Z. Erkin
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60 records found
1
Contrastive Self-Supervised Learning for Utility-Privacy Trade-off Navigation in Graph Neural Networks
Node-Level Vulnerability Analysis and DP Utility Recovery
This thesis extends adversarial robustness analysis to multigraph GNNs through three contributions. First, it reformulates GNN message passing and attack optimisation over the incidence matrix instead of the adjacency matrix, yielding the first gradient-based structural attack that retains multi-edge structure. Second, it introduces unnoticeability loss terms that constrain perturbations to maintain the graph's statistical fingerprint, including the frequency of characteristic patterns such as short transaction cycles, keeping the attack statistically plausible and unnoticeable at the macro level. Third, it scales the framework to large networks with projected randomised block coordinate descent. On the IBM synthetic anti-money laundering dataset, learned attacks substantially reduce detection accuracy compared to non-learnable perturbations, and adversarial training recovers robustness, showing that multigraph GNNs are both vulnerable to structural manipulation and defensible against it. ...
This thesis extends adversarial robustness analysis to multigraph GNNs through three contributions. First, it reformulates GNN message passing and attack optimisation over the incidence matrix instead of the adjacency matrix, yielding the first gradient-based structural attack that retains multi-edge structure. Second, it introduces unnoticeability loss terms that constrain perturbations to maintain the graph's statistical fingerprint, including the frequency of characteristic patterns such as short transaction cycles, keeping the attack statistically plausible and unnoticeable at the macro level. Third, it scales the framework to large networks with projected randomised block coordinate descent. On the IBM synthetic anti-money laundering dataset, learned attacks substantially reduce detection accuracy compared to non-learnable perturbations, and adversarial training recovers robustness, showing that multigraph GNNs are both vulnerable to structural manipulation and defensible against it.
Before Agda Core can be used as a true self-verifier for Agda and be integrated into Agda’s main compiler and type checker, more features from Agda need to be supported by it. In this thesis, we focus on Agda’s η-conversion for function types and record types. We formalize η-conversion for function types and record types with at least one field using untyped conversion: we also add support for records to Agda Core along the way. We also show progress towards a formalization of Agda’s η-conversion using typed conversion, which allows for formalizing the often tricky-considered η-conversion for Agda’s unit type. For all of these formalizations, we show that they can be added to Agda Core with reasonable effort. Overall, this work therefore provides an important step towards the ultimate goal of a self-verified type checker for Agda with support for all of Agda’s features, which decreases the future potential for bugs in Agda’s implementation with relation to η-conversion, and teaches us how to self-verify η-conversion for a dependently-typed language. ...
Before Agda Core can be used as a true self-verifier for Agda and be integrated into Agda’s main compiler and type checker, more features from Agda need to be supported by it. In this thesis, we focus on Agda’s η-conversion for function types and record types. We formalize η-conversion for function types and record types with at least one field using untyped conversion: we also add support for records to Agda Core along the way. We also show progress towards a formalization of Agda’s η-conversion using typed conversion, which allows for formalizing the often tricky-considered η-conversion for Agda’s unit type. For all of these formalizations, we show that they can be added to Agda Core with reasonable effort. Overall, this work therefore provides an important step towards the ultimate goal of a self-verified type checker for Agda with support for all of Agda’s features, which decreases the future potential for bugs in Agda’s implementation with relation to η-conversion, and teaches us how to self-verify η-conversion for a dependently-typed language.
Plantard Multiplication for ML-KEM Hardware Acceleration
An FPGA Implementation and Area-Time Evaluation
Layer-Wise Exchange for Subgraph Federated Learning
An Application to Financial Crime Detection
We identify three failure modes that a single-model analysis would hide. First, the way an evaluation metric is measured or implemented can influence the metric as much as switching the model under test. Second, predictive accuracy should be interpreted separately from biologically correct reasoning. Third, an encoder’s prior can exert a stronger influence on the result than the model built on top of it. These findings suggest that explanations of microbiome models should be evaluated across multiple measurement methods, considered separately from accuracy, and interpreted with representation effects in mind. Otherwise, any single explanation may reflect substantial artefacts inherent to its implementation or measurement method. ...
We identify three failure modes that a single-model analysis would hide. First, the way an evaluation metric is measured or implemented can influence the metric as much as switching the model under test. Second, predictive accuracy should be interpreted separately from biologically correct reasoning. Third, an encoder’s prior can exert a stronger influence on the result than the model built on top of it. These findings suggest that explanations of microbiome models should be evaluated across multiple measurement methods, considered separately from accuracy, and interpreted with representation effects in mind. Otherwise, any single explanation may reflect substantial artefacts inherent to its implementation or measurement method.
