arXiv subjects

Mete Akgün

Publications and source records attributed to Mete Akgün.

At least 19 recordsLinked to original sources

arXiv2026

Privacy-Preserving Detection of Rare Disease-Associated Cell Subsets via Secure Multi-Party Computation

The detection of rare disease-associated cell subsets from high-dimensional single-cell measurements is critical for understanding diseases such as leukaemia and viral infections. CellCnn, a convolutional neural network (CNN) designed for this task, has demonstrated the ability to identify phenotype-associated cell populations at frequencies as low as 0.01\%. Training such models reliably requires patient cohorts that are larger and more diverse than any single institution can typically assemble, and the underlying single-cell data is too sensitive to share across institutional boundaries under existing privacy regulations. We propose a secure multi-party computation (MPC) framework that enables the training and inference of CellCnn entirely on secret-shared data. This ensures that neither the participants nor the computing servers ever observe raw patient data or intermediate values. Evaluated on benchmark single-cell datasets for cytomegalovirus infection (CMV) and acute myeloid leukaemia (AML), our implementation preserves accuracy close to its plaintext counterpart while outperforming the prior privacy-preserving baseline. In contrast to earlier privacy-preserving approaches that removed components such as ReLU activations and bias terms, our method retains these key parts of the CellCnn architecture and supports accurate analysis without exposing raw patient data.

cs.CR↗

arXiv2026

Empirical Evidence for Simply Connected Decision Regions in Image Classifiers

Understanding the topology of decision regions is central to explaining the inner workings of deep neural networks. Prior empirical work has provided evidence that these regions are path connected. We study a stronger topological question: whether closed loops inside a decision region can be contracted without leaving that region. To this end, we propose an iterative quad-mesh filling procedure that constructs a finite-resolution label-preserving surface bounded by a given loop and lying entirely within the same decision region. We further connect this construction to natural Coons patches in order to quantify its deviation from a canonical geometric interpolation of the loop. By evaluating our method across several modern image-classification models, we provide empirical evidence supporting the hypothesis that decision regions in deep neural networks are not only path connected, but also simply connected.

cs.CV↗

arXiv2026

Scaling Unsupervised Multi-Source Federated Domain Adaptation through Group-Wise Discrepancy Minimization

Unsupervised multi-source domain adaptation (UMDA) leverages labeled data from multiple source domains to generalize to an unlabeled target. While federated UMDA addresses privacy by avoiding raw data sharing, existing methods scale poorly as the number of sources increases, often suffering from high computational overhead or training instability. We propose GALA, a scalable and robust federated UMDA framework designed for high-diversity settings. GALA achieves scalability by coupling a novel inter-group discrepancy minimization objective that approximates pairwise alignment with linear complexity alongside a temperature-controlled, centroid-based weighting strategy for dynamic source prioritization. These components enable stable, parallelizable training across many heterogeneous sources, addressing a critical scalability bottleneck that remains largely unaddressed in current literature. To evaluate performance in high-diversity scenarios, we introduce Digit-18, a new benchmark comprising 18 datasets with varied synthetic and real-world domain shifts. Extensive experiments demonstrate that GALA achieves state-of-the-art results on standard benchmarks and significantly outperforms prior methods in large-scale settings where others either fail to converge or become computationally infeasible.

cs.LG↗

arXiv2026

Accelerating Targeted Hard-Label Adversarial Attacks in Low-Query Black-Box Settings

Deep neural networks for image classification remain vulnerable to adversarial examples -- small, imperceptible perturbations that induce misclassifications. In black-box settings, where only the final prediction is accessible, crafting targeted attacks that aim to misclassify into a specific target class is particularly challenging due to narrow decision regions. Current state-of-the-art methods often exploit the geometric properties of the decision boundary separating a source image and a target image rather than incorporating information from the images themselves. In contrast, we propose Targeted Edge-informed Attack (TEA), a novel attack that utilizes edge information from the target image to carefully perturb it, thereby producing an adversarial image that is closer to the source image while still achieving the desired target classification. Our approach consistently outperforms current state-of-the-art methods across different models in low query settings (nearly 70% fewer queries are used), a scenario especially relevant in real-world applications with limited queries and black-box access. Furthermore, by efficiently generating a suitable adversarial example, TEA provides an improved target initialization for established geometry-based attacks.

