arXiv subjects

Shuo Zhou

Publications and source records attributed to Shuo Zhou.

At least 37 records · Page 2Linked to original sources

arXiv2025

MeDSLIP: Medical Dual-Stream Language-Image Pre-training with Pathology-Anatomy Semantic Alignment

Pathology and anatomy are two essential groups of semantics in medical data. Pathology describes what the diseases are, while anatomy explains where the diseases occur. They describe diseases from different perspectives, providing complementary insights into diseases. Thus, properly understanding these semantics and their relationships can enhance medical vision-language models (VLMs). However, pathology and anatomy semantics are usually entangled in medical data, hindering VLMs from explicitly modeling these semantics and their relationships. To address this challenge, we propose MeDSLIP, a novel Medical Dual-Stream Language-Image Pre-training pipeline, to disentangle pathology and anatomy semantics and model the relationships between them. We introduce a dual-stream mechanism in MeDSLIP to explicitly disentangle medical semantics into pathology-relevant and anatomy-relevant streams and align visual and textual information within each stream. Furthermore, we propose an interaction modeling module with prototypical contrastive learning loss and intra-image contrastive learning loss to regularize the relationships between pathology and anatomy semantics. We apply MeDSLIP to chest X-ray analysis and conduct comprehensive evaluations with four benchmark datasets: NIH CXR14, RSNA Pneumonia, SIIM-ACR Pneumothorax, and COVIDx CXR-4. The results demonstrate MeDSLIP's superior generalizability and transferability across different scenarios. The code is available at https://github.com/Shef-AIRE/MeDSLIP, and the pre-trained model is released at https://huggingface.co/pykale/MeDSLIP.

cs.CV↗

arXiv2025

Foundation-Model-Boosted Multimodal Learning for fMRI-based Neuropathic Pain Drug Response Prediction

Neuropathic pain, affecting up to 10% of adults, remains difficult to treat due to limited therapeutic efficacy and tolerability. Although resting-state functional MRI (rs-fMRI) is a promising non-invasive measurement of brain biomarkers to predict drug response in therapeutic development, the complexity of fMRI demands machine learning models with substantial capacity. However, extreme data scarcity in neuropathic pain research limits the application of high-capacity models. To address the challenge of data scarcity, we propose FMM$_{TC}$, a Foundation-Model-boosted Multimodal learning framework for fMRI-based neuropathic pain drug response prediction, which leverages both internal multimodal information in pain-specific data and external knowledge from large pain-agnostic data. Specifically, to maximize the value of limited pain-specific data, FMM$_{TC}$ integrates complementary information from two rs-fMRI modalities: Time series and functional Connectivity. FMM$_{TC}$ is further boosted by an fMRI foundation model with its external knowledge from extensive pain-agnostic fMRI datasets enriching limited pain-specific information. Evaluations with an in-house dataset and a public dataset from OpenNeuro demonstrate FMM$_{TC}$'s superior representation ability, generalizability, and cross-dataset adaptability over existing unimodal fMRI models that only consider one of the rs-fMRI modalities. The ablation study validates the effectiveness of multimodal learning and foundation-model-powered external knowledge transfer in FMM$_{TC}$. An integrated gradient-based interpretation study explains how FMM$_{TC}$'s cross-dataset dynamic behaviors enhance its adaptability. In conclusion, FMM$_{TC}$ boosts clinical trials in neuropathic pain therapeutic development by accurately predicting drug responses to improve the participant stratification efficiency.

cs.LG↗

arXiv2025

Classifying the Stoichiometry of Virus-like Particles with Interpretable Machine Learning

Virus-like particles (VLPs) are valuable for vaccine development due to their immune-triggering properties. Understanding their stoichiometry, the number of protein subunits to form a VLP, is critical for vaccine optimisation. However, current experimental methods to determine stoichiometry are time-consuming and require highly purified proteins. To efficiently classify stoichiometry classes in proteins, we curate a new dataset and propose an interpretable, data-driven pipeline leveraging linear machine learning models. We also explore the impact of feature encoding on model performance and interpretability, as well as methods to identify key protein sequence features influencing classification. The evaluation of our pipeline demonstrates that it can classify stoichiometry while revealing protein features that possibly influence VLP assembly. The data and code used in this work are publicly available at https://github.com/Shef-AIRE/StoicIML.