This study compares an autoencoder, a variational autoencoder, a transformer-based autoencoder, and a pretrained MGM benchmark on the same genus-level gut microbiome dataset. Models are evaluated using held-out AUROC for disease-status prediction and silhouette scores for latent-space structure.
The results show that representation learning does not substantially improve prediction over directly using preprocessed abundance features. The transformer-based autoencoder achieves the highest AUROC, but only marginally outperforms the random forest baseline. The autoencoder performs similarly, while MGM with limited fine-tuning and especially the variational autoencoder perform worse. Silhouette scores are close to zero for control--disease separation and negative for disease-label and disease-category clustering, indicating weak biological structure in all embedding spaces.
Overall, this study shows that architectural complexity alone does not guarantee better microbiome representations. ...
This study compares an autoencoder, a variational autoencoder, a transformer-based autoencoder, and a pretrained MGM benchmark on the same genus-level gut microbiome dataset. Models are evaluated using held-out AUROC for disease-status prediction and silhouette scores for latent-space structure.
The results show that representation learning does not substantially improve prediction over directly using preprocessed abundance features. The transformer-based autoencoder achieves the highest AUROC, but only marginally outperforms the random forest baseline. The autoencoder performs similarly, while MGM with limited fine-tuning and especially the variational autoencoder perform worse. Silhouette scores are close to zero for control--disease separation and negative for disease-label and disease-category clustering, indicating weak biological structure in all embedding spaces.
Overall, this study shows that architectural complexity alone does not guarantee better microbiome representations.
Benchmarking Microbiome Classifiers Across Studies and Disease Contexts
A comparative evaluation of Random Forest, TabPFN, and MGM for cross-study and cross-context transfer
To address this, this study benchmarked crossstudy microbiome classification under four evaluation settings: study-to-study transfer, leave-onestudy-out transfer, disease-context transfer, and within-study prediction. Random Forest was compared with TabPFN and MGM, two foundationstyle models, under multiple feature-space alignment strategies, including union, intersection, and
prevalence-based filtering.
The results show that external validation is harder than within-study prediction (average ROC-AUC: 0.56–0.66 vs. 0.75). Random Forest consistently achieved the strongest performance on the external transfer tasks, generally outperforming both TabPFN and MGM. Feature-space alignment affected performance, but its impact was modest compared with the much larger effect of the evaluation setting itself.
Overall, this study provides a reproducible benchmark for microbiome generalization and shows that robust transfer across heterogeneous cohorts remains harder than achieving high performance within a single dataset. The benchmark offers a starting point for future work on stronger transferoriented models and more realistic evaluation protocols. ...
To address this, this study benchmarked crossstudy microbiome classification under four evaluation settings: study-to-study transfer, leave-onestudy-out transfer, disease-context transfer, and within-study prediction. Random Forest was compared with TabPFN and MGM, two foundationstyle models, under multiple feature-space alignment strategies, including union, intersection, and
prevalence-based filtering.
The results show that external validation is harder than within-study prediction (average ROC-AUC: 0.56–0.66 vs. 0.75). Random Forest consistently achieved the strongest performance on the external transfer tasks, generally outperforming both TabPFN and MGM. Feature-space alignment affected performance, but its impact was modest compared with the much larger effect of the evaluation setting itself.
Overall, this study provides a reproducible benchmark for microbiome generalization and shows that robust transfer across heterogeneous cohorts remains harder than achieving high performance within a single dataset. The benchmark offers a starting point for future work on stronger transferoriented models and more realistic evaluation protocols.
Benchmarking Compositional Preprocessing for Microbiome-Based IBD Classification
A Systematic Comparison of 15 Preprocessing Methods Across 8 Classifiers on the HMP2 Dataset
Preprocessing sensitivity was strongly classifier-dependent. Tree-based methods were robust over all variants, with standard deviations across preprocessing below 0.01 and no significant pairwise differences after Benjamini-Hochberg correction. Scale-sensitive classifiers showed substantial effects, with the MLP exhibiting a standard deviation of 0.052 across preprocessing variants and SVM-RBF showing 73 significant pairwise differences out of 105. Distribution shape emerged as the primary driver of scale-sensitive classifier performance. Rank and quantile normalization consistently matched or exceeded theoretically motivated log-ratio transforms, while raw count-based variants such as TSS and log-TSS were actively harmful for MLP. Feature importance rankings were highly stable across preprocessing choices for tree-based models (RF mean Spearman ρ = 0.986, XGBoost ρ = 0.948), with greater variability for linear models (Elastic Net ρ = 0.772, SVM-linearρ = 0.838). This indicates that preprocessing affects scale-sensitive classifiers not only in performance but also in which features are prioritised. These results suggest that tree-based models can be used with any preprocessing choice, while scale-sensitive classifiers require careful selection of a distribution-normalising transform. ...
