arXiv subjects

Ali Burak Ünal

Publications and source records attributed to Ali Burak Ünal.

18 recordsLinked to original sources

arXiv2026

FedCKA: Representation-Guided Layer Personalization for Federated 3D Perception Across Driving Domains

Robust perception in intelligent vehicles demands 3D object detectors that remain dependable under domain shifts, such as changes in time of day, location, or weather. However, due to costly annotation and rare shifts, some environments lack sufficient data to train a standalone detector. Federated learning offers a privacy-preserving framework for collaborative model training, enabling clients to benefit from shared learning across diverse environments. Yet, this framework traditionally relies on a single global consensus model, which struggles to perform across heterogeneous local data distributions. Local conditions are better captured by adapting a subset of the model, but many personalization approaches rely on predefined layer partitions or fixed personalization ratios, thereby limiting adaptation to client-specific divergence. To reduce this rigidity, we propose FedCKA, a Centered Kernel Alignment (CKA)-based strategy that dynamically handles the personalization-globalization trade-off. Specifically, FedCKA computes layer-wise feature similarities between local client models and the global consensus model during training. By converting layer-wise similarity scores into client-specific aggregation masks, FedCKA selectively shares representation-consistent layers. Evaluation on a unified multi-domain benchmark based on nuScenes shows that FedCKA outperforms established federated baselines, including FedBN, FedRep, and FedSelect, improving average NDS by 7 percentage points over the strongest baseline. The findings offer both a comparative benchmark and a promising direction for robust federated 3D perception across shifts in location, weather, and illumination. Code is available at https://github.com/j-verhoog/FedCKA.

cs.CV↗

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

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↗

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

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↗

arXiv2021

Privacy Preserving Gaze Estimation using Synthetic Images via a Randomized Encoding Based Framework

Eye tracking is handled as one of the key technologies for applications that assess and evaluate human attention, behavior, and biometrics, especially using gaze, pupillary, and blink behaviors. One of the challenges with regard to the social acceptance of eye tracking technology is however the preserving of sensitive and personal information. To tackle this challenge, we employ a privacy-preserving framework based on randomized encoding to train a Support Vector Regression model using synthetic eye images privately to estimate the human gaze. During the computation, none of the parties learn about the data or the result that any other party has. Furthermore, the party that trains the model cannot reconstruct pupil, blinks or visual scanpath. The experimental results show that our privacy-preserving framework is capable of working in real-time, with the same accuracy as compared to non-private version and could be extended to other eye tracking related problems.

cs.CV↗

arXiv2020

ESCAPED: Efficient Secure and Private Dot Product Framework for Kernel-based Machine Learning Algorithms with Applications in Healthcare

To train sophisticated machine learning models one usually needs many training samples. Especially in healthcare settings these samples can be very expensive, meaning that one institution alone usually does not have enough on its own. Merging privacy-sensitive data from different sources is usually restricted by data security and data protection measures. This can lead to approaches that reduce data quality by putting noise onto the variables (e.g., in $ε$-differential privacy) or omitting certain values (e.g., for $k$-anonymity). Other measures based on cryptographic methods can lead to very time-consuming computations, which is especially problematic for larger multi-omics data. We address this problem by introducing ESCAPED, which stands for Efficient SeCure And PrivatE Dot product framework, enabling the computation of the dot product of vectors from multiple sources on a third-party, which later trains kernel-based machine learning algorithms, while neither sacrificing privacy nor adding noise. We evaluated our framework on drug resistance prediction for HIV-infected people and multi-omics dimensionality reduction and clustering problems in precision medicine. In terms of execution time, our framework significantly outperforms the best-fitting existing approaches without sacrificing the performance of the algorithm. Even though we only show the benefit for kernel-based algorithms, our framework can open up new research opportunities for further machine learning models that require the dot product of vectors from multiple sources.

cs.LG↗

arXiv2016

Identification of Cancer Patient Subgroups via Smoothed Shortest Path Graph Kernel

Characterizing patient somatic mutations through next-generation sequencing technologies opens up possibilities for refining cancer subtypes. However, catalogues of mutations reveal that only a small fraction of the genes are altered frequently in patients. On the other hand different genomic alterations may perturb the same pathways. We propose a novel clustering procedure that quantifies the similarities of patients from their mutational profile on pathways via a novel graph kernel. We represent each KEGG pathway as an undirected graph. For each patient the vertex labels are assigned based on her altered genes. Smoothed shortest path graph kernel (smSPK) evaluates each pair of patients by comparing their vertex labeled pathway graphs. Our clustering procedure involves two steps: the smSPK kernel matrix derived for each pathway are input to kernel k-means algorithm and each pathway is evaluated individually. In the next step, only those pathways that are successful are combined in to a single kernel input to kernel k-means to stratify patients. Evaluating the procedure on simulated data showed that smSPK clusters patients up to 88\% accuracy. Finally to identify ovarian cancer patient subgroups, we apply our methodology to the cancer genome atlas ovarian data that involves 481 patients. The identified subgroups are evaluated through survival analysis. Grouping patients into four clusters results with patients groups that are significantly different in their survival times ($p$-value $\le 0.005$).

cs.CE↗