cs.LG↗

arXiv2024

Quantum Neural Network for Accelerated Magnetic Resonance Imaging

Magnetic resonance image reconstruction starting from undersampled k-space data requires the recovery of many potential nonlinear features, which is very difficult for algorithms to recover these features. In recent years, the development of quantum computing has discovered that quantum convolution can improve network accuracy, possibly due to potential quantum advantages. This article proposes a hybrid neural network containing quantum and classical networks for fast magnetic resonance imaging, and conducts experiments on a quantum computer simulation system. The experimental results indicate that the hybrid network has achieved excellent reconstruction results, and also confirm the feasibility of applying hybrid quantum-classical neural networks into the image reconstruction of rapid magnetic resonance imaging.

eess.IV↗

arXiv2024

Pediatric TSC-Related Epilepsy Classification from Clinical MR Images Using Quantum Neural Network

Tuberous sclerosis complex (TSC) manifests as a multisystem disorder with significant neurological implications. This study addresses the critical need for robust classification models tailored to TSC in pediatric patients, introducing QResNet,a novel deep learning model seamlessly integrating conventional convolutional neural networks with quantum neural networks. The model incorporates a two-layer quantum layer (QL), comprising ZZFeatureMap and Ansatz layers, strategically designed for processing classical data within a quantum framework. A comprehensive evaluation, demonstrates the superior performance of QResNet in TSC MRI image classification compared to conventional 3D-ResNet models. These compelling findings underscore the potential of quantum computing to revolutionize medical imaging and diagnostics.Remarkably, this method surpasses conventional CNNs in accuracy and Area Under the Curve (AUC) metrics with the current dataset. Future research endeavors may focus on exploring the scalability and practical implementation of quantum algorithms in real-world medical imaging scenarios.

eess.IV↗

arXiv2024

DPA-2: a large atomic model as a multi-task learner

The rapid advancements in artificial intelligence (AI) are catalyzing transformative changes in atomic modeling, simulation, and design. AI-driven potential energy models have demonstrated the capability to conduct large-scale, long-duration simulations with the accuracy of ab initio electronic structure methods. However, the model generation process remains a bottleneck for large-scale applications. We propose a shift towards a model-centric ecosystem, wherein a large atomic model (LAM), pre-trained across multiple disciplines, can be efficiently fine-tuned and distilled for various downstream tasks, thereby establishing a new framework for molecular modeling. In this study, we introduce the DPA-2 architecture as a prototype for LAMs. Pre-trained on a diverse array of chemical and materials systems using a multi-task approach, DPA-2 demonstrates superior generalization capabilities across multiple downstream tasks compared to the traditional single-task pre-training and fine-tuning methodologies. Our approach sets the stage for the development and broad application of LAMs in molecular and materials simulation research.

physics.chem-ph↗

arXiv2024

Complexity of Digital Quantum Simulation in the Low-Energy Subspace: Applications and a Lower Bound

Digital quantum simulation has broad applications in approximating unitary evolution of Hamiltonians. In practice, many simulation tasks for quantum systems focus on quantum states in the low-energy subspace instead of the entire Hilbert space. In this paper, we systematically investigate the complexity of digital quantum simulation based on product formulas in the low-energy subspace. We show that the simulation error depends on the effective low-energy norm of the Hamiltonian for a variety of digital quantum simulation algorithms and quantum systems, allowing improvements over the previous complexities for full unitary simulations even for imperfect state preparations due to thermalization. In particular, for simulating spin models in the low-energy subspace, we prove that randomized product formulas such as qDRIFT and random permutation require smaller Trotter numbers. Such improvement also persists in symmetry-protected digital quantum simulations. We prove a similar improvement in simulating the dynamics of power-law quantum interactions. We also provide a query lower bound for general digital quantum simulations in the low-energy subspace.

quant-ph↗

arXiv2024

Multimodal Variational Autoencoder for Low-cost Cardiac Hemodynamics Instability Detection

