Research Papers

Advancements in high-throughput technologies have led to a shift from traditional hypothesis-driven methodologies to data-driven approaches. Multi-omics refers to the integrative analysis of data derived from multiple 'omes', such as genomics, proteomics, transcriptomics, metabolomics, and microbiomics. This approach enables a comprehensive understanding of biological systems by capturing different layers of biological information. Deep learning methods are increasingly utilized to integrate multi-omics data, offering insights into molecular interactions and enhancing research into complex diseases. However, these models, with their numerous interconnected layers and nonlinear relationships, often function as black boxes, lacking transparency in decision-making processes. To overcome this challenge, explainable artificial intelligence (xAI) methods are crucial for creating transparent models that allow clinicians to interpret and work with complex data more effectively. This review explores how xAI can improve the interpretability of deep learning models in multi-omics research, highlighting its potential to provide clinicians with clear insights, thereby facilitating the effective application of such models in clinical settings.

Inherited retinal diseases (IRDs) are a diverse group of genetic disorders that lead to progressive vision loss and are a major cause of blindness in working-age adults. The complexity and heterogeneity of IRDs pose significant challenges in diagnosis, prognosis, and management. Recent advancements in artificial intelligence (AI) offer promising solutions to these challenges. However, the rapid development of AI techniques and their varied applications have led to fragmented knowledge in this field. This review consolidates existing studies, identifies gaps, and provides an overview of AI's potential in diagnosing and managing IRDs. It aims to structure pathways for advancing clinical applications by exploring AI techniques like machine learning and deep learning, particularly in disease detection, progression prediction, and personalized treatment planning. Special focus is placed on the effectiveness of convolutional neural networks in these areas. Additionally, the integration of explainable AI is discussed, emphasizing its importance in clinical settings to improve transparency and trust in AI-based systems. The review addresses the need to bridge existing gaps in focused studies on AI's role in IRDs, offering a structured analysis of current AI techniques and outlining future research directions. It concludes with an overview of the challenges and opportunities in deploying AI for IRDs, highlighting the need for interdisciplinary collaboration and the continuous development of robust, interpretable AI models to advance clinical applications.

Objective: Mitigating algorithmic disparities is a critical challenge in healthcare research, where ensuring equity and fairness is paramount. While large-scale healthcare data exist across multiple institutions, cross-institutional collaborations often face privacy constraints, highlighting the need for privacy-preserving solutions that also promote fairness. Materials and Methods: In this study, we present Fair Federated Machine Learning (FairFML), a model-agnostic solution designed to reduce algorithmic bias in cross-institutional healthcare collaborations while preserving patient privacy. As a proof of concept, we validated FairFML using a real-world clinical case study focused on reducing gender disparities in cardiac arrest outcome prediction. Results: We demonstrate that the proposed FairFML framework enhances fairness in federated learning (FL) models without compromising predictive performance. Our findings show that FairFML improves model fairness by up to 65% compared to the centralized model, while maintaining performance comparable to both local and centralized models, as measured by receiver operating characteristic analysis. Discussion and Conclusion: FairFML offers a promising and flexible solution for FL collaborations, with its adaptability allowing seamless integration with various FL frameworks and models, from traditional statistical methods to deep learning techniques. This makes FairFML a robust approach for developing fairer FL models across diverse clinical and biomedical applications.

The rapid expansion of e-commerce and the widespread use of credit cards in online purchases and financial transactions have significantly heightened the importance of promptly and accurately detecting credit card fraud (CCF). Not only do fraudulent activities in financial transactions lead to substantial monetary losses for banks and financial institutions, but they also undermine user trust in digital services. This study presents a new stacking-based approach for CCF detection by adding two extra layers to the usual classification process: an attention layer and a confidence-based combination layer. In the attention layer, we combine soft outputs from a convolutional neural network (CNN) and a recurrent neural network (RNN) using the dependent ordered weighted averaging (DOWA) operator, and from a graph neural network (GNN) and a long short-term memory (LSTM) network using the induced ordered weighted averaging (IOWA) operator. These weighted outputs capture different predictive signals, increasing the model's accuracy. Next, in the confidence-based layer, we select whichever aggregate (DOWA or IOWA) shows lower uncertainty to feed into a meta-learner. To make the model more explainable, we use shapley additive explanations (SHAP) to identify the top ten most important features for distinguishing between fraud and normal transactions. These features are then used in our attention-based model. Experiments on three datasets show that our method achieves high accuracy and robust generalization, making it effective for CCF detection.