Preprocessing sensitivity was strongly classifier-dependent. Tree-based methods were robust over all variants, with standard deviations across preprocessing below 0.01 and no significant pairwise differences after Benjamini-Hochberg correction. Scale-sensitive classifiers showed substantial effects, with the MLP exhibiting a standard deviation of 0.052 across preprocessing variants and SVM-RBF showing 73 significant pairwise differences out of 105. Distribution shape emerged as the primary driver of scale-sensitive classifier performance. Rank and quantile normalization consistently matched or exceeded theoretically motivated log-ratio transforms, while raw count-based variants such as TSS and log-TSS were actively harmful for MLP. Feature importance rankings were highly stable across preprocessing choices for tree-based models (RF mean Spearman ρ = 0.986, XGBoost ρ = 0.948), with greater variability for linear models (Elastic Net ρ = 0.772, SVM-linearρ = 0.838). This indicates that preprocessing affects scale-sensitive classifiers not only in performance but also in which features are prioritised. These results suggest that tree-based models can be used with any preprocessing choice, while scale-sensitive classifiers require careful selection of a distribution-normalising transform.
Offline Digital Euro
A Minimum Viable CBDC using Groth-Sahai proofs
digital euro. The protocol has a working initial implementation showcasing its usability and demonstrating functionality. ...
digital euro. The protocol has a working initial implementation showcasing its usability and demonstrating functionality.
Using EBAT, we conducted a large-scale analysis of over 36,000 firmware images publicly crawled from the Internet and successfully unpacked over 60% of them. The created dataset of firmware images includes more than 5,000 different products across 33 vendors, spanning more than 20 years and a plethora of various device types. Our findings show that ARM and MIPS are the most prevailed CPU architecture in the IoT/embedded industry. We compared identical binaries across all vendors, revealing a significant percentage of similar binaries used across different vendors' firmware images. Our analysis of firmware binaries reveals a notable absence of exploit mitigation techniques in IoT/embedded firmware images, and we present many firmware images containing private keys, posing potential security threats. Additionally, versions of open-source cryptographic libraries used in firmware images are identified, and the CVEs of the cryptographic libraries are evaluated. Two real-world case studies on hard-coded credentials demonstrate the significance of the large-scale attack presented in this thesis. Hashed passwords, predominantly using outdated algorithms, have also been discovered, and several have been cracked.
The main goal of EBAT is to identify cryptographic misuses in cross-architectural binaries. By applying static taint analysis (backward tracking) to well-defined APIs on specific functions and arguments for 10 open-source cryptographic libraries, we can identify potential violations of cryptographic rules. This analysis was executed on over 1.4 million binaries, revealing that approximately 50% of examined firmware images violated at least one cryptographic rule. Various case studies on real-world vulnerabilities in firmware images are presented, including recent CVEs that are found in various vendors' products. Executing EBAT on those vulnerable firmware images, we tested the effectiveness of our tool to evaluate the automatic capturing of these known vulnerabilities. In addition, performing large-scale analysis on an extensive corpus of firmware images allows us to discover that other firmware images are affected by these known vulnerabilities, in some cases also across various product lines not covered on the public CVEs reports.
In conclusion, EBAT is a valuable resource for researchers working on firmware security. Its automated analysis process, comprehensive modules, and ability to discover possible vulnerabilities, cryptographic misuses at a binary level, and other security weaknesses make it a powerful tool for identifying and mitigating security risks in IoT/embedded devices. ...
Using EBAT, we conducted a large-scale analysis of over 36,000 firmware images publicly crawled from the Internet and successfully unpacked over 60% of them. The created dataset of firmware images includes more than 5,000 different products across 33 vendors, spanning more than 20 years and a plethora of various device types. Our findings show that ARM and MIPS are the most prevailed CPU architecture in the IoT/embedded industry. We compared identical binaries across all vendors, revealing a significant percentage of similar binaries used across different vendors' firmware images. Our analysis of firmware binaries reveals a notable absence of exploit mitigation techniques in IoT/embedded firmware images, and we present many firmware images containing private keys, posing potential security threats. Additionally, versions of open-source cryptographic libraries used in firmware images are identified, and the CVEs of the cryptographic libraries are evaluated. Two real-world case studies on hard-coded credentials demonstrate the significance of the large-scale attack presented in this thesis. Hashed passwords, predominantly using outdated algorithms, have also been discovered, and several have been cracked.
