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Oliver Y. Chén

Publications and source records attributed to Oliver Y. Chén.

At least 19 recordsLinked to original sources

MemoCare: An Interactive Multimodal Mobile System for Automated Cognitive Screening

MemoCare is an interactive mobile system for automated multimodal cognitive screening. A React Native application combines spoken responses, temporal and spatial orientation, touchscreen actions, and visuoconstruction in complete English and Vietnamese workflows. Speech is transcribed by Google Speech-to-Text and scored locally with deterministic task-specific natural language processing rules; GPS coordinates are resolved by the MemoCare spatial module before answer matching; touch tasks are scored from interaction events; and the drawing task uses a three-model convolutional neural network consensus with separate visual interpretation. Software tests pass 151/151 predefined cases across speech/language, spatial-answer, and touch-interaction scoring, while spatial regression passes 48/48 four-country coordinate-resolution cases. For the drawing module, validation-selected ShuffleNetV2 x1.5 achieved 91.33% mean balanced accuracy and 78.87% exact three-criterion accuracy on a locked 71-image test set. Four clinician co-authors additionally inspected the end-to-end workflow, yielding a pooled median rating of 4/5 across eight criteria, with item-level medians ranging from 3 to 4.5. At MMM, attendees can directly try a shortened multimodal screening workflow and inspect automatic item-level and total scoring.

cs.MM↗

Explainable Graph-theoretical Machine Learning with Application to Alzheimer's Disease Prediction

Dementia affects over 55 million people worldwide, projected to reach 139 million by 2050, with Alzheimer's disease (AD) accounting for 60-70% of cases. AD is associated with disruptions in metabolic brain connectivity. Detecting these disruptions early is crucial for AD management. FDG-PET is a useful tool for identifying such impairments. However, most studies rely on group-level analyses or thresholding, potentially masking individual differences and overlooking weaker yet biologically critical brain connections. Moreover, AD prediction largely focuses on univariate rather than multivariate outcomes. To address this, we introduce explainable graph-theoretical machine learning (XGML), a framework for constructing individual metabolic brain graphs and identifying subgraphs most predictive of multivariate disease-related outcomes. Using Alzheimer's Disease Neuroimaging Initiative (ADNI) FDG-PET data, we compared six graph representations against three non-graph baselines, each with six machine learning models using repeated stratified 3-fold cross-validation (10 repeats). The best configuration combined kernel density estimation with Hellinger distance and random forest. Across eight cognitive scores, it reached an overall Fisher-z-averaged Pearson correlation of r=0.595, with strongest performance for ADAS13 (r=0.67), ADAS11 (r=0.65), and ADASQ4 (r=0.62). We identified key edges that were jointly but differentially predictive across outcomes, suggesting their potential as network biomarkers of cognitive decline. Preliminary external feasibility validation on an OASIS3 cohort yielded weak predictive performance for CDRSB (r=0.26) and MMSE (r=0.18), likely reflecting cohort, protocol, and diagnostic differences. Overall, our results suggest the promise of graph-theoretical machine learning for biomarker discovery, disease prediction, and understanding the neural mechanisms underlying AD.

cs.LG↗

Imputation-free transformer learning enables robust Alzheimer's disease prediction and calibrated uncertainty quantification across heterogeneous clinical cohorts

Accurate diagnostic classification and disease-severity prediction for Alzheimer's disease are hampered by the incompleteness and heterogeneity of real-world clinical data. Left unaddressed, these barriers prevent reliable disease modelling and hinder effective clinical evaluation. Conventional imputation strategies introduce systematic bias, distort inter-feature relationships, and yield overconfident predictions, limitations especially consequential in diagnostic settings. Here, we propose NITROGEN, an imputation-free transformer that jointly models within-patient feature dependencies and between-patient relational structure through masked and intersample attention, enabling robust multimodal learning directly from partially observed records. We trained NITROGEN on ADNI (N=7858 scans), and evaluated it on two independent cohorts: OASIS-3 (N=2675 scans) and AIBL (N=1286 scans). Across cohorts and diagnostic and cognitive score prediction tasks, NITROGEN showed robust calibration and uncertainty quantification advantages over tree-based ensemble methods, while maintaining competitive discriminative performance. Cross-cohort and cross-method analyses identified cortical thickness in the temporal pole, age, and APOE genotype as important, though not individually sufficient, features for AD classification. We further introduced a modality-aware uncertainty adjustment that augments predictive uncertainty proportionally to the importance of absent modalities, enabling calibrated confidence when diagnostic information is unavailable. Together, our results show that imputation-free attention learning preserved meaningful discrimination under cohort shift, revealing expected degradation on more distributionally different cohorts, and demonstrate that evaluating models along calibration, interpretability, and cross-cohort reliability, not accuracy alone, is essential for clinical deployment.