Social interactions promote well-being, yet barriers like geographic distance, time limitations, and mental health conditions can limit face-to-face interactions. Emotionally responsive AI systems, such as chatbots, offer new opportunities for social and emotional support, but raise critical questions about how empathy is perceived and experienced in human-AI interactions. This study examines how empathy is evaluated in AI-generated versus human responses. Using personal narratives, we explored how persona attributes (e.g., gender, empathic traits, shared experiences) and story qualities affect empathy ratings. We compared responses from standard and fine-tuned AI models with human judgments. Results show that while humans are highly sensitive to emotional vividness and shared experience, AI-responses are less influenced by these cues, often lack nuance in empathic expression. These findings highlight challenges in designing emotionally intelligent systems that respond meaningfully across diverse users and contexts, and informs the design of ethically aware tools to support social connection and well-being.

The use of transformer-based models is growing rapidly throughout society. With this growth, it is important to understand how they work, and in particular, how the attention mechanisms represent concepts. Though there are many interpretability methods, many look at models through their neuronal activations, which are poorly understood. We describe different lenses through which to view neuron activations, and investigate the effectiveness in language models and vision transformers through various methods of neural ablation: zero ablation, mean ablation, activation resampling, and a novel approach we term 'peak ablation'. Through experimental analysis, we find that in different regimes and models, each method can offer the lowest degradation of model performance compared to other methods, with resampling usually causing the most significant performance deterioration. We make our code available at https://github.com/nickypro/investigating-ablation.

With the rapid advancement of AI, there is a growing trend to integrate AI into decision-making processes. However, AI systems may exhibit biases that lead decision-makers to draw unfair conclusions. Notably, the COMPAS system used in the American justice system to evaluate recidivism was found to favor racial majority groups; specifically, it violates a fairness standard called equalized odds. Various measures have been proposed to assess AI fairness. We present a framework for auditing AI fairness, involving third-party auditors and AI system providers, and we have created a tool to facilitate systematic examination of AI systems. The tool is open-sourced and publicly available. Unlike traditional AI systems, we advocate a transparent white-box and statistics-based approach. It can be utilized by third-party auditors, AI developers, or the general public for reference when judging the fairness criterion of AI systems.

As AI-enhanced academic search systems become increasingly popular among researchers, investigating their AI transparency is crucial to ensure trust in the search outcomes, as well as the reliability and integrity of scholarly work. This study employs a qualitative content analysis approach to examine the websites of a sample of 10 AI-enhanced academic search systems identified through university library guides. The assessed level of transparency varies across these systems: five provide detailed information about their mechanisms, three offer partial information, and two provide little to no information. These findings indicate that the academic community is recommending and using tools with opaque functionalities, raising concerns about research integrity, including issues of reproducibility and researcher responsibility.

Recent generative models produce images with a level of authenticity that makes them nearly indistinguishable from real photos and artwork. Potential harmful use cases of these models, necessitate the creation of robust synthetic image detectors. However, current datasets in the field contain generated images with questionable quality or have examples from one predominant content type which leads to poor generalizability of the underlying detectors. We find that the curation of a balanced amount of high-resolution generated images across various content types is crucial for the generalizability of detectors, and introduce ImagiNet, a dataset of 200K examples, spanning four categories: photos, paintings, faces, and miscellaneous. Synthetic images in ImagiNet are produced with both open-source and proprietary generators, whereas real counterparts for each content type are collected from public datasets. The structure of ImagiNet allows for a two-track evaluation system: i) classification as real or synthetic and ii) identification of the generative model. To establish a strong baseline, we train a ResNet-50 model using a self-supervised contrastive objective (SelfCon) for each track which achieves evaluation AUC of up to 0.99 and balanced accuracy ranging from 86% to 95%, even under conditions that involve compression and resizing. The provided model is generalizable enough to achieve zero-shot state-of-the-art performance on previous synthetic detection benchmarks. We provide ablations to demonstrate the importance of content types and publish code and data.