Recent advancements in non-invasive detection of cardiac hemodynamic instability (CHDI) primarily focus on applying machine learning techniques to a single data modality, e.g. cardiac magnetic resonance imaging (MRI). Despite their potential, these approaches often fall short especially when the size of labeled patient data is limited, a common challenge in the medical domain. Furthermore, only a few studies have explored multimodal methods to study CHDI, which mostly rely on costly modalities such as cardiac MRI and echocardiogram. In response to these limitations, we propose a novel multimodal variational autoencoder ($\text{CardioVAE}_\text{X,G}$) to integrate low-cost chest X-ray (CXR) and electrocardiogram (ECG) modalities with pre-training on a large unlabeled dataset. Specifically, $\text{CardioVAE}_\text{X,G}$ introduces a novel tri-stream pre-training strategy to learn both shared and modality-specific features, thus enabling fine-tuning with both unimodal and multimodal datasets. We pre-train $\text{CardioVAE}_\text{X,G}$ on a large, unlabeled dataset of $50,982$ subjects from a subset of MIMIC database and then fine-tune the pre-trained model on a labeled dataset of $795$ subjects from the ASPIRE registry. Comprehensive evaluations against existing methods show that $\text{CardioVAE}_\text{X,G}$ offers promising performance (AUROC $=0.79$ and Accuracy $=0.77$), representing a significant step forward in non-invasive prediction of CHDI. Our model also excels in producing fine interpretations of predictions directly associated with clinical features, thereby supporting clinical decision-making.

cs.LG↗

arXiv2024

Group-specific discriminant analysis reveals statistically validated sex differences in lateralization of brain functional network

Lateralization is a fundamental feature of the human brain, where sex differences have been observed. Conventional studies in neuroscience on sex-specific lateralization are typically conducted on univariate statistical comparisons between male and female groups. However, these analyses often lack effective validation of group specificity. Here, we formulate modeling sex differences in lateralization of functional networks as a dual-classification problem, consisting of first-order classification for left vs. right functional networks and second-order classification for male vs. female models. To capture sex-specific patterns, we develop the Group-Specific Discriminant Analysis (GSDA) for first-order classification. The evaluation on two public neuroimaging datasets demonstrates the efficacy of GSDA in learning sex-specific models from functional networks, achieving a significant improvement in group specificity over baseline methods. The major sex differences are in the strength of lateralization and the interactions within and between lobes. The GSDA-based method is generic in nature and can be adapted to other group-specific analyses such as handedness-specific or disease-specific analyses.

q-bio.NC↗

arXiv2024

Interpretable Multimodal Learning for Cardiovascular Hemodynamics Assessment

Pulmonary Arterial Wedge Pressure (PAWP) is an essential cardiovascular hemodynamics marker to detect heart failure. In clinical practice, Right Heart Catheterization is considered a gold standard for assessing cardiac hemodynamics while non-invasive methods are often needed to screen high-risk patients from a large population. In this paper, we propose a multimodal learning pipeline to predict PAWP marker. We utilize complementary information from Cardiac Magnetic Resonance Imaging (CMR) scans (short-axis and four-chamber) and Electronic Health Records (EHRs). We extract spatio-temporal features from CMR scans using tensor-based learning. We propose a graph attention network to select important EHR features for prediction, where we model subjects as graph nodes and feature relationships as graph edges using the attention mechanism. We design four feature fusion strategies: early, intermediate, late, and hybrid fusion. With a linear classifier and linear fusion strategies, our pipeline is interpretable. We validate our pipeline on a large dataset of $2,641$ subjects from our ASPIRE registry. The comparative study against state-of-the-art methods confirms the superiority of our pipeline. The decision curve analysis further validates that our pipeline can be applied to screen a large population. The code is available at https://github.com/prasunc/hemodynamics.

cs.CV↗

arXiv2024

Tensor-based Multimodal Learning for Prediction of Pulmonary Arterial Wedge Pressure from Cardiac MRI