q-bio.NC↗

High-dimensional Many-to-many-to-many Mediation Analysis

We study high-dimensional mediation analysis in which exposures, mediators, and outcomes are all multivariate, and both exposures and mediators may be high-dimensional. We formalize this as a many (exposures)-to-many (mediators)-to-many (outcomes) (MMM) mediation analysis problem. Methodologically, MMM mediation analysis simultaneously performs variable selection for high-dimensional exposures and mediators, estimates the indirect effect matrix (i.e., the coefficient matrices linking exposure-to-mediator and mediator-to-outcome pathways), and enables prediction of multivariate outcomes. Theoretically, we show that the estimated indirect effect matrices are consistent and element-wise asymptotically normal, and we derive error bounds for the estimators. To evaluate the efficacy of the MMM mediation framework, we first investigate its finite-sample performance, including convergence properties, the behavior of the asymptotic approximations, and robustness to noise, via simulation studies. We then apply MMM mediation analysis to data from the Alzheimer's Disease Neuroimaging Initiative to study how cortical thickness of 202 brain regions may mediate the effects of 688 genome-wide significant single nucleotide polymorphisms (SNPs) (selected from approximately 1.5 million SNPs) on eleven cognitive-behavioral and diagnostic outcomes. The MMM mediation framework identifies biologically interpretable, many-to-many-to-many genetic-neural-cognitive pathways and improves downstream out-of-sample classification and prediction performance. Taken together, our results demonstrate the potential of MMM mediation analysis and highlight the value of statistical methodology for investigating complex, high-dimensional multi-layer pathways in science. The MMM package is available at https://github.com/THELabTop/MMM-Mediation.

stat.ME↗

Generative Model via Quantile Assignment

Deep Generative models (DGMs) play two key roles in modern machine learning: (i) producing new information (e.g., image synthesis) and (ii) reducing dimensionality. However, traditional architectures often rely on auxiliary networks such as encoders in Variational Autoencoders (VAEs) or discriminators in Generative Adversarial Networks (GANs), which introduce training instability, computational overhead, and risks like mode collapse. We present NeuroSQL, a new generative paradigm that eliminates the need for auxiliary networks by learning low-dimensional latent representations implicitly. NeuroSQL leverages an asymptotic approximation that expresses the latent variables as the solution to an optimal transportation problem. Specifically, NeuroSQL learns the latent variables by solving a linear assignment problem and then passes the latent information to a standalone generator. We benchmark its performance against GANs, VAEs, and a budget-matched diffusion baseline on four datasets: handwritten digits (MNIST), faces (CelebA), animal faces (AFHQ), and brain images (OASIS). Compared to VAEs, GANs, and diffusion models: (1) in terms of image quality, NeuroSQL achieves overall lower mean pixel distance between synthetic and authentic images and stronger perceptual/structural fidelity; (2) computationally, NeuroSQL requires the least training time; and (3) practically, NeuroSQL provides an effective solution for generating synthetic data with limited training samples. By embracing quantile assignment rather than an encoder, NeuroSQL provides a fast, stable, and robust way to generate synthetic data with minimal information loss.

cs.LG↗

Physics-Informed Neural Koopman Machine for Interpretable Longitudinal Personalized Alzheimer's Disease Forecasting

