Research on the Proximity Relationships of Psychosomatic Disease Knowledge Graph Modules Extracted by Large Language Models

As social changes accelerate, the incidence of psychosomatic disorders has significantly increased, becoming a major challenge in global health issues. This necessitates an innovative knowledge system and analytical methods to aid in diagnosis and treatment. Here, we establish the ontology model and entity types, using the BERT model and LoRA-tuned LLM for named entity recognition, constructing the knowledge graph with 9668 triples. Next, by analyzing the network distances between disease, symptom, and drug modules, it was found that closer network distances among diseases can predict greater similarities in their clinical manifestations, treatment approaches, and psychological mechanisms, and closer distances between symptoms indicate that they are more likely to co-occur. Lastly, by comparing the proximity d and proximity z score, it was shown that symptom-disease pairs in primary diagnostic relationships have a stronger association and are of higher referential value than those in diagnostic relationships. The research results revealed the potential connections between diseases, co-occurring symptoms, and similarities in treatment strategies, providing new perspectives for the diagnosis and treatment of psychosomatic disorders and valuable information for future mental health research and practice.

QuLTSF: Long-Term Time Series Forecasting with Quantum Machine Learning

Long-term time series forecasting (LTSF) involves predicting a large number of future values of a time series based on the past values and is an essential task in a wide range of domains including weather forecasting, stock market analysis, disease outbreak prediction. Over the decades LTSF algorithms have transitioned from statistical models to deep learning models like transformer models. Despite the complex architecture of transformer based LTSF models `Are Transformers Effective for Time Series Forecasting? (Zeng et al., 2023)' showed that simple linear models can outperform the state-of-the-art transformer based LTSF models. Recently, quantum machine learning (QML) is evolving as a domain to enhance the capabilities of classical machine learning models. In this paper we initiate the application of QML to LTSF problems by proposing QuLTSF, a simple hybrid QML model for multivariate LTSF. Through extensive experiments on a widely used weather dataset we show the advantages of QuLTSF over the state-of-the-art classical linear models, in terms of reduced mean squared error and mean absolute error.

GraphSeqLM: A Unified Graph Language Framework for Omic Graph Learning

The integration of multi-omic data is pivotal for understanding complex diseases, but its high dimensionality and noise present significant challenges. Graph Neural Networks (GNNs) offer a robust framework for analyzing large-scale signaling pathways and protein-protein interaction networks, yet they face limitations in expressivity when capturing intricate biological relationships. To address this, we propose Graph Sequence Language Model (GraphSeqLM), a framework that enhances GNNs with biological sequence embeddings generated by Large Language Models (LLMs). These embeddings encode structural and biological properties of DNA, RNA, and proteins, augmenting GNNs with enriched features for analyzing sample-specific multi-omic data. By integrating topological, sequence-derived, and biological information, GraphSeqLM demonstrates superior predictive accuracy and outperforms existing methods, paving the way for more effective multi-omic data integration in precision medicine.

NeuralPLexer3: Accurate Biomolecular Complex Structure Prediction with Flow Models

Structure determination is essential to a mechanistic understanding of diseases and the development of novel therapeutics. Machine-learning-based structure prediction methods have made significant advancements by computationally predicting protein and bioassembly structures from sequences and molecular topology alone. Despite substantial progress in the field, challenges remain to deliver structure prediction models to real-world drug discovery. Here, we present NeuralPLexer3 -- a physics-inspired flow-based generative model that achieves state-of-the-art prediction accuracy on key biomolecular interaction types and improves training and sampling efficiency compared to its predecessors and alternative methodologies. Examined through newly developed benchmarking strategies, NeuralPLexer3 excels in vital areas that are crucial to structure-based drug design, such as physical validity and ligand-induced conformational changes.

Accelerated Patient-Specific Calibration via Differentiable Hemodynamics Simulations

One of the goals of personalized medicine is to tailor diagnostics to individual patients. Diagnostics are performed in practice by measuring quantities, called biomarkers, that indicate the existence and progress of a disease. In common cardiovascular diseases, such as hypertension, biomarkers that are closely related to the clinical representation of a patient can be predicted using computational models. Personalizing computational models translates to considering patient-specific flow conditions, for example, the compliance of blood vessels that cannot be a priori known and quantities such as the patient geometry that can be measured using imaging. Therefore, a patient is identified by a set of measurable and nonmeasurable parameters needed to well-define a computational model; else, the computational model is not personalized, meaning it is prone to large prediction errors. Therefore, to personalize a computational model, sufficient information needs to be extracted from the data. The current methods by which this is done are either inefficient, due to relying on slow-converging optimization methods, or hard to interpret, due to using `black box` deep-learning algorithms. We propose a personalized diagnostic procedure based on a differentiable 0D-1D Navier-Stokes reduced order model solver and fast parameter inference methods that take advantage of gradients through the solver. By providing a faster method for performing parameter inference and sensitivity analysis through differentiability while maintaining the interpretability of well-understood mathematical models and numerical methods, the best of both worlds is combined. The performance of the proposed solver is validated against a well-established process on different geometries, and different parameter inference processes are successfully performed.

Efficient Fine-Tuning of Single-Cell Foundation Models Enables Zero-Shot Molecular Perturbation Prediction

Predicting transcriptional responses to novel drugs provides a unique opportunity to accelerate biomedical research and advance drug discovery efforts. However, the inherent complexity and high dimensionality of cellular responses, combined with the extremely limited available experimental data, makes the task challenging. In this study, we leverage single-cell foundation models (FMs) pre-trained on tens of millions of single cells, encompassing multiple cell types, states, and disease annotations, to address molecular perturbation prediction. We introduce a drug-conditional adapter that allows efficient fine-tuning by training less than 1% of the original foundation model, thus enabling molecular conditioning while preserving the rich biological representation learned during pre-training. The proposed strategy allows not only the prediction of cellular responses to novel drugs, but also the zero-shot generalization to unseen cell lines. We establish a robust evaluation framework to assess model performance across different generalization tasks, demonstrating state-of-the-art results across all settings, with significant improvements in the few-shot and zero-shot generalization to new cell lines compared to existing baselines.

