Computationally predicting protein-protein interactions (PPIs) is challenging due to the lack of integrated, multimodal protein representations. DPEB is a curated collection of 22,043 human proteins that integrates four embedding types: structural (AlphaFold2), transformer-based sequence (BioEmbeddings), contextual amino acid patterns (ESM-2: Evolutionary Scale Modeling), and sequence-based n-gram statistics (ProtVec]). AlphaFold2 protein structures are available through public databases (e.g., AlphaFold2 Protein Structure Database), but the internal neural network embeddings are not. DPEB addresses this gap by providing AlphaFold2-derived embeddings for computational modeling. Our benchmark evaluations show GraphSAGE with BioEmbedding achieved the highest PPI prediction performance (87.37% AUROC, 79.16% accuracy). The framework also achieved 77.42% accuracy for enzyme classification and 86.04% accuracy for protein family classification. DPEB supports multiple graph neural network methods for PPI prediction, enabling applications in systems biology, drug target identification, pathway analysis, and disease mechanism studies.

Stack Overflow (SO), a leading online community forum, is a rich source of software development knowledge. However, locating architectural knowledge, such as architectural solutions remains challenging due to the overwhelming volume of unstructured content and fragmented discussions. Developers must manually sift through posts to find relevant architectural insights, which is time-consuming and error-prone. This study introduces ArchISMiner, a framework for mining architectural knowledge from SO. The framework comprises two complementary components: ArchPI and ArchISPE. ArchPI trains and evaluates multiple models, including conventional ML/DL models, Pre-trained Language Models (PLMs), and Large Language Models (LLMs), and selects the best-performing model to automatically identify Architecture-Related Posts (ARPs) among programming-related discussions. ArchISPE employs an indirect supervised approach that leverages diverse features, including BERT embeddings and local TextCNN features, to extract architectural issue-solution pairs. Our evaluation shows that the best model in ArchPI achieves an F1-score of 0.960 in ARP detection, and ArchISPE outperforms baselines in both SE and NLP fields, achieving F1-scores of 0.883 for architectural issues and 0.894 for solutions. A user study further validated the quality (e.g., relevance and usefulness) of the identified ARPs and the extracted issue-solution pairs. Moreover, we applied ArchISMiner to three additional forums, releasing a dataset of over 18K architectural issue-solution pairs. Overall, ArchISMiner can help architects and developers identify ARPs and extract succinct, relevant, and useful architectural knowledge from developer communities more accurately and efficiently. The replication package of this study has been provided at https://github.com/JeanMusenga/ArchISPE

Abstract--Ransomware has become a critical threat to cy-bersecurity due to its rapid evolution, the necessity for early detection, and growing diversity, posing significant challenges to traditional detection methods. While AI-based approaches had been proposed by prior works to assist ransomware detection, existing methods suffer from three major limitations, ad-hoc feature dependencies, delayed response, and limited adaptability to unseen variants. In this paper, we propose a framework that integrates self-supervised contrastive learning with neural architecture search (NAS) to address these challenges. Specifically, this paper offers three important contributions. Experimental results show that our proposed method achieves significant improvements in both detection accuracy (up to 16.1%) and response time (up to 6x) compared to existing approaches while maintaining robustness under evasive attacks. Ransomware has emerged as one of the most pervasive threats in cybersecurity. It encrypts files on infected machines and demands a ransom for decryption, resulting in significant financial losses. According to a recent study [1], global ransomware-related damages have exceeded $6 trillion, highlighting an urgent need for efficient defense frameworks. Compared with conventional malware, ransomware poses a greater threat due to its stealth and urgency for immediate response. As illustrated in Figure 1, a typical ransomware attack involves two major phases: a stealthy initialization phase where the malware registers itself and loads encryption algorithms, along with the infection phase where encryption begins and causes damage within milliseconds.

