arXiv subjects

Athanasios Angelakis

Publications and source records attributed to Athanasios Angelakis.

13 recordsLinked to original sources

arXiv2026

REDE: A Quantitative Framework for Differential-Expression Reproducibility and Diagnostic Transfer Across Nine Cohorts and Three Cancers

Differential-expression analyses often turn cohort-specific significance into claims of stable gene signatures or diagnostic biomarkers. We evaluated which layers of evidence reproduce across independent datasets and whether discovery-derived panels retain locked tumor-versus-non-tumor classification performance. Nine public microarray cohorts were organized into fixed discovery, validation, and external-test experiments for pancreatic ductal adenocarcinoma, breast cancer, and lung cancer. Reproducibility was assessed for DEG burden, exact membership, top-rank overlap, signed effects, prespecified gene confirmation, and Hallmark pathways. We also introduced REDE-2Fold, in which each discovery cohort is split once at patient level, differential expression is performed independently in both folds, and only same-direction genes selected in both are retained. Four training-only panels were then evaluated with locked logistic models and thresholds: all discovery DEGs, the top 19 discovery DEGs, all REDE-2Fold genes, and the top 19 REDE-2Fold genes. Broad DEG-list confirmation in both independent cohorts ranged from 15.5% to 39.5%, rising to 50.1% to 84.3% for large effects. Pathway replication ranged from 52.2% to 88.9%. Compact 19-gene panels retained high external ROC-AUC, but locked operating points were often unstable: some models with ROC-AUC near 1.0 showed zero specificity or very low sensitivity. These results define a hierarchy from thresholded membership through effect, pathway, discrimination, and operating-point transfer. REDE provides a seven-level quantitative framework for matching transcriptomic claims to the evidence actually tested, while REDE-2Fold offers a minimum internal feature-stability procedure that strengthens but does not replace independent validation.

q-bio.QM↗

arXiv2026

qZACH-ViT: Quantization-Aware Intrinsic Explanations with Recursive Attribution-Stabilized Optimization

Compact medical-image classifiers need efficiency and interpretable evidence, yet these goals are often addressed separately. We introduce qZACH-ViT, a quantization-aware extension of the zero-token (CLS-token-free), position-free ZACH-ViT backbone with recursive intrinsic patch-level class evidence. We also introduce Recursive Attribution-Stabilized Optimization (RASO), which norm-matches classification and attribution gradients and removes attribution components that conflict with classification. We evaluate four controlled conditions on seven MedMNIST datasets using 50 training images per class and ten fixed seeds, completing 280 runs. All 210 qZACH-ViT checkpoints are converted to executable mixed-precision ONNX INT8 graphs containing 16 signed INT8 MatMulInteger projections with INT32 accumulation. Deployed mixed-precision INT8 qZACH-ViT with Adam improves the FP32 ZACH-ViT baseline mean on all seven datasets, with a mean paired gain of 0.0313 in the dataset-specific primary metric; qZACH-ViT with RASO yields a mean gain of 0.0368. Across 964,920 source-to-INT8 test comparisons, prediction agreement is 99.9751\%, with a mean absolute primary-metric change of 0.000133 and a maximum of 0.004386. Across 3,600 matched intrinsic maps, mean cosine similarity is 0.999955, mean rank correlation is 0.9944, and mean top-10\% overlap is 0.9692. ONNX artifacts are 70.0\% smaller than source checkpoints and provide $1.41\times$ and $2.39\times$ end-to-end CPU speedups with one and four threads. RASO significantly reduces sufficiency error and improves input-noise stability over Adam with the same attribution loss, but does not dominate every predictive or explainable artificial intelligence (XAI) metric. These results establish qZACH-ViT as a deployable compact intrinsically explainable model and RASO as a targeted stability-oriented optimization procedure.

cs.LG↗

arXiv2026

The $\alpha$-Index: A Penalized Authorship-Integrity Framework for Position-Weighted Scientific Contribution

Publication and citation indicators commonly assign full credit to every coauthor, obscuring differences in authorship role and potentially rewarding accumulated authorship rather than identifiable intellectual contribution. We propose the $\alpha$-index as a conserved, position-weighted, and penalized authorship-integrity framework. Each publication contributes one unit of credit, allocated across first-author execution, senior-author leadership, and residual middle authorship. Its defining feature is a senior-author responsibility penalty: senior credit decreases as the residual middle-author list expands, expressing the normative principle that leadership credit should be accompanied by responsibility for authorship discipline. The paper formalizes local $\alpha$-credit allocation and the cumulative $\alpha$-index; presents a parameterized family of weight blocks and penalty functions; and compares the framework with fractional, harmonic, and h-$\alpha$-type approaches. Synthetic examples and selected public byline illustrations demonstrate mathematical behavior, including large-team variants. The default values are not empirical constants but transparent, testable hypotheses within a calibratable family. The framework is presented as a methodological and ethical proposal requiring field-specific validation against contribution statements, expert assessments, author surveys, and bibliographic data. It is intended to complement, not replace, peer review, contributor statements, acknowledgements, and citation-based metrics.