Heartbeat Detection from Ballistocardiogram using Transformer Network

Longitudinal monitoring of heart rate (HR) and heart rate variability (HRV) can aid in tracking cardiovascular diseases (CVDs), sleep quality, sleep disorders, and reflect autonomic nervous system activity, stress levels, and overall well-being. These metrics are valuable in both clinical and everyday settings. In this paper, we present a transformer network aimed primarily at detecting the precise timing of heart beats from predicted electrocardiogram (ECG), derived from input Ballistocardiogram (BCG). We compared the performance of segment and subject models across three datasets: a lab dataset with 46 young subjects, an elder dataset with 28 elderly adults, and a combined dataset. The segment model demonstrated superior performance, with correlation coefficients of 0.97 for HR and mean heart beat interval (MHBI) when compared to ground truth. This non-invasive method offers significant potential for long-term, in-home HR and HRV monitoring, aiding in the early indication and prevention of cardiovascular issues.

A Novel Machine Learning Classifier Based on Genetic Algorithms and Data Importance Reformatting

In this paper, a novel classification algorithm that is based on Data Importance (DI) reformatting and Genetic Algorithms (GA) named GADIC is proposed to overcome the issues related to the nature of data which may hinder the performance of the Machine Learning (ML) classifiers. GADIC comprises three phases which are data reformatting phase which depends on DI concept, training phase where GA is applied on the reformatted training dataset, and testing phase where the instances of the reformatted testing dataset are being averaged based on similar instances in the training dataset. GADIC is an approach that utilizes the exiting ML classifiers with involvement of data reformatting, using GA to tune the inputs, and averaging the similar instances to the unknown instance. The averaging of the instances becomes the unknown instance to be classified in the stage of testing. GADIC has been tested on five existing ML classifiers which are Support Vector Machine (SVM), K-Nearest Neighbour (KNN), Logistic Regression (LR), Decision Tree (DT), and Na\"ive Bayes (NB). All were evaluated using seven open-source UCI ML repository and Kaggle datasets which are Cleveland heart disease, Indian liver patient, Pima Indian diabetes, employee future prediction, telecom churn prediction, bank customer churn, and tech students. In terms of accuracy, the results showed that, with the exception of approximately 1% decrease in the accuracy of NB classifier in Cleveland heart disease dataset, GADIC significantly enhanced the performance of most ML classifiers using various datasets. In addition, KNN with GADIC showed the greatest performance gain when compared with other ML classifiers with GADIC followed by SVM while LR had the lowest improvement. The lowest average improvement that GADIC could achieve is 5.96%, whereas the maximum average improvement reached 16.79%.

Catalysts of Conversation: Examining Interaction Dynamics Between Topic Initiators and Commentors in Alzheimer's Disease Online Communities

Informal caregivers (e.g.,family members or friends) of people living with Alzheimers Disease and Related Dementias (ADRD) face substantial challenges and often seek informational or emotional support through online communities. Understanding the factors that drive engagement within these platforms is crucial, as it can enhance their long-term value for caregivers by ensuring that these communities effectively meet their needs. This study investigated the user interaction dynamics within two large, popular ADRD communities, TalkingPoint and ALZConnected, focusing on topic initiator engagement, initial post content, and the linguistic patterns of comments at the thread level. Using analytical methods such as propensity score matching, topic modeling, and predictive modeling, we found that active topic initiator engagement drives higher comment volumes, and reciprocal replies from topic initiators encourage further commentor engagement at the community level. Practical caregiving topics prompt more re-engagement of topic initiators, while emotional support topics attract more comments from other commentors. Additionally, the linguistic complexity and emotional tone of a comment influence its likelihood of receiving replies from topic initiators. These findings highlight the importance of fostering active and reciprocal engagement and providing effective strategies to enhance sustainability in ADRD caregiving and broader health-related online communities.

Reliable Breast Cancer Molecular Subtype Prediction based on uncertainty-aware Bayesian Deep Learning by Mammography

Breast cancer is a heterogeneous disease with different molecular subtypes, clinical behavior, treatment responses as well as survival outcomes. The development of a reliable, accurate, available and inexpensive method to predict the molecular subtypes using medical images plays an important role in the diagnosis and prognosis of breast cancer. Recently, deep learning methods have shown good performance in the breast cancer classification tasks using various medical images. Despite all that success, classical deep learning cannot deliver the predictive uncertainty. The uncertainty represents the validity of the predictions.Therefore, the high predicted uncertainty might cause a negative effect in the accurate diagnosis of breast cancer molecular subtypes. To overcome this, uncertainty quantification methods are used to determine the predictive uncertainty. Accordingly, in this study, we proposed an uncertainty-aware Bayesian deep learning model using the full mammogram images. In addition, to increase the performance of the multi-class molecular subtype classification task, we proposed a novel hierarchical classification strategy, named the two-stage classification strategy. The separate AUC of the proposed model for each subtype was 0.71, 0.75 and 0.86 for HER2-enriched, luminal and triple-negative classes, respectively. The proposed model not only has a comparable performance to other studies in the field of breast cancer molecular subtypes prediction, even using full mammography images, but it is also more reliable, due to quantify the predictive uncertainty.