The growing adoption of machine learning (ML) in sensitive domains has heightened the demand for transparent and interpretable artificial intelligence. Large Language Models (LLMs) are increasingly capable of producing natural language explanations, yet it remains unclear whether these rationales faithfully capture the predictive signals that underlie decisions. This paper introduces RACE-Reasoning Alignment for Completeness of Explanations, a systematic framework to evaluate the alignment between LLM-generated explanations and interpretable feature importance scores derived from a logistic regression baseline. We analyze four widely used text classification datasets-WIKI ONTOLOGY, AG NEWS, IMDB, and GOEMOTIONS-and compare LLM rationales against top-ranked supporting and contradicting lexical features. To capture alignment at multiple levels of granularity, RACE implements token-aware, exact string, and edit-distance matching techniques. Empirical results reveal a consistent asymmetry: correct predictions exhibit higher coverage of supporting features, while incorrect predictions are associated with elevated coverage of contradicting features. Edit-distance matching further uncovers paraphrastic overlaps, boosting coverage while preserving this asymmetry. These findings demonstrate that LLM rationales combine both surface-level and flexible evidence reuse, yet can also amplify misleading cues in error cases. RACE provides new insights into the faithfulness of LLM explanations and establishes a quantitative basis for evaluating reasoning completeness in neural language models.

Membership inference attacks (MIAs) test whether a data point was part of a model's training set, posing serious privacy risks. Existing methods often depend on shadow models or heavy query access, which limits their practicality. We propose GP-MIA, an efficient and interpretable approach based on Gaussian process (GP) meta-modeling. Using post-hoc metrics such as accuracy, entropy, dataset statistics, and optional sensitivity features (e.g. gradients, NTK measures) from a single trained model, GP-MIA trains a GP classifier to distinguish members from non-members while providing calibrated uncertainty estimates. Experiments on synthetic data, real-world fraud detection data, CIFAR-10, and WikiText-2 show that GP-MIA achieves high accuracy and generalizability, offering a practical alternative to existing MIAs.

In the last decade, due to high resolution cameras and accurate meta - phase analyzes, the accuracy of chromosome classification has improved substantially. However, current Karyotyping systems demand large number of high quality train data to have an adequa tely plausible Precision per each chromosome. Such provision of high quality train data with accurate devices are not yet accomplished in some out - reached pathological laboratories. To prevent false positive detections in low - cost systems and low - quality i mages settings, this paper improves the classification Precision of chromosomes using proposed reliability thresholding metrics and deliberately engineered features. The proposed method has been evaluated using a variation of deep Alex - Net neural network, SVM, K - Nearest - Neighbors, and their cascade pipelines to an automated filtering of semi - straight chromosome. The classification results have highly improved over 90% for the chromosomes with more common defections and translocations. Furthermore, a compara tive analysis over the proposed thresholding metrics has been conducted and the best metric is bolded with its salient characteristics. The high Precision results provided for a very low - quality G - banding database verifies suitability of the proposed metri cs and pruning method for Karyotyping facilities in poor countries and low - budget pathological laboratories. Keywords: G - banded Karyotyping, Precision, Reliability metrics, Pattern Recognition, Medical Imaging 1 Introduction One of the ways to study and dia gnose birth - defects and biological disorders is through using Cytogenetics. This branch of science endeavors to analyze chromosome shapes and patterns to find out common defects. The methods used for such analyzes includes G - Banding, Fluorescent In - Situ Hy bridization (FISH), Comparative Genomic Hybridization (CGH) and Chromosome - specific unique - sequence probes [27] . While Molecular Cytogenetics methods are effective in biological disorders, they do not necessarily manifest specific chromosome defects. FISH methods, though having higher accuracy results in stains, are costly and unable to identify all chromosome abnorm alities. Being temporary in sustaining fluorescence detector, they demand higher provision effort and substance supply that might not be affordable for some countries . Furthermore, detecting some abnormalities implies having G - banding technique involved an d not merely using stains.

The proliferation of high-dimensional datasets in fields such as genomics, healthcare, and finance has created an urgent need for machine learning models that are both highly accurate and inherently interpretable. While traditional deep learning approaches deliver strong predictive performance, their lack of transparency often impedes their deployment in critical, decision-sensitive applications. In this work, we introduce the Hierarchical Attention-based Interpretable Network (HAIN), a novel architecture that unifies multi-level attention mechanisms, dimensionality reduction, and explanation-driven loss functions to deliver interpretable and robust analysis of complex biomedical data. HAIN provides feature-level interpretability via gradientweighted attention and offers global model explanations through prototype-based representations. Comprehensive evaluation on The Cancer Genome Atlas (TCGA) dataset demonstrates that HAIN achieves a classification accuracy of 94.3%, surpassing conventional post-hoc interpretability approaches such as SHAP and LIME in both transparency and explanatory power. Furthermore, HAIN effectively identifies biologically relevant cancer biomarkers, supporting its utility for clinical and research applications. By harmonizing predictive accuracy with interpretability, HAIN advances the development of transparent AI solutions for precision medicine and regulatory compliance.