Heart failure is a serious and life-threatening condition that can lead to elevated pressure in the left ventricle. Pulmonary Arterial Wedge Pressure (PAWP) is an important surrogate marker indicating high pressure in the left ventricle. PAWP is determined by Right Heart Catheterization (RHC) but it is an invasive procedure. A non-invasive method is useful in quickly identifying high-risk patients from a large population. In this work, we develop a tensor learning-based pipeline for identifying PAWP from multimodal cardiac Magnetic Resonance Imaging (MRI). This pipeline extracts spatial and temporal features from high-dimensional scans. For quality control, we incorporate an epistemic uncertainty-based binning strategy to identify poor-quality training samples. To improve the performance, we learn complementary information by integrating features from multimodal data: cardiac MRI with short-axis and four-chamber views, and Electronic Health Records. The experimental analysis on a large cohort of $1346$ subjects who underwent the RHC procedure for PAWP estimation indicates that the proposed pipeline has a diagnostic value and can produce promising performance with significant improvement over the baseline in clinical practice (i.e., $Δ$AUC $=0.10$, $Δ$Accuracy $=0.06$, and $Δ$MCC $=0.39$). The decision curve analysis further confirms the clinical utility of our method.

cs.LG↗

arXiv2022

A Machine Learning Method for Material Property Prediction: Example Polymer Compatibility

Prediction of material property is a key problem because of its significance to material design and screening. We present a brand-new and general machine learning method for material property prediction. As a representative example, polymer compatibility is chosen to demonstrate the effectiveness of our method. Specifically, we mine data from related literature to build a specific database and give a prediction based on the basic molecular structures of blending polymers and, as auxiliary, the blending composition. Our model obtains at least 75% accuracy on the dataset consisting of thousands of entries. We demonstrate that the relationship between structure and properties can be learned and simulated by machine learning method.

cs.LG↗

arXiv2021

Channel-Temporal Attention for First-Person Video Domain Adaptation

Unsupervised Domain Adaptation (UDA) can transfer knowledge from labeled source data to unlabeled target data of the same categories. However, UDA for first-person action recognition is an under-explored problem, with lack of datasets and limited consideration of first-person video characteristics. This paper focuses on addressing this problem. Firstly, we propose two small-scale first-person video domain adaptation datasets: ADL$_{small}$ and GTEA-KITCHEN. Secondly, we introduce channel-temporal attention blocks to capture the channel-wise and temporal-wise relationships and model their inter-dependencies important to first-person vision. Finally, we propose a Channel-Temporal Attention Network (CTAN) to integrate these blocks into existing architectures. CTAN outperforms baselines on the two proposed datasets and one existing dataset EPIC$_{cvpr20}$.

cs.CV↗

arXiv2021

Team PyKale (xy9) Submission to the EPIC-Kitchens 2021 Unsupervised Domain Adaptation Challenge for Action Recognition

This report describes the technical details of our submission to the EPIC-Kitchens 2021 Unsupervised Domain Adaptation Challenge for Action Recognition. The EPIC-Kitchens dataset is more difficult than other video domain adaptation datasets due to multi-tasks with more modalities. Firstly, to participate in the challenge, we employ a transformer to capture the spatial information from each modality. Secondly, we employ a temporal attention module to model temporal-wise inter-dependency. Thirdly, we employ the adversarial domain adaptation network to learn the general features between labeled source and unlabeled target domain. Finally, we incorporate multiple modalities to improve the performance by a three-stream network with late fusion. Our network achieves the comparable performance with the state-of-the-art baseline T$A^3$N and outperforms the baseline on top-1 accuracy for verb class and top-5 accuracies for all three tasks which are verb, noun and action. Under the team name xy9, our submission achieved 5th place in terms of top-1 accuracy for verb class and all top-5 accuracies.

cs.CV↗

arXiv2021

A Behavior-aware Graph Convolution Network Model for Video Recommendation

Interactions between users and videos are the major data source of performing video recommendation. Despite lots of existing recommendation methods, user behaviors on videos, which imply the complex relations between users and videos, are still far from being fully explored. In the paper, we present a model named Sagittarius. Sagittarius adopts a graph convolutional neural network to capture the influence between users and videos. In particular, Sagittarius differentiates between different user behaviors by weighting and fuses the semantics of user behaviors into the embeddings of users and videos. Moreover, Sagittarius combines multiple optimization objectives to learn user and video embeddings and then achieves the video recommendation by the learned user and video embeddings. The experimental results on multiple datasets show that Sagittarius outperforms several state-of-the-art models in terms of recall, unique recall and NDCG.

