Large language models have already demonstrated their formidable capabilities in general domains, ushering in a revolutionary transformation. However, exploring and exploiting the extensive knowledge of these models to comprehend multi-omics biology remains underexplored. To fill this research gap, we first introduce Biology-Instructions, the first large-scale multi-omics biological sequences-related instruction-tuning dataset including DNA, RNA, proteins, and multi-molecules, designed to bridge the gap between large language models (LLMs) and complex biological sequences-related tasks. This dataset can enhance the versatility of LLMs by integrating diverse biological sequenced-based prediction tasks with advanced reasoning capabilities, while maintaining conversational fluency. Additionally, we reveal significant performance limitations in even state-of-the-art LLMs on biological sequence-related multi-omics tasks without specialized pre-training and instruction-tuning. We further develop a strong baseline called ChatMultiOmics with a novel three-stage training pipeline, demonstrating the powerful ability to understand biology by using Biology-Instructions. Biology-Instructions and ChatMultiOmics are publicly available and crucial resources for enabling more effective integration of LLMs with multi-omics sequence analysis.

Dementia is a neurodegenerative disorder that has been growing among elder people over the past decades. This growth profoundly impacts the quality of life for patients and caregivers due to the symptoms arising from it. Agitation and aggression (AA) are some of the symptoms of people with severe dementia (PwD) in long-term care or hospitals. AA not only causes discomfort but also puts the patients or others at potential risk. Existing monitoring solutions utilizing different wearable sensors integrated with Artificial Intelligence (AI) offer a way to detect AA early enough for timely and adequate medical intervention. However, most studies are limited by the availability of accurately labeled datasets, which significantly affects the efficacy of such solutions in real-world scenarios. This study presents a novel comprehensive approach to detect AA in PwD using physiological data from the Empatica E4 wristbands. The research creates a diverse dataset, consisting of three distinct datasets gathered from 14 participants across multiple hospitals in Canada. These datasets have not been extensively explored due to their limited labeling. We propose a novel approach employing self-training and a variational autoencoder (VAE) to detect AA in PwD effectively. The proposed approach aims to learn the representation of the features extracted using the VAE and then uses a semi-supervised block to generate labels, classify events, and detect AA. We demonstrate that combining Self-Training and Variational Autoencoder mechanism significantly improves model performance in classifying AA in PwD. Among the tested techniques, the XGBoost classifier achieved the highest accuracy of 90.16\%. By effectively addressing the challenge of limited labeled data, the proposed system not only learns new labels but also proves its superiority in detecting AA.

Instance selection (IS) is a crucial technique in machine learning that aims to reduce dataset size while maintaining model performance. This paper introduces a novel method called Graph Attention-based Instance Selection (GAIS), which leverages Graph Attention Networks (GATs) to identify the most informative instances in a dataset. GAIS represents the data as a graph and uses GATs to learn node representations, enabling it to capture complex relationships between instances. The method processes data in chunks, applies random masking and similarity thresholding during graph construction, and selects instances based on confidence scores from the trained GAT model. Experiments on 13 diverse datasets demonstrate that GAIS consistently outperforms traditional IS methods in terms of effectiveness, achieving high reduction rates (average 96\%) while maintaining or improving model performance. Although GAIS exhibits slightly higher computational costs, its superior performance in maintaining accuracy with significantly reduced training data makes it a promising approach for graph-based data selection.