cs.CV↗

arXiv2025

PP-GWAS: Privacy Preserving Multi-Site Genome-wide Association Studies

Genome-wide association studies are pivotal in understanding the genetic underpinnings of complex traits and diseases. Collaborative, multi-site GWAS aim to enhance statistical power but face obstacles due to the sensitive nature of genomic data sharing. Current state-of-the-art methods provide a privacy-focused approach utilizing computationally expensive methods such as Secure Multi-Party Computation and Homomorphic Encryption. In this context, we present a novel algorithm PP-GWAS designed to improve upon existing standards in terms of computational efficiency and scalability without sacrificing data privacy. This algorithm employs randomized encoding within a distributed architecture to perform stacked ridge regression on a Linear Mixed Model to ensure rigorous analysis. Experimental evaluation with real world and synthetic data indicates that PP-GWAS can achieve computational speeds twice as fast as similar state-of-the-art algorithms while using lesser computational resources, all while adhering to a robust security model that caters to an all-but-one semi-honest adversary setting. We have assessed its performance using various datasets, emphasizing its potential in facilitating more efficient and private genomic analyses.

cs.CR↗

arXiv2025

Accurate and Private Diagnosis of Rare Genetic Syndromes from Facial Images with Federated Deep Learning

Machine learning has shown promise in facial dysmorphology, where characteristic facial features provide diagnostic clues for rare genetic disorders. GestaltMatcher, a leading framework in this field, has demonstrated clinical utility across multiple studies, but its reliance on centralized datasets limits further development, as patient data are siloed across institutions and subject to strict privacy regulations. We introduce a federated GestaltMatcher service based on a cross-silo horizontal federated learning framework, which allows hospitals to collaboratively train a global ensemble feature extractor without sharing patient images. Patient data are mapped into a shared latent space, and a privacy-preserving kernel matrix computation framework enables syndrome inference and discovery while safeguarding confidentiality. New participants can directly benefit from and contribute to the system by adopting the global feature extractor and kernel configuration from previous training rounds. Experiments show that the federated service retains over 90% of centralized performance and remains robust to both varying silo numbers and heterogeneous data distributions.

cs.LG↗

arXiv2025

Enabling Privacy-preserving Model Evaluation in Federated Learning via Fully Homomorphic Encryption

Federated learning has become increasingly widespread due to its ability to train models collaboratively without centralizing sensitive data. While most research on FL emphasizes privacy-preserving techniques during training, the evaluation phase also presents significant privacy risks that have not been adequately addressed in the literature. In particular, the state-of-the-art solution for computing the area under the curve (AUC) in FL systems employs differential privacy, which not only fails to protect against a malicious aggregator but also suffers from severe performance degradation on smaller datasets. To overcome these limitations, we propose a novel evaluation method that leverages fully homomorphic encryption. To the best of our knowledge, this is the first work to apply FHE to privacy-preserving model evaluation in federated learning while providing verifiable security guarantees. In our approach, clients encrypt their true-positive and false-positive counts based on predefined thresholds and submit them to an aggregator, which then performs homomorphic operations to compute the global AUC without ever seeing intermediate or final results in plaintext. We offer two variants of our protocol: one secure against a semi-honest aggregator and one that additionally detects and prevents manipulations by a malicious aggregator. Besides providing verifiable security guarantees, our solution achieves superior accuracy across datasets of any size and distribution, eliminating the performance issues faced by the existing state-of-the-art method on small datasets and its runtime is negligibly small and independent of the test-set size. Experimental results confirm that our method can compute the AUC among 100 parties in under two seconds with near-perfect (99.93%) accuracy while preserving complete data privacy.

cs.CR↗

arXiv2025

Federated Learning for Epileptic Seizure Prediction Across Heterogeneous EEG Datasets