The main goal of EBAT is to identify cryptographic misuses in cross-architectural binaries. By applying static taint analysis (backward tracking) to well-defined APIs on specific functions and arguments for 10 open-source cryptographic libraries, we can identify potential violations of cryptographic rules. This analysis was executed on over 1.4 million binaries, revealing that approximately 50% of examined firmware images violated at least one cryptographic rule. Various case studies on real-world vulnerabilities in firmware images are presented, including recent CVEs that are found in various vendors' products. Executing EBAT on those vulnerable firmware images, we tested the effectiveness of our tool to evaluate the automatic capturing of these known vulnerabilities. In addition, performing large-scale analysis on an extensive corpus of firmware images allows us to discover that other firmware images are affected by these known vulnerabilities, in some cases also across various product lines not covered on the public CVEs reports.
In conclusion, EBAT is a valuable resource for researchers working on firmware security. Its automated analysis process, comprehensive modules, and ability to discover possible vulnerabilities, cryptographic misuses at a binary level, and other security weaknesses make it a powerful tool for identifying and mitigating security risks in IoT/embedded devices.
Creating New Train Timetables in Case of Disruptions
Optimising a Branch & Bound Algorithm
Various alternative formulations of the heuristic value, used to determine the likeliness of a node leading to a good solution, showed promising results.
One of these formulas resulted in solutions for 96% more scenarios than before, and improved the quality of solutions for other scenarios.
Using machine learning, a decision tree was created to predict whether applying another new formula for the heuristic value gives better results than the old formula. This classifier achieved an accuracy of 73.5% on the test data. Having the solver choose between the old and new formula based on that classification resulted in some scenarios with worse scores, but twice as many improved, and the average improvement was higher than the average deterioration.
Recommendations are made to conduct further experiments related to the heuristic value calculation. Furthermore, it is suggested to separate the scores for evaluating solution quality from the heuristic value formula, to facilitate more fine-grained changes to the calculation of the heuristic value.
...
Various alternative formulations of the heuristic value, used to determine the likeliness of a node leading to a good solution, showed promising results.
One of these formulas resulted in solutions for 96% more scenarios than before, and improved the quality of solutions for other scenarios.
Using machine learning, a decision tree was created to predict whether applying another new formula for the heuristic value gives better results than the old formula. This classifier achieved an accuracy of 73.5% on the test data. Having the solver choose between the old and new formula based on that classification resulted in some scenarios with worse scores, but twice as many improved, and the average improvement was higher than the average deterioration.
Recommendations are made to conduct further experiments related to the heuristic value calculation. Furthermore, it is suggested to separate the scores for evaluating solution quality from the heuristic value formula, to facilitate more fine-grained changes to the calculation of the heuristic value.
This research aims to get insight into the robustness vulnerabilities of a method name prediction model. We use a genetic search algorithm that looks for these robustness problems. The main question this thesis tries to answer is to what extent the performance metrics are affected by applying metamorphic transformations to the test set of a trained code2vec model. Besides this, this thesis also proposes an alternative metric called percentage MRR, which might better reflect the robustness of a model. The main idea behind this metric is that it penalizes the prediction certainty of a model instead of penalizing the prediction rank.
To answer this research question, a tool is created that runs a genetic algorithm applying these metamorphic transformations to a dataset that a trained model is then evaluating. With this tool, we conducted 22 genetic search experiments on primary metrics and combinations of metrics to see the trade-offs in the Pareto fronts. The guided search of applying metamorphic transformations on the test set results in an average performance decrease of around 19%. This thesis also compares this drop in performance to the performance decrease a random search algorithm would create. Notably, for every transformer added, the average decrease in performance becomes smaller, and there are transformations, e.g., the if-false-else transformation, that have a bigger effect than others. This thesis concludes that the trained model is not robust against metamorphic transformations and has a significant performance drop. ...
This research aims to get insight into the robustness vulnerabilities of a method name prediction model. We use a genetic search algorithm that looks for these robustness problems. The main question this thesis tries to answer is to what extent the performance metrics are affected by applying metamorphic transformations to the test set of a trained code2vec model. Besides this, this thesis also proposes an alternative metric called percentage MRR, which might better reflect the robustness of a model. The main idea behind this metric is that it penalizes the prediction certainty of a model instead of penalizing the prediction rank.
To answer this research question, a tool is created that runs a genetic algorithm applying these metamorphic transformations to a dataset that a trained model is then evaluating. With this tool, we conducted 22 genetic search experiments on primary metrics and combinations of metrics to see the trade-offs in the Pareto fronts. The guided search of applying metamorphic transformations on the test set results in an average performance decrease of around 19%. This thesis also compares this drop in performance to the performance decrease a random search algorithm would create. Notably, for every transformer added, the average decrease in performance becomes smaller, and there are transformations, e.g., the if-false-else transformation, that have a bigger effect than others. This thesis concludes that the trained model is not robust against metamorphic transformations and has a significant performance drop.
Revisit Attacks on Searchable Symmetric Encryption
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