Early forecasting of individual cognitive decline in Alzheimer's disease (AD) is central to disease evaluation and management. Despite advances, it is as of yet challenging for existing methodological frameworks to integrate multimodal data for longitudinal personalized forecasting while maintaining interpretability. To address this gap, we present the Neural Koopman Machine (NKM), a new machine learning architecture inspired by dynamical systems and attention mechanisms, designed to forecast multiple cognitive scores simultaneously using multimodal genetic, neuroimaging, proteomic, and demographic data. NKM integrates analytical ($α$) and biological ($β$) knowledge to guide feature grouping and control the hierarchical attention mechanisms to extract relevant patterns. By implementing Fusion Group-Aware Hierarchical Attention within the Koopman operator framework, NKM transforms complex nonlinear trajectories into interpretable linear representations. To demonstrate NKM's efficacy, we applied it to study the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset. Our results suggest that NKM consistently outperforms both traditional machine learning methods and deep learning models in forecasting trajectories of cognitive decline. Specifically, NKM (1) forecasts changes of multiple cognitive scores simultaneously, (2) quantifies differential biomarker contributions to predicting distinctive cognitive scores, and (3) identifies brain regions most predictive of cognitive deterioration. Together, NKM advances personalized, interpretable forecasting of future cognitive decline in AD using past multimodal data through an explainable, explicit system and reveals potential multimodal biological underpinnings of AD progression.

cs.LG↗

MUDI: A Multimodal Biomedical Dataset for Understanding Pharmacodynamic Drug-Drug Interactions

Understanding the interaction between different drugs (drug-drug interaction or DDI) is critical for ensuring patient safety and optimizing therapeutic outcomes. Existing DDI datasets primarily focus on textual information, overlooking multimodal data that reflect complex drug mechanisms. In this paper, we (1) introduce MUDI, a large-scale Multimodal biomedical dataset for Understanding pharmacodynamic Drug-drug Interactions, and (2) benchmark learning methods to study it. In brief, MUDI provides a comprehensive multimodal representation of drugs by combining pharmacological text, chemical formulas, molecular structure graphs, and images across 310,532 annotated drug pairs labeled as Synergism, Antagonism, or New Effect. Crucially, to effectively evaluate machine-learning based generalization, MUDI consists of unseen drug pairs in the test set. We evaluate benchmark models using both late fusion voting and intermediate fusion strategies. All data, annotations, evaluation scripts, and baselines are released under an open research license.

cs.LG↗

REMEMBER: Retrieval-based Explainable Multimodal Evidence-guided Modeling for Brain Evaluation and Reasoning in Zero- and Few-shot Neurodegenerative Diagnosis

Timely and accurate diagnosis of neurodegenerative disorders, such as Alzheimer's disease, is central to disease management. Existing deep learning models require large-scale annotated datasets and often function as "black boxes". Additionally, datasets in clinical practice are frequently small or unlabeled, restricting the full potential of deep learning methods. Here, we introduce REMEMBER -- Retrieval-based Explainable Multimodal Evidence-guided Modeling for Brain Evaluation and Reasoning -- a new machine learning framework that facilitates zero- and few-shot Alzheimer's diagnosis using brain MRI scans through a reference-based reasoning process. Specifically, REMEMBER first trains a contrastively aligned vision-text model using expert-annotated reference data and extends pseudo-text modalities that encode abnormality types, diagnosis labels, and composite clinical descriptions. Then, at inference time, REMEMBER retrieves similar, human-validated cases from a curated dataset and integrates their contextual information through a dedicated evidence encoding module and attention-based inference head. Such an evidence-guided design enables REMEMBER to imitate real-world clinical decision-making process by grounding predictions in retrieved imaging and textual context. Specifically, REMEMBER outputs diagnostic predictions alongside an interpretable report, including reference images and explanations aligned with clinical workflows. Experimental results demonstrate that REMEMBER achieves robust zero- and few-shot performance and offers a powerful and explainable framework to neuroimaging-based diagnosis in the real world, especially under limited data.

cs.CV↗

OPTIMUS: Predicting Multivariate Outcomes in Alzheimer's Disease Using Multi-modal Data amidst Missing Values