Developing accurate and generalizable epileptic seizure prediction models from electroencephalography (EEG) data across multiple clinical sites is hindered by patient privacy regulations and significant data heterogeneity (non-IID characteristics). Federated Learning (FL) offers a privacy-preserving framework for collaborative training, but standard aggregation methods like Federated Averaging (FedAvg) can be biased by dominant datasets in heterogeneous settings. This paper investigates FL for seizure prediction using a single EEG channel across four diverse public datasets (Siena, CHB-MIT, Helsinki, NCH), representing distinct patient populations (adult, pediatric, neonate) and recording conditions. We implement privacy-preserving global normalization and propose a Random Subset Aggregation strategy, where each client trains on a fixed-size random subset of its data per round, ensuring equal contribution during aggregation. Our results show that locally trained models fail to generalize across sites, and standard weighted FedAvg yields highly skewed performance (e.g., 89.0% accuracy on CHB-MIT but only 50.8% on Helsinki and 50.6% on NCH). In contrast, Random Subset Aggregation significantly improves performance on under-represented clients (accuracy increases to 81.7% on Helsinki and 68.7% on NCH) and achieves a superior macro-average accuracy of 77.1% and pooled accuracy of 80.0% across all sites, demonstrating a more robust and fair global model. This work highlights the potential of balanced FL approaches for building effective and generalizable seizure prediction systems in realistic, heterogeneous multi-hospital environments while respecting data privacy.

cs.LG↗

arXiv2025

Distributed and Secure Kernel-Based Quantum Machine Learning

Quantum computing promises to revolutionize machine learning, offering significant efficiency gains in tasks such as clustering and distance estimation. Additionally, it provides enhanced security through fundamental principles like the measurement postulate and the no-cloning theorem, enabling secure protocols such as quantum teleportation and quantum key distribution. While advancements in secure quantum machine learning are notable, the development of secure and distributed quantum analogues of kernel-based machine learning techniques remains underexplored. In this work, we present a novel approach for securely computing common kernels, including polynomial, radial basis function (RBF), and Laplacian kernels, when data is distributed, using quantum feature maps. Our methodology introduces a robust framework that leverages quantum teleportation to ensure secure and distributed kernel learning. The proposed architecture is validated using IBM's Qiskit Aer Simulator on various public datasets.

quant-ph↗

arXiv2025

Privacy-Preserving Federated Unsupervised Domain Adaptation for Regression on Small-Scale and High-Dimensional Biological Data

Machine learning models often struggle with generalization in small, heterogeneous datasets due to domain shifts caused by variations in data collection and population differences. This challenge is particularly pronounced in biological data, where data is high-dimensional, small-scale, and decentralized across institutions. While federated domain adaptation methods (FDA) aim to address these challenges, most existing approaches rely on deep learning and focus on classification tasks, making them unsuitable for small-scale, high-dimensional applications. In this work, we propose freda, a privacy-preserving federated method for unsupervised domain adaptation in regression tasks. Unlike deep learning-based FDA approaches, freda is the first method to enable the federated training of Gaussian Processes to model complex feature relationships while ensuring complete data privacy through randomized encoding and secure aggregation. This allows for effective domain adaptation without direct access to raw data, making it well-suited for applications involving high-dimensional, heterogeneous datasets. We evaluate freda on the challenging task of age prediction from DNA methylation data, demonstrating that it achieves performance comparable to the centralized state-of-the-art method while preserving complete data privacy.

cs.LG↗

arXiv2024

Accelerating Privacy-Preserving Medical Record Linkage: A Three-Party MPC Approach

Record linkage is a crucial concept for integrating data from multiple sources, particularly when datasets lack exact identifiers, and it has diverse applications in real-world data analysis. Privacy-Preserving Record Linkage (PPRL) ensures this integration occurs securely, protecting sensitive information from unauthorized access. This is especially important in sectors such as healthcare, where datasets include private identity information (IDAT) governed by strict privacy laws. However, maintaining both privacy and efficiency in large-scale record linkage poses significant challenges. Consequently, researchers must develop advanced methods to protect data privacy while optimizing processing performance. This paper presents a novel and efficient PPRL method based on a secure 3-party computation (MPC) framework. Our approach allows multiple parties to compute linkage results without exposing their private inputs and significantly improves the speed of linkage process compared to existing privacy-preserving solutions. We demonstrated that our method preserves the linkage quality of the state-of-the-art PPRL method while achieving up to 14 times faster performance. For example, linking a record against a database of 10,000 records takes just 8.74 seconds in a realistic network with 700 Mbps bandwidth and 60 ms latency. Even on a slower internet connection with 100 Mbps bandwidth and 60 ms latency, the linkage completes in 28 seconds, highlighting the scalability and efficiency of our solution.

