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Researcher profile

Oya Beyan

Oya Beyan contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine LearningArtificial IntelligenceComputer VisionDatabasesDistributed, Parallel, and Cluster Computingeess.IVQuantitative Methods

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Published work

4 published item(s)

preprint2026arXiv

Autonomous FAIR Digital Objects: From Passive Assertions to Active Knowledge

Scientific knowledge on the Web is published as passive assertions and cannot decide when to validate evidence, reconcile contradictions, or update confidence as findings accumulate. Curation depends on centralised middleware and institutional continuity, but when registries close, active stewardship stops even when data remain online. We advance the concept of Autonomous FAIR Digital Objects (aFDOs) from an abstract idea to an operational model, to offer a route from passive scientific publication toward accountable, standards-aligned automation that can outlive its publishing institutions. aFDO augments FDOs with three capabilities anchored in Semantic Web standards, namely 1) a policy layer over RDF-star aligned with PROV-O, SHACL, and ODRL for portable condition-action rules, 2) an announcement layer over ActivityStreams 2.0 that bounds per-announcement evaluation cost, and 3) an agreement layer that resolves multi-source contradictions through reputation and confidence weighted agreement under a bounded adversarial model. We provide a formal definition that distinguishes policy specifications, event handlers, and communication interfaces. We evaluate an open reference implementation on 4,305 FDOs grounded in rare-disease ontologies, namely ClinVar, HPO, and Orphanet, combined with controlled synthetic observations. The consensus mechanism resolves 56.3% of 3,914 naturally occurring ClinVar conflicts where multiple submitters disagree and an expert panel has subsequently adjudicated. Under Sybil, collusion, and poisoning attacks, the mechanism degrades gracefully within its design Byzantine-tolerance bound (f < n/5), and fails as predicted beyond that bound.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Towards General Deep Leakage in Federated Learning

Unlike traditional central training, federated learning (FL) improves the performance of the global model by sharing and aggregating local models rather than local data to protect the users&#39; privacy. Although this training approach appears secure, some research has demonstrated that an attacker can still recover private data based on the shared gradient information. This on-the-fly reconstruction attack deserves to be studied in depth because it can occur at any stage of training, whether at the beginning or at the end of model training; no relevant dataset is required and no additional models need to be trained. We break through some unrealistic assumptions and limitations to apply this reconstruction attack in a broader range of scenarios. We propose methods that can reconstruct the training data from shared gradients or weights, corresponding to the FedSGD and FedAvg usage scenarios, respectively. We propose a zero-shot approach to restore labels even if there are duplicate labels in the batch. We study the relationship between the label and image restoration. We find that image restoration fails even if there is only one incorrectly inferred label in the batch; we also find that when batch images have the same label, the corresponding image is restored as a fusion of that class of images. Our approaches are evaluated on classic image benchmarks, including CIFAR-10 and ImageNet. The batch size, image quality, and the adaptability of the label distribution of our approach exceed those of GradInversion, the state-of-the-art.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Convolutional Embedded Networks for Population Scale Clustering and Bio-ancestry Inferencing

The study of genetic variants can help find correlating population groups to identify cohorts that are predisposed to common diseases and explain differences in disease susceptibility and how patients react to drugs. Machine learning algorithms are increasingly being applied to identify interacting GVs to understand their complex phenotypic traits. Since the performance of a learning algorithm not only depends on the size and nature of the data but also on the quality of underlying representation, deep neural networks can learn non-linear mappings that allow transforming GVs data into more clustering and classification friendly representations than manual feature selection. In this paper, we proposed convolutional embedded networks in which we combine two DNN architectures called convolutional embedded clustering and convolutional autoencoder classifier for clustering individuals and predicting geographic ethnicity based on GVs, respectively. We employed CAE-based representation learning on 95 million GVs from the 1000 genomes and Simons genome diversity projects. Quantitative and qualitative analyses with a focus on accuracy and scalability show that our approach outperforms state-of-the-art approaches such as VariantSpark and ADMIXTURE. In particular, CEC can cluster targeted population groups in 22 hours with an adjusted rand index of 0.915, the normalized mutual information of 0.92, and the clustering accuracy of 89%. Contrarily, the CAE classifier can predict the geographic ethnicity of unknown samples with an F1 and Mathews correlation coefficient(MCC) score of 0.9004 and 0.8245, respectively. To provide interpretations of the predictions, we identify significant biomarkers using gradient boosted trees(GBT) and SHAP. Overall, our approach is transparent and faster than the baseline methods, and scalable for 5% to 100% of the full human genome.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

DeepCOVIDExplainer: Explainable COVID-19 Diagnosis Based on Chest X-ray Images

Amid the coronavirus disease(COVID-19) pandemic, humanity experiences a rapid increase in infection numbers across the world. Challenge hospitals are faced with, in the fight against the virus, is the effective screening of incoming patients. One methodology is the assessment of chest radiography(CXR) images, which usually requires expert radiologist&#39;s knowledge. In this paper, we propose an explainable deep neural networks(DNN)-based method for automatic detection of COVID-19 symptoms from CXR images, which we call DeepCOVIDExplainer. We used 15,959 CXR images of 15,854 patients, covering normal, pneumonia, and COVID-19 cases. CXR images are first comprehensively preprocessed, before being augmented and classified with a neural ensemble method, followed by highlighting class-discriminating regions using gradient-guided class activation maps(Grad-CAM++) and layer-wise relevance propagation(LRP). Further, we provide human-interpretable explanations of the predictions. Evaluation results based on hold-out data show that our approach can identify COVID-19 confidently with a positive predictive value(PPV) of 91.6%, 92.45%, and 96.12%; precision, recall, and F1 score of 94.6%, 94.3%, and 94.6%, respectively for normal, pneumonia, and COVID-19 cases, respectively, making it comparable or improved results over recent approaches. We hope that our findings will be a useful contribution to the fight against COVID-19 and, in more general, towards an increasing acceptance and adoption of AI-assisted applications in the clinical practice.

0 citations0 reviewsNo code linkedOpen access