Speech pathology has impacts on communication abilities and quality of life. While deep learning-based models have shown potential in diagnosing these disorders, the use of sensitive data raises critical privacy concerns. Although differential privacy (DP) has been explored in the medical imaging domain, its application in pathological speech analysis remains largely unexplored despite the equally critical privacy concerns. This study is the first to investigate DP's impact on pathological speech data, focusing on the trade-offs between privacy, diagnostic accuracy, and fairness. Using a large, real-world dataset of 200 hours of recordings from 2,839 German-speaking participants, we observed a maximum accuracy reduction of 3.85% when training with DP with high privacy levels. To highlight real-world privacy risks, we demonstrated the vulnerability of non-private models to explicit gradient inversion attacks, reconstructing identifiable speech samples and showcasing DP's effectiveness in mitigating these risks. To generalize our findings across languages and disorders, we validated our approach on a dataset of Spanish-speaking Parkinson's disease patients, leveraging pretrained models from healthy English-speaking datasets, and demonstrated that careful pretraining on large-scale task-specific datasets can maintain favorable accuracy under DP constraints. A comprehensive fairness analysis revealed minimal gender bias at reasonable privacy levels but underscored the need for addressing age-related disparities. Our results establish that DP can balance privacy and utility in speech disorder detection, while highlighting unique challenges in privacy-fairness trade-offs for speech data. This provides a foundation for refining DP methodologies and improving fairness across diverse patient groups in real-world deployments.

The entropic risk measure is widely used in high-stakes decision making to account for tail risks associated with an uncertain loss. With limited data, the empirical entropic risk estimator, i.e. replacing the expectation in the entropic risk measure with a sample average, underestimates the true risk. To mitigate the bias in the empirical entropic risk estimator, we propose a strongly asymptotically consistent bootstrapping procedure. The first step of the procedure involves fitting a distribution to the data, whereas the second step estimates the bias of the empirical entropic risk estimator using bootstrapping, and corrects for it. Two methods are proposed to fit a Gaussian Mixture Model to the data, a computationally intensive one that fits the distribution of empirical entropic risk, and a simpler one with a component that fits the tail of the empirical distribution. As an application of our approach, we study distributionally robust entropic risk minimization problems with type-$\infty$ Wasserstein ambiguity set and apply our bias correction to debias validation performance. Furthermore, we propose a distributionally robust optimization model for an insurance contract design problem that takes into account the correlations of losses across households. We show that choosing regularization parameters based on the cross validation methods can result in significantly higher out-of-sample risk for the insurer if the bias in validation performance is not corrected for. This improvement in performance can be explained from the observation that our methods suggest a higher (and more accurate) premium to homeowners.

Trajectory anomaly detection, aiming to estimate the anomaly risk of trajectories given the Source-Destination (SD) pairs, has become a critical problem for many real-world applications. Existing solutions directly train a generative model for observed trajectories and calculate the conditional generative probability $P({T}|{C})$ as the anomaly risk, where ${T}$ and ${C}$ represent the trajectory and SD pair respectively. However, we argue that the observed trajectories are confounded by road network preference which is a common cause of both SD distribution and trajectories. Existing methods ignore this issue limiting their generalization ability on out-of-distribution trajectories. In this paper, we define the debiased trajectory anomaly detection problem and propose a causal implicit generative model, namely CausalTAD, to solve it. CausalTAD adopts do-calculus to eliminate the confounding bias of road network preference and estimates $P({T}|do({C}))$ as the anomaly criterion. Extensive experiments show that CausalTAD can not only achieve superior performance on trained trajectories but also generally improve the performance of out-of-distribution data, with improvements of $2.1\% \sim 5.7\%$ and $10.6\% \sim 32.7\%$ respectively.

Recent years have witnessed the emerging trend of extensions in modern Integrated Development Environments (IDEs) like Visual Studio Code (VSCode) that significantly enhance developer productivity. Especially, popular AI coding assistants like GitHub Copilot and Tabnine provide conveniences like automated code completion and debugging. While these extensions offer numerous benefits, they may introduce privacy and security concerns to software developers. However, there is no existing work that systematically analyzes the security and privacy concerns, including the risks of data exposure in VSCode extensions. In this paper, we investigate on the security issues of cross-extension interactions in VSCode and shed light on the vulnerabilities caused by data exposure among different extensions. Our study uncovers high-impact security flaws that could allow adversaries to stealthily acquire or manipulate credential-related data (e.g., passwords, API keys, access tokens) from other extensions if not properly handled by extension vendors. To measure their prevalence, we design a novel automated risk detection framework that leverages program analysis and natural language processing techniques to automatically identify potential risks in VSCode extensions. By applying our tool to 27,261 real-world VSCode extensions, we discover that 8.5% of them (i.e., 2,325 extensions) are exposed to credential-related data leakage through various vectors, such as commands, user input, and configurations. Our study sheds light on the security challenges and flaws of the extension-in-IDE paradigm and provides suggestions and recommendations for improving the security of VSCode extensions and mitigating the risks of data exposure.