cs.DL↗

arXiv2026

hZACH-ViT: Curved Latent Geometry for Compact Vision Transformers in Low-Data Medical Imaging

Compact Vision Transformers are attractive for medical imaging in low-data and resource-constrained settings, but most existing variants assume that Euclidean latent geometry is sufficient for organizing image representations. We introduce hZACH-ViT, a family of curved-geometry extensions of ZACH-ViT, a compact zero-token Vision Transformer that removes positional embeddings and the class token and relies on global average pooling over patch representations. To isolate the role of geometry, we preserve the verified ZACH-ViT backbone and modify only the final representation space and prototype-based classifier head, enabling a controlled comparison between Euclidean, hyperbolic, and spherical latent geometries. We evaluate Poincar\'e, Klein, and spherical hZACH-ViT heads on seven MedMNIST datasets under an identical few-shot protocol with 50 samples per class and five random seeds. The completed benchmark contains 770 training runs spanning seven datasets, three non-Euclidean geometries, seven curvature magnitudes, and a Euclidean baseline. Across all seven datasets, the best non-Euclidean hZACH-ViT configuration improves over Euclidean ZACH-ViT, with an average gain of +0.021 in the dataset-specific primary metric and the largest improvement on OCTMNIST (+0.055 MacroF1). Fixed low-curvature configurations retain positive gains on the majority of datasets, and low curvature values (c = 0.1 or 0.2) account for six of the seven dataset-level winners. Rather than identifying a universally optimal manifold, our results establish geometry and curvature as dataset-dependent model-selection variables, with fixed low-curvature analyses confirming that gains persist beyond exhaustive per-dataset tuning.

cs.CV↗

arXiv2026

Machine-Learning-Enhanced Non-Invasive Testing for MASLD Fibrosis: Shallow-Deep Neural Networks Versus FIB-4, Tabular Foundation Models, and Large Language Models

Advanced fibrosis is a major determinant of liver-related morbidity in metabolic dysfunction-associated steatotic liver disease (MASLD). FIB-4 is widely used as a first-line non-invasive test, but its fixed formula may underuse diagnostic information contained in age, aspartate aminotransferase, alanine aminotransferase, and platelet count. We evaluated whether machine-learning-enhanced non-invasive testing (MLE-NIT) can improve advanced fibrosis detection while preserving this FIB-4 variable space. We used three biopsy-confirmed MASLD cohorts from China, Malaysia, and India (n=784). The Chinese cohort was split into 486 training and 54 internal validation/tuning patients; final performance was reported only on the Malaysian and Indian external cohorts. Models used five variables: age, FIB-4, aspartate aminotransferase, platelet count, and alanine aminotransferase. We compared FIB-4 with a shallow-deep neural network (s-DNN), TabPFN, and gpt-4o-2024-08-06. FIB-4 achieved external ROC-AUCs of 0.75 and 0.60 in Malaysia and India, respectively. TabPFN achieved 0.69 and 0.66, fine-tuned GPT-4o achieved 0.75 and 0.63, and the s-DNN achieved 0.77 and 0.67, respectively. The s-DNN contained only 354 trainable parameters, compared with 7,244,554 for TabPFN, yet provided a more balanced external operating profile. Calibration showed s-DNN Brier scores of 0.18 and 0.22, and permutation importance identified AST and FIB-4 as dominant variables. Compact non-linear MLE-NITs may enhance FIB-4-based fibrosis assessment without increasing clinical data requirements.

cs.LG↗

arXiv2026

Extending ZACH-ViT to Robust Medical Imaging: Corruption and Adversarial Stress Testing in Low-Data Regimes