Alzheimer's disease, a neurodegenerative disorder, is associated with neural, genetic, and proteomic factors while affecting multiple cognitive and behavioral faculties. Traditional AD prediction largely focuses on univariate disease outcomes, such as disease stages and severity. Multimodal data encode broader disease information than a single modality and may, therefore, improve disease prediction; but they often contain missing values. Recent "deeper" machine learning approaches show promise in improving prediction accuracy, yet the biological relevance of these models needs to be further charted. Integrating missing data analysis, predictive modeling, multimodal data analysis, and explainable AI, we propose OPTIMUS, a predictive, modular, and explainable machine learning framework, to unveil the many-to-many predictive pathways between multimodal input data and multivariate disease outcomes amidst missing values. OPTIMUS first applies modality-specific imputation to uncover data from each modality while optimizing overall prediction accuracy. It then maps multimodal biomarkers to multivariate outcomes using machine-learning and extracts biomarkers respectively predictive of each outcome. Finally, OPTIMUS incorporates XAI to explain the identified multimodal biomarkers. Using data from 346 cognitively normal subjects, 608 persons with mild cognitive impairment, and 251 AD patients, OPTIMUS identifies neural and transcriptomic signatures that jointly but differentially predict multivariate outcomes related to executive function, language, memory, and visuospatial function. Our work demonstrates the potential of building a predictive and biologically explainable machine-learning framework to uncover multimodal biomarkers that capture disease profiles across varying cognitive landscapes. The results improve our understanding of the complex many-to-many pathways in AD.

cs.LG↗

VisTA: Vision-Text Alignment Model with Contrastive Learning using Multimodal Data for Evidence-Driven, Reliable, and Explainable Alzheimer's Disease Diagnosis

Objective: Assessing Alzheimer's disease (AD) using high-dimensional radiology images is clinically important but challenging. Although Artificial Intelligence (AI) has advanced AD diagnosis, it remains unclear how to design AI models embracing predictability and explainability. Here, we propose VisTA, a multimodal language-vision model assisted by contrastive learning, to optimize disease prediction and evidence-based, interpretable explanations for clinical decision-making. Methods: We developed VisTA (Vision-Text Alignment Model) for AD diagnosis. Architecturally, we built VisTA from BiomedCLIP and fine-tuned it using contrastive learning to align images with verified abnormalities and their descriptions. To train VisTA, we used a constructed reference dataset containing images, abnormality types, and descriptions verified by medical experts. VisTA produces four outputs: predicted abnormality type, similarity to reference cases, evidence-driven explanation, and final AD diagnoses. To illustrate VisTA's efficacy, we reported accuracy metrics for abnormality retrieval and dementia prediction. To demonstrate VisTA's explainability, we compared its explanations with human experts' explanations. Results: Compared to 15 million images used for baseline pretraining, VisTA only used 170 samples for fine-tuning and obtained significant improvement in abnormality retrieval and dementia prediction. For abnormality retrieval, VisTA reached 74% accuracy and an AUC of 0.87 (26% and 0.74, respectively, from baseline models). For dementia prediction, VisTA achieved 88% accuracy and an AUC of 0.82 (30% and 0.57, respectively, from baseline models). The generated explanations agreed strongly with human experts' and provided insights into the diagnostic process. Taken together, VisTA optimize prediction, clinical reasoning, and explanation.

cs.CV↗

Enhancing Uncertain Demand Prediction in Hospitals Using Simple and Advanced Machine Learning

Early and timely prediction of patient care demand not only affects effective resource allocation but also influences clinical decision-making as well as patient experience. Accurately predicting patient care demand, however, is a ubiquitous challenge for hospitals across the world due, in part, to the demand's time-varying temporal variability, and, in part, to the difficulty in modelling trends in advance. To address this issue, here, we develop two methods, a relatively simple time-vary linear model, and a more advanced neural network model. The former forecasts patient arrivals hourly over a week based on factors such as day of the week and previous 7-day arrival patterns. The latter leverages a long short-term memory (LSTM) model, capturing non-linear relationships between past data and a three-day forecasting window. We evaluate the predictive capabilities of the two proposed approaches compared to two naïve approaches - a reduced-rank vector autoregressive (VAR) model and the TBATS model. Using patient care demand data from Rambam Medical Center in Israel, our results show that both proposed models effectively capture hourly variations of patient demand. Additionally, the linear model is more explainable thanks to its simple architecture, whereas, by accurately modelling weekly seasonal trends, the LSTM model delivers lower prediction errors. Taken together, our explorations suggest the utility of machine learning in predicting time-varying patient care demand; additionally, it is possible to predict patient care demand with good accuracy (around 4 patients) three days or a week in advance using machine learning.