cs.CR↗

arXiv2024

Private, Efficient and Scalable Kernel Learning for Medical Image Analysis

Medical imaging is key in modern medicine. From magnetic resonance imaging (MRI) to microscopic imaging for blood cell detection, diagnostic medical imaging reveals vital insights into patient health. To predict diseases or provide individualized therapies, machine learning techniques like kernel methods have been widely used. Nevertheless, there are multiple challenges for implementing kernel methods. Medical image data often originates from various hospitals and cannot be combined due to privacy concerns, and the high dimensionality of image data presents another significant obstacle. While randomised encoding offers a promising direction, existing methods often struggle with a trade-off between accuracy and efficiency. Addressing the need for efficient privacy-preserving methods on distributed image data, we introduce OKRA (Orthonormal K-fRAmes), a novel randomized encoding-based approach for kernel-based machine learning. This technique, tailored for widely used kernel functions, significantly enhances scalability and speed compared to current state-of-the-art solutions. Through experiments conducted on various clinical image datasets, we evaluated model quality, computational performance, and resource overhead. Additionally, our method outperforms comparable approaches

cs.CR↗

arXiv2024

CECILIA: Comprehensive Secure Machine Learning Framework

Since ML algorithms have proven their success in many different applications, there is also a big interest in privacy preserving (PP) ML methods for building models on sensitive data. Moreover, the increase in the number of data sources and the high computational power required by those algorithms force individuals to outsource the training and/or the inference of a ML model to the clouds providing such services. To address this, we propose a secure 3-party computation framework, CECILIA, offering PP building blocks to enable complex operations privately. In addition to the adapted and common operations like addition and multiplication, it offers multiplexer, most significant bit and modulus conversion. The first two are novel in terms of methodology and the last one is novel in terms of both functionality and methodology. CECILIA also has two complex novel methods, which are the exact exponential of a public base raised to the power of a secret value and the inverse square root of a secret Gram matrix. We use CECILIA to realize the private inference on pre-trained RKNs, which require more complex operations than most other DNNs, on the structural classification of proteins as the first study ever accomplishing the PP inference on RKNs. In addition to the successful private computation of basic building blocks, the results demonstrate that we perform the exact and fully private exponential computation, which is done by approximation in the literature so far. Moreover, they also show that we compute the exact inverse square root of a secret Gram matrix up to a certain privacy level, which has not been addressed in the literature at all. We also analyze the scalability of CECILIA to various settings on a synthetic dataset. The framework shows a great promise to make other ML algorithms as well as further computations privately computable by the building blocks of the framework.

cs.LG↗

arXiv2024

Privacy Preserving Data Imputation via Multi-party Computation for Medical Applications

Handling missing data is crucial in machine learning, but many datasets contain gaps due to errors or non-response. Unlike traditional methods such as listwise deletion, which are simple but inadequate, the literature offers more sophisticated and effective methods, thereby improving sample size and accuracy. However, these methods require accessing the whole dataset, which contradicts the privacy regulations when the data is distributed among multiple sources. Especially in the medical and healthcare domain, such access reveals sensitive information about patients. This study addresses privacy-preserving imputation methods for sensitive data using secure multi-party computation, enabling secure computations without revealing any party's sensitive information. In this study, we realized the mean, median, regression, and kNN imputation methods in a privacy-preserving way. We specifically target the medical and healthcare domains considering the significance of protection of the patient data, showcasing our methods on a diabetes dataset. Experiments on the diabetes dataset validated the correctness of our privacy-preserving imputation methods, yielding the largest error around $3 \times 10^{-3}$, closely matching plaintext methods. We also analyzed the scalability of our methods to varying numbers of samples, showing their applicability to real-world healthcare problems. Our analysis demonstrated that all our methods scale linearly with the number of samples. Except for kNN, the runtime of all our methods indicates that they can be utilized for large datasets.

cs.CR↗

arXiv2023

Robust Representation Learning for Privacy-Preserving Machine Learning: A Multi-Objective Autoencoder Approach

