Better Opioid Antagonists Using Deep Reinforcement Learning

Naloxone, an opioid antagonist, has been widely used to save lives from opioid overdose, a leading cause for death in the opioid epidemic. However, naloxone has short brain retention ability, which limits its therapeutic efficacy. Developing better opioid antagonists is critical in combating the opioid epidemic.Instead of exhaustively searching in a huge chemical space for better opioid antagonists, we adopt reinforcement learning which allows efficient gradient-based search towards molecules with desired physicochemical and/or biological properties. Specifically, we implement a deep reinforcement learning framework to discover potential lead compounds as better opioid antagonists with enhanced brain retention ability. A customized multi-objective reward function is designed to bias the generation towards molecules with both sufficient opioid antagonistic effect and enhanced brain retention ability. Thorough evaluation demonstrates that with this framework, we are able to identify valid, novel and feasible molecules with multiple desired properties, which has high potential in drug discovery.

q-bio.BM↗

arXiv2019

An Informatics-based Approach to Identify Key Pharmacological Components in Drug-Drug Interactions

Drug-drug interactions (DDI) can cause severe adverse drug reactions and pose a major challenge to medication therapy. Recently, informatics-based approaches are emerging for DDI studies. In this paper, we aim to identify key pharmacological components in DDI based on large-scale data from DrugBank, a comprehensive DDI database. With pharmacological components as features, logistic regression is used to perform DDI classification with a focus on searching for most predictive features, a process of identifying key pharmacological components. Using univariate feature selection with chi-squared statistic as the ranking criteria, our study reveals that top 10% features can achieve comparable classification performance compared to that using all features. The top 10% features are identified to be key pharmacological components. Furthermore, their importance is quantified by feature coefficients in the classifier, which measures the DDI potential and provides a novel perspective to evaluate pharmacological components.

q-bio.QM↗

arXiv2019

Liver Steatosis Segmentation with Deep Learning Methods

Liver steatosis is known as the abnormal accumulation of lipids within cells. An accurate quantification of steatosis area within the liver histopathological microscopy images plays an important role in liver disease diagnosis and trans-plantation assessment. Such a quantification analysis often requires a precise steatosis segmentation that is challenging due to abundant presence of highly overlapped steatosis droplets. In this paper, a deep learning model Mask-RCNN is used to segment the steatosis droplets in clumps. Extended from Faster R-CNN, Mask-RCNN can predict object masks in addition to bounding box detection. With transfer learning, the resulting model is able to segment overlapped steatosis regions at 75.87% by Average Precision, 60.66% by Recall,65.88% by F1-score, and 76.97% by Jaccard index, promising to support liver disease diagnosis and allograft rejection prediction in future clinical practice.

eess.IV↗