cs.LG↗

L-SeqSleepNet: Whole-cycle Long Sequence Modelling for Automatic Sleep Staging

Human sleep is cyclical with a period of approximately 90 minutes, implying long temporal dependency in the sleep data. Yet, exploring this long-term dependency when developing sleep staging models has remained untouched. In this work, we show that while encoding the logic of a whole sleep cycle is crucial to improve sleep staging performance, the sequential modelling approach in existing state-of-the-art deep learning models are inefficient for that purpose. We thus introduce a method for efficient long sequence modelling and propose a new deep learning model, L-SeqSleepNet, which takes into account whole-cycle sleep information for sleep staging. Evaluating L-SeqSleepNet on four distinct databases of various sizes, we demonstrate state-of-the-art performance obtained by the model over three different EEG setups, including scalp EEG in conventional Polysomnography (PSG), in-ear EEG, and around-the-ear EEG (cEEGrid), even with a single EEG channel input. Our analyses also show that L-SeqSleepNet is able to alleviate the predominance of N2 sleep (the major class in terms of classification) to bring down errors in other sleep stages. Moreover the network becomes much more robust, meaning that for all subjects where the baseline method had exceptionally poor performance, their performance are improved significantly. Finally, the computation time only grows at a sub-linear rate when the sequence length increases.

eess.SP↗

Uniting Machine Intelligence, Brain and Behavioural Sciences to Assist Criminal Justice

I discuss here three important roles where machine intelligence, brain and behaviour studies together may facilitate criminal law. First, predictive modelling using brain and behaviour data may support legal investigations by predicting categorical, continuous, and longitudinal legal outcomes of interests related to brain injury and mental illnesses. Second, psychological, psychiatric, and behavioural studies supported by machine learning algorithms may help predict human behaviour and actions, such as lies, biases, and visits to crime scenes. Third, machine learning models have been used to predict recidivism using clinical and criminal data whereas brain decoding is beginning to uncover one's thoughts and intentions based on brain imaging data. Having dispensed with achievements and promises, I examine concerns regarding the accuracy, reliability, and reproducibility of the brain- and behaviour-based assessments in criminal law, as well as questions regarding data possession, ethics, free will (and automatism), privacy, and security. Further, I will discuss issues related to predictability vs. explainability, population-level prediction vs. personalised prediction, and predicting future actions, and outline three potential scenarios where brain and behaviour data may be used as court evidence. Taken together, brain and behaviour decoding in legal exploration and decision-making at present is promising but primitive. The derived evidence is limited and should not be used to generate definitive conclusions, although it can be potentially used in addition, or parallel, to existing evidence. Finally, I suggest that there needs to be (more precise) definitions and regulations regarding when and when not brain and behaviour data can be used in a predictive manner in legal cases.

cs.CY↗

Personalized Longitudinal Assessment of Multiple Sclerosis Using Smartphones

Personalized longitudinal disease assessment is central to quickly diagnosing, appropriately managing, and optimally adapting the therapeutic strategy of multiple sclerosis (MS). It is also important for identifying the idiosyncratic subject-specific disease profiles. Here, we design a novel longitudinal model to map individual disease trajectories in an automated way using sensor data that may contain missing values. First, we collect digital measurements related to gait and balance, and upper extremity functions using sensor-based assessments administered on a smartphone. Next, we treat missing data via imputation. We then discover potential markers of MS by employing a generalized estimation equation. Subsequently, parameters learned from multiple training datasets are ensembled to form a simple, unified longitudinal predictive model to forecast MS over time in previously unseen people with MS. To mitigate potential underestimation for individuals with severe disease scores, the final model incorporates additional subject-specific fine-tuning using data from the first day. The results show that the proposed model is promising to achieve personalized longitudinal MS assessment; they also suggest that features related to gait and balance as well as upper extremity function, remotely collected from sensor-based assessments, may be useful digital markers for predicting MS over time.