Several domains increasingly rely on machine learning in their applications. The resulting heavy dependence on data has led to the emergence of various laws and regulations around data ethics and privacy and growing awareness of the need for privacy-preserving machine learning (ppML). Current ppML techniques utilize methods that are either purely based on cryptography, such as homomorphic encryption, or that introduce noise into the input, such as differential privacy. The main criticism given to those techniques is the fact that they either are too slow or they trade off a model s performance for improved confidentiality. To address this performance reduction, we aim to leverage robust representation learning as a way of encoding our data while optimizing the privacy-utility trade-off. Our method centers on training autoencoders in a multi-objective manner and then concatenating the latent and learned features from the encoding part as the encoded form of our data. Such a deep learning-powered encoding can then safely be sent to a third party for intensive training and hyperparameter tuning. With our proposed framework, we can share our data and use third party tools without being under the threat of revealing its original form. We empirically validate our results on unimodal and multimodal settings, the latter following a vertical splitting system and show improved performance over state-of-the-art.

cs.LG↗

arXiv2023

ppAURORA: Privacy Preserving Area Under Receiver Operating Characteristic and Precision-Recall Curves

Computing an AUC as a performance measure to compare the quality of different machine learning models is one of the final steps of many research projects. Many of these methods are trained on privacy-sensitive data and there are several different approaches like $ε$-differential privacy, federated machine learning and cryptography if the datasets cannot be shared or used jointly at one place for training and/or testing. In this setting, it can also be a problem to compute the global AUC, since the labels might also contain privacy-sensitive information. There have been approaches based on $ε$-differential privacy to address this problem, but to the best of our knowledge, no exact privacy preserving solution has been introduced. In this paper, we propose an MPC-based solution, called ppAURORA, with private merging of individually sorted lists from multiple sources to compute the exact AUC as one could obtain on the pooled original test samples. With ppAURORA, the computation of the exact area under precision-recall and receiver operating characteristic curves is possible even when ties between prediction confidence values exist. We use ppAURORA to evaluate two different models predicting acute myeloid leukemia therapy response and heart disease, respectively. We also assess its scalability via synthetic data experiments. All these experiments show that we efficiently and privately compute the exact same AUC with both evaluation metrics as one can obtain on the pooled test samples in plaintext according to the semi-honest adversary setting.

cs.LG↗

arXiv2023

A Privacy-Preserving Federated Learning Approach for Kernel methods

It is challenging to implement Kernel methods, if the data sources are distributed and cannot be joined at a trusted third party for privacy reasons. It is even more challenging, if the use case rules out privacy-preserving approaches that introduce noise. An example for such a use case is machine learning on clinical data. To realize exact privacy preserving computation of kernel methods, we propose FLAKE, a Federated Learning Approach for KErnel methods on horizontally distributed data. With FLAKE, the data sources mask their data so that a centralized instance can compute a Gram matrix without compromising privacy. The Gram matrix allows to calculate many kernel matrices, which can be used to train kernel-based machine learning algorithms such as Support Vector Machines. We prove that FLAKE prevents an adversary from learning the input data or the number of input features under a semi-honest threat model. Experiments on clinical and synthetic data confirm that FLAKE is outperforming the accuracy and efficiency of comparable methods. The time needed to mask the data and to compute the Gram matrix is several orders of magnitude less than the time a Support Vector Machine needs to be trained. Thus, FLAKE can be applied to many use cases.

cs.LG↗

arXiv2022

Bringing the Algorithms to the Data -- Secure Distributed Medical Analytics using the Personal Health Train (PHT-meDIC)

The need for data privacy and security -- enforced through increasingly strict data protection regulations -- renders the use of healthcare data for machine learning difficult. In particular, the transfer of data between different hospitals is often not permissible and thus cross-site pooling of data not an option. The Personal Health Train (PHT) paradigm proposed within the GO-FAIR initiative implements an 'algorithm to the data' paradigm that ensures that distributed data can be accessed for analysis without transferring any sensitive data. We present PHT-meDIC, a productively deployed open-source implementation of the PHT concept. Containerization allows us to easily deploy even complex data analysis pipelines (e.g, genomics, image analysis) across multiple sites in a secure and scalable manner. We discuss the underlying technological concepts, security models, and governance processes. The implementation has been successfully applied to distributed analyses of large-scale data, including applications of deep neural networks to medical image data.

cs.LG↗