In this study, we present an interpretable deep learning framework for the early detection of breast cancer using quantitative features extracted from digitized fine needle aspirate (FNA) images of breast masses. Our deep neural network, using ReLU activations, the Adam optimizer, and a binary cross-entropy loss, delivers state-of-the-art classification performance, achieving an accuracy of 0.992, precision of 1.000, recall of 0.977, and an F1 score of 0.988. These results substantially exceed the benchmarks reported in the literature. We evaluated the model under identical protocols against a suite of well-established algorithms (logistic regression, decision trees, random forests, stochastic gradient descent, K-nearest neighbors, and XGBoost) and found the deep model consistently superior on the same metrics. Recognizing that high predictive accuracy alone is insufficient for clinical adoption due to the black-box nature of deep learning models, we incorporated model-agnostic Explainable AI techniques such as SHAP and LIME to produce feature-level attributions and human-readable visualizations. These explanations quantify the contribution of each feature to individual predictions, support error analysis, and increase clinician trust, thus bridging the gap between performance and interpretability for real-world clinical use. The concave points feature of the cell nuclei is found to be the most influential feature positively impacting the classification task. This insight can be very helpful in improving the diagnosis and treatment of breast cancer by highlighting the key characteristics of breast tumor.

Transformers trained in low precision can suffer forward-error amplification. We give a first-order, module-wise theory that predicts when and where errors grow. For self-attention we derive a per-layer bound that factorizes into three interpretable diagnostics: a score-scale ratio $κ_{\rm score}$, a rowwise softmax sensitivity $κ_{\rm softmax}$, and value conditioning $κ(V)$. We prove a residual relaxation inequality showing that residual blocks attenuate depth-wise accumulation, and we introduce a precision- and width-aware LayerNorm indicator $ρ_{\rm LN}$ with a matching first-order bound in the $ε$-dominated regime. These pieces yield a unified forward-stability bound whose right-hand side is directly estimable during training. On Tiny-ViT/CIFAR-10 we evaluate the bound and components. (1) The combined predictor $κ_{\rm softmax},(1+κ_{\rm score}),κ(V),|W_O|2+κ{\rm eff}+C_{\rm LN}$ tracks FP32$\leftrightarrow$LP mismatches across seeds, widths, and precisions; scaling by $ε_{\rm mach}$ collapses mixed-precision points. (2) The time-series maximum of $κ_{\rm softmax}$ acts as an early-warning signal, leading error spikes by 16-24 steps (corr. 0.65-0.82; permutation $p!\approx!10^{-3}$; Precision@K 0.89-1.00). (3) Guided by $ρ_{\rm LN}$, a small LayerNorm-$ε$ tweak targeting $ρ_\star$ gives consistent stabilization (mean tail-loss $\downarrow\ \approx0.010$ at $ρ_\star!=!0.6$, cap$=10^{-2}$) with negligible overhead. Overall, our theory supplies actionable, unitless diagnostics that (i) explain when self-attention is fragile, (ii) forecast instability, and (iii) motivate a minimally invasive mitigation.

Internal combustion engine (ICE) vehicles and electric vehicles (EVs) exhibit distinct vehicle dynamics. EVs provide rapid acceleration, with electric motors producing peak power across a wider speed range, and achieve swift deceleration through regenerative braking. While existing microscopic models effectively capture the driving behavior of ICE vehicles, a modeling framework that accurately describes the unique car-following dynamics of EVs is lacking. Developing such a model is essential given the increasing presence of EVs in traffic, yet creating an easy-to-use and accurate analytical model remains challenging. To address these gaps, this study develops and validates a Phase-Aware AI (PAAI) car-following model specifically for EVs. The proposed model enhances traditional physics-based frameworks with an AI component that recognizes and adapts to different driving phases, such as rapid acceleration and regenerative braking. Using real-world trajectory data from vehicles equipped with adaptive cruise control (ACC), we conduct comprehensive simulations to validate the model's performance. The numerical results demonstrate that the PAAI model significantly improves prediction accuracy over traditional car-following models, providing an effective tool for accurately representing EV behavior in traffic simulations.