cs.CV↗

arXiv2021

PyKale: Knowledge-Aware Machine Learning from Multiple Sources in Python

Machine learning is a general-purpose technology holding promises for many interdisciplinary research problems. However, significant barriers exist in crossing disciplinary boundaries when most machine learning tools are developed in different areas separately. We present Pykale - a Python library for knowledge-aware machine learning on graphs, images, texts, and videos to enable and accelerate interdisciplinary research. We formulate new green machine learning guidelines based on standard software engineering practices and propose a novel pipeline-based application programming interface (API). PyKale focuses on leveraging knowledge from multiple sources for accurate and interpretable prediction, thus supporting multimodal learning and transfer learning (particularly domain adaptation) with latest deep learning and dimensionality reduction models. We build PyKale on PyTorch and leverage the rich PyTorch ecosystem. Our pipeline-based API design enforces standardization and minimalism, embracing green machine learning concepts via reducing repetitions and redundancy, reusing existing resources, and recycling learning models across areas. We demonstrate its interdisciplinary nature via examples in bioinformatics, knowledge graph, image/video recognition, and medical imaging.

cs.LG↗

arXiv2021

On local intrinsic dimensionality of deformation in complex materials

We propose a new metric called s-LID based on the concept of Local Intrinsic Dimensionality to identify and quantify hierarchies of kinematic patterns in heterogeneous media. s-LID measures how outlying a grain's motion is relative to its s nearest neighbors in displacement state space. To demonstrate the merits of s-LID over the conventional measure of strain, we apply it to data on individual grain motions in a set of deforming granular materials. Several new insights into the evolution of failure are uncovered. First, s-LID reveals a hierarchy of concurrent deformation bands that prevails throughout loading history. These structures vary not only in relative dominance but also spatial and kinematic scales. Second, in the nascent stages of the pre-failure regime, s-LID uncovers a set of system-spanning, criss-crossing bands: microbands for small s and embryonic-shearbands at large s, with the former being dominant. At the opposite extreme, in the failure regime, fully formed shearbands at large s dominate over the microbands. The novel patterns uncovered from s-LID contradict the common belief of a causal sequence where a subset of microbands coalesce and/or grow to form shearbands. Instead, s-LID suggests that the deformation of the sample in the lead-up to failure is governed by a complex symbiosis among these different coexisting structures, which amplifies and promotes the progressive dominance of the embryonic-shearbands over microbands. Third, we probed this transition from the microband-dominated regime to the shearband-dominated regime by systematically suppressing grain rotations. We found particle rotation to be an essential enabler of the transition to the shearband-dominated regime. When grain rotations are completely suppressed, this transition is prevented: microbands and shearbands coexist in relative parity.

cond-mat.mtrl-sci↗

arXiv2020

Neuropsychiatric Disease Classification Using Functional Connectomics -- Results of the Connectomics in NeuroImaging Transfer Learning Challenge

Large, open-source consortium datasets have spurred the development of new and increasingly powerful machine learning approaches in brain connectomics. However, one key question remains: are we capturing biologically relevant and generalizable information about the brain, or are we simply overfitting to the data? To answer this, we organized a scientific challenge, the Connectomics in NeuroImaging Transfer Learning Challenge (CNI-TLC), held in conjunction with MICCAI 2019. CNI-TLC included two classification tasks: (1) diagnosis of Attention-Deficit/Hyperactivity Disorder (ADHD) within a pre-adolescent cohort; and (2) transference of the ADHD model to a related cohort of Autism Spectrum Disorder (ASD) patients with an ADHD comorbidity. In total, 240 resting-state fMRI time series averaged according to three standard parcellation atlases, along with clinical diagnosis, were released for training and validation (120 neurotypical controls and 120 ADHD). We also provided demographic information of age, sex, IQ, and handedness. A second set of 100 subjects (50 neurotypical controls, 25 ADHD, and 25 ASD with ADHD comorbidity) was used for testing. Models were submitted in a standardized format as Docker images through ChRIS, an open-source image analysis platform. Utilizing an inclusive approach, we ranked the methods based on 16 different metrics. The final rank was calculated using the rank product for each participant across all measures. Furthermore, we assessed the calibration curves of each method. Five participants submitted their model for evaluation, with one outperforming all other methods in both ADHD and ASD classification. However, further improvements are needed to reach the clinical translation of functional connectomics. We are keeping the CNI-TLC open as a publicly available resource for developing and validating new classification methodologies in the field of connectomics.

q-bio.NC↗