stat.ME↗

Thou Shalt Not Reject the P-value

Since its debut in the 18th century, the P-value has been an important part of hypothesis testing-based scientific discoveries. As the statistical engine accelerates, questions are beginning to be raised, asking to what extent scientific discoveries based on P-values are reliable and reproducible, and the voice calling for adjusting the significance level or banning the P-value has been increasingly heard. Inspired by these questions and discussions, here we enquire into the useful roles and misuses of the P-value in scientific studies. For common misuses and misinterpretations, we provide modest recommendations for practitioners. Additionally, we compare statistical significance with clinical relevance. In parallel, we review the Bayesian alternatives for seeking evidence. Finally, we discuss the promises and risks of using meta-analysis to pool P-values from multiple studies to aggregate evidence. Taken together, the P-value underpins a useful probabilistic decision-making system and provides evidence at a continuous scale. But its interpretation must be contextual, considering the scientific question, experimental design (including the model specification, sample size, and significance level), statistical power, effect size, and reproducibility.

stat.ME↗

SleepTransformer: Automatic Sleep Staging with Interpretability and Uncertainty Quantification

Background: Black-box skepticism is one of the main hindrances impeding deep-learning-based automatic sleep scoring from being used in clinical environments. Methods: Towards interpretability, this work proposes a sequence-to-sequence sleep-staging model, namely SleepTransformer. It is based on the transformer backbone and offers interpretability of the model's decisions at both the epoch and sequence level. We further propose a simple yet efficient method to quantify uncertainty in the model's decisions. The method, which is based on entropy, can serve as a metric for deferring low-confidence epochs to a human expert for further inspection. Results: Making sense of the transformer's self-attention scores for interpretability, at the epoch level, the attention scores are encoded as a heat map to highlight sleep-relevant features captured from the input EEG signal. At the sequence level, the attention scores are visualized as the influence of different neighboring epochs in an input sequence (i.e. the context) to recognition of a target epoch, mimicking the way manual scoring is done by human experts. Conclusion: Additionally, we demonstrate that SleepTransformer performs on par with existing methods on two databases of different sizes. Significance: Equipped with interpretability and the ability of uncertainty quantification, SleepTransformer holds promise for being integrated into clinical settings.

cs.LG↗

XSleepNet: Multi-View Sequential Model for Automatic Sleep Staging

Automating sleep staging is vital to scale up sleep assessment and diagnosis to serve millions experiencing sleep deprivation and disorders and enable longitudinal sleep monitoring in home environments. Learning from raw polysomnography signals and their derived time-frequency image representations has been prevalent. However, learning from multi-view inputs (e.g., both the raw signals and the time-frequency images) for sleep staging is difficult and not well understood. This work proposes a sequence-to-sequence sleep staging model, XSleepNet, that is capable of learning a joint representation from both raw signals and time-frequency images. Since different views may generalize or overfit at different rates, the proposed network is trained such that the learning pace on each view is adapted based on their generalization/overfitting behavior. In simple terms, the learning on a particular view is speeded up when it is generalizing well and slowed down when it is overfitting. View-specific generalization/overfitting measures are computed on-the-fly during the training course and used to derive weights to blend the gradients from different views. As a result, the network is able to retain the representation power of different views in the joint features which represent the underlying distribution better than those learned by each individual view alone. Furthermore, the XSleepNet architecture is principally designed to gain robustness to the amount of training data and to increase the complementarity between the input views. Experimental results on five databases of different sizes show that XSleepNet consistently outperforms the single-view baselines and the multi-view baseline with a simple fusion strategy. Finally, XSleepNet also outperforms prior sleep staging methods and improves previous state-of-the-art results on the experimental databases.

eess.SP↗

Multi-view Audio and Music Classification

We propose in this work a multi-view learning approach for audio and music classification. Considering four typical low-level representations (i.e. different views) commonly used for audio and music recognition tasks, the proposed multi-view network consists of four subnetworks, each handling one input types. The learned embedding in the subnetworks are then concatenated to form the multi-view embedding for classification similar to a simple concatenation network. However, apart from the joint classification branch, the network also maintains four classification branches on the single-view embedding of the subnetworks. A novel method is then proposed to keep track of the learning behavior on the classification branches and adapt their weights to proportionally blend their gradients for network training. The weights are adapted in such a way that learning on a branch that is generalizing well will be encouraged whereas learning on a branch that is overfitting will be slowed down. Experiments on three different audio and music classification tasks show that the proposed multi-view network not only outperforms the single-view baselines but also is superior to the multi-view baselines based on concatenation and late fusion.

cs.SD↗