Neuroimaging data, particularly from techniques like MRI or PET, offer rich but complex information about brain structure and activity. To manage this complexity, latent representation models - such as Autoencoders, Generative Adversarial Networks (GANs), and Latent Diffusion Models (LDMs) - are increasingly applied. These models are designed to reduce high-dimensional neuroimaging data to lower-dimensional latent spaces, where key patterns and variations related to brain function can be identified. By modeling these latent spaces, researchers hope to gain insights into the biology and function of the brain, including how its structure changes with age or disease, or how it encodes sensory information, predicts and adapts to new inputs. This review discusses how these models are used for clinical applications, like disease diagnosis and progression monitoring, but also for exploring fundamental brain mechanisms such as active inference and predictive coding. These approaches provide a powerful tool for both understanding and simulating the brain's complex computational tasks, potentially advancing our knowledge of cognition, perception, and neural disorders.

Graph Mamba, a powerful graph embedding technique, has emerged as a cornerstone in various domains, including bioinformatics, social networks, and recommendation systems. This survey represents the first comprehensive study devoted to Graph Mamba, to address the critical gaps in understanding its applications, challenges, and future potential. We start by offering a detailed explanation of the original Graph Mamba architecture, highlighting its key components and underlying mechanisms. Subsequently, we explore the most recent modifications and enhancements proposed to improve its performance and applicability. To demonstrate the versatility of Graph Mamba, we examine its applications across diverse domains. A comparative analysis of Graph Mamba and its variants is conducted to shed light on their unique characteristics and potential use cases. Furthermore, we identify potential areas where Graph Mamba can be applied in the future, highlighting its potential to revolutionize data analysis in these fields. Finally, we address the current limitations and open research questions associated with Graph Mamba. By acknowledging these challenges, we aim to stimulate further research and development in this promising area. This survey serves as a valuable resource for both newcomers and experienced researchers seeking to understand and leverage the power of Graph Mamba.

ABSTRACT: Early detection of cancer is critical in improving treatment outcomes and increasing survival rates, particularly for common cancers such as lung, breast and prostate which collectively contribute to a significant global mortality burden. With advancements in imaging technologies and data processing, Convolutional Neural Networks (CNNs) have emerged as a powerful tool for analyzing and classifying medical images, enabling more precise cancer detection. This paper provides a comprehensive review of recent studies leveraging CNN models for detecting ten different types of cancer. Each study employs distinct CNN architectures to identify patterns associated with these cancers, utilizing diverse datasets. Key differences and strengths of these architectures are meticulously compared and analyzed, highlighting their efficacy in improving early detection. Beyond reviewing the performance and limitations of CNN-based cancer detection methods, this study explores the feasibility of integrating CNNs into clinical settings as an early detection tool, potentially complementing or replacing traditional methods. Despite significant progress, challenges remain, including data diversity, result interpretation, and ethical considerations. By identifying the best-performing CNN architectures and providing a comparative analysis, this study aims to contribute a comprehensive perspective on the application of CNNs in cancer detection and their role in advancing diagnostic capabilities in healthcare. I. INTRODUCTION Cancer is one of the most complex and deadly diseases of the present century, and due to its increasing prevalence, it has become a global crisis. This disease is characterized by the uncontrolled growth of cells, which can spread to other parts of the body, leading to disability and death. The exact causes of cancer are highly diverse and are a combination of genetic, environmental, and lifestyle factors. 2 In this study, we focus on some of the most common types of cancer, including prostate cancer, blood cancers (leukemia and lymphoma), bladder cancer, skin cancer (melanoma and non-melanoma), colorectal cancer, liver cancer, breast cancer, ovarian cancer, thyroid cancer, and lung cancer. These cancers are of particular significance due to their high prevalence and considerable impact on public health. Global data indicate that the cancer burden is increasing annually.