The recently introduced ZACH-ViT (Zero-token Adaptive Compact Hierarchical Vision Transformer) formalized a compact permutation-invariant Vision Transformer for medical imaging and argued that architectural alignment with spatial structure can matter more than universal benchmark dominance. Its design was motivated by the observation that positional embeddings and a dedicated class token encode fixed spatial assumptions that may be suboptimal when spatial organization is weakly informative, locally distributed, or variable across biomedical images. The foundational study established a regime-dependent clean performance profile across MedMNIST, but did not examine robustness in detail. In this work, we present the first robustness-focused extension of ZACH-ViT by evaluating its behavior under common image corruptions and adversarial perturbations in the same low-data setting. We compare ZACH-ViT with three scratch-trained compact baselines, ABMIL, Minimal-ViT, and TransMIL, on seven MedMNIST datasets using 50 samples per class, fixed hyperparameters, and five random seeds. Across the benchmark, ZACH-ViT achieves the best overall mean rank on clean data (1.57) and under common corruptions (1.57), indicating a favorable balance between baseline predictive performance and robustness to realistic image degradation. Under adversarial stress, all models deteriorate substantially; nevertheless, ZACH-ViT remains competitive, ranking first under FGSM (2.00) and second under PGD (2.29), where ABMIL performs best overall. These results extend the original ZACH-ViT narrative: the advantages of compact permutation-invariant transformers are not limited to clean evaluation, but can persist under realistic perturbation stress in low-data medical imaging, while adversarial robustness remains an open challenge for all evaluated models.

cs.CV↗

arXiv2026

ZACH-ViT: Regime-Dependent Inductive Bias in Compact Vision Transformers for Medical Imaging

Vision Transformers rely on positional embeddings and class tokens encoding fixed spatial priors. While effective for natural images, these priors may be suboptimal when spatial layout is weakly informative, a frequent condition in medical imaging. We introduce ZACH-ViT (Zero-token Adaptive Compact Hierarchical Vision Transformer), a compact Vision Transformer that removes positional embeddings and the [CLS] token, achieving permutation-invariant patch processing via global average pooling. Zero-token denotes removal of the dedicated aggregation token and positional encodings. Patch tokens remain unchanged. Adaptive residual projections preserve training stability under strict parameter constraints. We evaluate ZACH-ViT across seven MedMNIST datasets under a strict few-shot protocol (50 samples/class, fixed hyperparameters, five seeds). Results reveal regime-dependent behavior: ZACH-ViT (0.25M parameters, trained from scratch) achieves strongest advantage on BloodMNIST and remains competitive on PathMNIST, while relative advantage decreases on datasets with stronger anatomical priors (OCTMNIST, OrganAMNIST), consistent with our hypothesis. Component and pooling ablations show positional support becomes mildly beneficial as spatial structure increases, whereas reintroducing a [CLS] token is consistently unfavorable. These findings support that architectural alignment with data structure can outweigh universal benchmark dominance. Despite minimal size and no pretraining, ZACH-ViT achieves competitive performance under data-scarce conditions, relevant for compact medical imaging and low-resource settings. Code: https://github.com/Bluesman79/ZACH-ViT

cs.CV↗

arXiv2025

ZACH-ViT: A Zero-Token Vision Transformer with ShuffleStrides Data Augmentation for Robust Lung Ultrasound Classification

Differentiating cardiogenic pulmonary oedema (CPE) from non-cardiogenic and structurally normal lungs in lung ultrasound (LUS) videos remains challenging due to the high visual variability of non-cardiogenic inflammatory patterns (NCIP/ARDS-like), interstitial lung disease, and healthy lungs. This heterogeneity complicates automated classification as overlapping B-lines and pleural artefacts are common. We introduce ZACH-ViT (Zero-token Adaptive Compact Hierarchical Vision Transformer), a 0.25 M-parameter Vision Transformer variant that removes both positional embeddings and the [CLS] token, making it fully permutation-invariant and suitable for unordered medical image data. To enhance generalization, we propose ShuffleStrides Data Augmentation (SSDA), which permutes probe-view sequences and frame orders while preserving anatomical validity. ZACH-ViT was evaluated on 380 LUS videos from 95 critically ill patients against nine state-of-the-art baselines. Despite the heterogeneity of the non-cardiogenic group, ZACH-ViT achieved the highest validation and test ROC-AUC (0.80 and 0.79) with balanced sensitivity (0.60) and specificity (0.91), while all competing models collapsed to trivial classification. It trains 1.35x faster than Minimal ViT (0.62M parameters) with 2.5x fewer parameters, supporting real-time clinical deployment. These results show that aligning architectural design with data structure can outperform scale in small-data medical imaging.