In modern healthcare, addressing the complexities of accurate disease prediction and personalized recommendations is both crucial and challenging. This research introduces MLtoGAI, which integrates Semantic Web technology with Machine Learning (ML) to enhance disease prediction and offer user-friendly explanations through ChatGPT. The system comprises three key components: a reusable disease ontology that incorporates detailed knowledge about various diseases, a diagnostic classification model that uses patient symptoms to detect specific diseases accurately, and the integration of Semantic Web Rule Language (SWRL) with ontology and ChatGPT to generate clear, personalized health advice. This approach significantly improves prediction accuracy and ensures results that are easy to understand, addressing the complexity of diseases and diverse symptoms. The MLtoGAI system demonstrates substantial advancements in accuracy and user satisfaction, contributing to developing more intelligent and accessible healthcare solutions. This innovative approach combines the strengths of ML algorithms with the ability to provide transparent, human-understandable explanations through ChatGPT, achieving significant improvements in prediction accuracy and user comprehension. By leveraging semantic technology and explainable AI, the system enhances the accuracy of disease prediction and ensures that the recommendations are relevant and easily understood by individual patients. Our research highlights the potential of integrating advanced technologies to overcome existing challenges in medical diagnostics, paving the way for future developments in intelligent healthcare systems. Additionally, the system is validated using 200 synthetic patient data records, ensuring robust performance and reliability.

The advancement of machine learning (ML) models has led to the development of ML-based approaches to improve numerous software engineering tasks in software maintenance and evolution. Nevertheless, research indicates that despite their potential successes, ML models may not be employed in real-world scenarios because they often remain a black box to practitioners, lacking explainability in their reasoning. Recently, various rule-based model-agnostic Explainable AI (XAI) techniques, such as PyExplainer and LIME, have been employed to explain the predictions of ML models in software analytics tasks. This paper assesses the ability of these techniques (e.g., PyExplainer and LIME) to generate reliable and consistent explanations for ML models across various software analytics tasks, including Just-in-Time (JIT) defect prediction, clone detection, and the classification of useful code review comments. Our manual investigations find inconsistencies and anomalies in the explanations generated by these techniques. Therefore, we design a novel framework: Evaluation of Explainable AI (EvaluateXAI), along with granular-level evaluation metrics, to automatically assess the effectiveness of rule-based XAI techniques in generating reliable and consistent explanations for ML models in software analytics tasks. After conducting in-depth experiments involving seven state-of-the-art ML models trained on five datasets and six evaluation metrics, we find that none of the evaluation metrics reached 100\%, indicating the unreliability of the explanations generated by XAI techniques. Additionally, PyExplainer and LIME failed to provide consistent explanations for 86.11% and 77.78% of the experimental combinations, respectively. Therefore, our experimental findings emphasize the necessity for further research in XAI to produce reliable and consistent explanations for ML models in software analytics tasks.

Numerous fairness metrics have been proposed and employed by artificial intelligence (AI) experts to quantitatively measure bias and define fairness in AI models. Recognizing the need to accommodate stakeholders' diverse fairness understandings, efforts are underway to solicit their input. However, conveying AI fairness metrics to stakeholders without AI expertise, capturing their personal preferences, and seeking a collective consensus remain challenging and underexplored. To bridge this gap, we propose a new framework, EARN Fairness, which facilitates collective metric decisions among stakeholders without requiring AI expertise. The framework features an adaptable interactive system and a stakeholder-centered EARN Fairness process to Explain fairness metrics, Ask stakeholders' personal metric preferences, Review metrics collectively, and Negotiate a consensus on metric selection. To gather empirical results, we applied the framework to a credit rating scenario and conducted a user study involving 18 decision subjects without AI knowledge. We identify their personal metric preferences and their acceptable level of unfairness in individual sessions. Subsequently, we uncovered how they reached metric consensus in team sessions. Our work shows that the EARN Fairness framework enables stakeholders to express personal preferences and reach consensus, providing practical guidance for implementing human-centered AI fairness in high-risk contexts. Through this approach, we aim to harmonize fairness expectations of diverse stakeholders, fostering more equitable and inclusive AI fairness.