cs.LG↗

arXiv2025

LLMs for Drug-Drug Interaction Prediction: A Comprehensive Comparison

The increasing volume of drug combinations in modern therapeutic regimens needs reliable methods for predicting drug-drug interactions (DDIs). While Large Language Models (LLMs) have revolutionized various domains, their potential in pharmaceutical research, particularly in DDI prediction, remains largely unexplored. This study thoroughly investigates LLMs' capabilities in predicting DDIs by uniquely processing molecular structures (SMILES), target organisms, and gene interaction data as raw text input from the latest DrugBank dataset. We evaluated 18 different LLMs, including proprietary models (GPT-4, Claude, Gemini) and open-source variants (from 1.5B to 72B parameters), first assessing their zero-shot capabilities in DDI prediction. We then fine-tuned selected models (GPT-4, Phi-3.5 2.7B, Qwen-2.5 3B, Gemma-2 9B, and Deepseek R1 distilled Qwen 1.5B) to optimize their performance. Our comprehensive evaluation framework included validation across 13 external DDI datasets, comparing against traditional approaches such as l2-regularized logistic regression. Fine-tuned LLMs demonstrated superior performance, with Phi-3.5 2.7B achieving a sensitivity of 0.978 in DDI prediction, with an accuracy of 0.919 on balanced datasets (50% positive, 50% negative cases). This result represents an improvement over both zero-shot predictions and state-of-the-art machine-learning methods used for DDI prediction. Our analysis reveals that LLMs can effectively capture complex molecular interaction patterns and cases where drug pairs target common genes, making them valuable tools for practical applications in pharmaceutical research and clinical settings.

cs.LG↗

arXiv2024

HELIOT: LLM-Based CDSS for Adverse Drug Reaction Management

Medication errors significantly threaten patient safety, leading to adverse drug events and substantial economic burdens on healthcare systems. Clinical Decision Support Systems (CDSSs) aimed at mitigating these errors often face limitations when processing unstructured clinical data, including reliance on static databases and rule-based algorithms, frequently generating excessive alerts that lead to alert fatigue among healthcare providers. This paper introduces HELIOT, an innovative CDSS for adverse drug reaction management that processes free-text clinical information using Large Language Models (LLMs) integrated with a comprehensive pharmaceutical data repository. HELIOT leverages advanced natural language processing capabilities to interpret medical narratives, extract relevant drug reaction information from unstructured clinical notes, and learn from past patient-specific medication tolerances to reduce false alerts, enabling more nuanced and contextual adverse drug event warnings across primary care, specialist consultations, and hospital settings. An initial evaluation using a synthetic dataset of clinical narratives and expert-verified ground truth shows promising results. HELIOT achieves high accuracy in a controlled setting. In addition, by intelligently analyzing previous medication tolerance documented in clinical notes and distinguishing between cases requiring different alert types, HELIOT can potentially reduce interruptive alerts by over 50% compared to traditional CDSSs. While these preliminary findings are encouraging, real-world validation will be essential to confirm these benefits in clinical practice.

cs.AI↗

arXiv2024

A data-centric approach to class-specific bias in image data augmentation

Data augmentation (DA) enhances model generalization in computer vision but may introduce biases, impacting class accuracy unevenly. Our study extends this inquiry, examining DA's class-specific bias across various datasets, including those distinct from ImageNet, through random cropping. We evaluated this phenomenon with ResNet50, EfficientNetV2S, and SWIN ViT, discovering that while residual models showed similar bias effects, Vision Transformers exhibited greater robustness or altered dynamics. This suggests a nuanced approach to model selection, emphasizing bias mitigation. We also refined a "data augmentation robustness scouting" method to manage DA-induced biases more efficiently, reducing computational demands significantly (training 112 models instead of 1860; a reduction of factor 16.2) while still capturing essential bias trends.

cs.CV↗

arXiv2017

Adelic point groups of elliptic curves

We show that for an elliptic curve E defined over a number field K, the group E(A) of points of E over the adele ring A of K is a topological group that can be analyzed in terms of the Galois representation associated to the torsion points of E. An explicit description of E(A) is given, and we prove that for K of degree n, almost all elliptic curves over K have an adelic point group topologically isomorphic to a universal group depending on n. We also show that there exist infinitely many elliptic curves over K having a different adelic point group.

math.NT↗

arXiv2013

Imaginary quadratic fields with isomorphic abelian Galois groups

In 1976, Onabe discovered that, in contrast to the Neukirch-Uchida results that were proved around the same time, a number field $K$ is not completely characterized by its absolute abelian Galois group $A_K$. The first examples of non-isomorphic $K$ having isomorphic $A_K$ were obtained on the basis of a classification by Kubota of idele class character groups in terms of their infinite families of Ulm invariants, and did not yield a description of $A_K$. In this paper, we provide a direct `computation' of the profinite group $A_K$ for imaginary quadratic $K$, and use it to obtain many different $K$ that all have the same minimal absolute abelian Galois group.

math.NT↗