In this thesis, we introduce Bayesian filtering as a principled framework for tackling diverse sequential machine learning problems, including online (continual) learning, pre-quential (one-step-ahead) forecasting, and contextual bandits. To this end, this thesis addresses key challenges in applying Bayesian filtering to these problems: adaptivity to non-stationary environments, robustness to model misspecification and outliers, and scalability to the high-dimensional parameter space of deep neural networks. We develop novel tools within the Bayesian filtering framework to address each of these challenges, including: (i) a modular framework that enables the development adaptive approaches for online learning; (ii) a novel, provably robust filter with similar computational cost to standard filters, that employs Generalised Bayes; and (iii) a set of tools for sequentially updating model parameters using approximate second-order optimisation methods that exploit the overparametrisation of high-dimensional parametric models such as neural networks. Theoretical analysis and empirical results demonstrate the improved performance of our methods in dynamic, high-dimensional, and misspecified models.

Causal machine learning (CML) enables individualized estimation of treatment effects, offering critical advantages over traditional correlation-based methods. However, existing approaches for medical survival data with censoring such as causal survival forests estimate effects at fixed time points, limiting their ability to capture dynamic changes over time. We introduce Causal Analysis for Survival Trajectories (CAST), a novel framework that models treatment effects as continuous functions of time following treatment. By combining parametric and non-parametric methods, CAST overcomes the limitations of discrete time-point analysis to estimate continuous effect trajectories. Using the RADCURE dataset [1] of 2,651 patients with head and neck squamous cell carcinoma (HNSCC) as a clinically relevant example, CAST models how chemotherapy and radiotherapy effects evolve over time at the population and individual levels. By capturing the temporal dynamics of treatment response, CAST reveals how treatment effects rise, peak, and decline over the follow-up period, helping clinicians determine when and for whom treatment benefits are maximized. This framework advances the application of CML to personalized care in HNSCC and other life-threatening medical conditions. Source code/data available at: https://github.com/CAST-FW/HNSCC

Many classification performance metrics exist, each suited to a specific application. However, these metrics often differ in scale and can exhibit varying sensitivity to class imbalance rates in the test set. As a result, it is difficult to use the nominal values of these metrics to interpret and evaluate classification performances, especially when imbalance rates vary. To address this problem, we introduce the outperformance score function, a universal standardization method for confusion-matrix-based classification performance (CMBCP) metrics. It maps any given metric to a common scale of $[0,1]$, while providing a clear and consistent interpretation. Specifically, the outperformance score represents the percentile rank of the observed classification performance within a reference distribution of possible performances. This unified framework enables meaningful comparison and monitoring of classification performance across test sets with differing imbalance rates. We illustrate how the outperformance scores can be applied to a variety of commonly used classification performance metrics and demonstrate the robustness of our method through experiments on real-world datasets spanning multiple classification applications.

Small nucleolar RNAs (snoRNAs) are increasingly recognized for their critical role in the pathogenesis and characterization of various human diseases. Consequently, the precise identification of snoRNA-disease associations (SDAs) is essential for the progression of diseases and the advancement of treatment strategies. However, conventional biological experimental approaches are costly, time-consuming, and resource-intensive; therefore, machine learning-based computational methods offer a promising solution to mitigate these limitations. This paper proposes a model called 'GBDTSVM', representing a novel and efficient machine learning approach for predicting snoRNA-disease associations by leveraging a Gradient Boosting Decision Tree (GBDT) and Support Vector Machine (SVM). 'GBDTSVM' effectively extracts integrated snoRNA-disease feature representations utilizing GBDT and SVM is subsequently utilized to classify and identify potential associations. Furthermore, the method enhances the accuracy of these predictions by incorporating Gaussian kernel profile similarity for both snoRNAs and diseases. Experimental evaluation of the GBDTSVM model demonstrated superior performance compared to state-of-the-art methods in the field, achieving an area under the receiver operating characteristic (AUROC) of 0.96 and an area under the precision-recall curve (AUPRC) of 0.95 on MDRF dataset. Moreover, our model shows superior performance on two more datasets named LSGT and PsnoD. Additionally, a case study on the predicted snoRNA-disease associations verified the top 10 predicted snoRNAs across nine prevalent diseases, further validating the efficacy of the GBDTSVM approach. These results underscore the model's potential as a robust tool for advancing snoRNA-related disease research. Source codes and datasets our proposed framework can be obtained from: https://github.com/mariamuna04/gbdtsvm

This paper presents a novel methodology for enhancing Automated Program Repair (APR) through synthetic data generation utilizing Large Language Models (LLMs). Current APR systems are constrained by the limited availability of high-quality training data encompassing diverse bug types across multiple programming languages. The proposed approach addresses this limitation through a two-phase process: a synthetic sample generation followed by a rigorous quality assessment. Multiple state-of-the-art LLMs were employed to generate approximately 30,000 paired examples of buggy and fixed code across 12 programming languages and 13 bug categories. Subsequently, these samples underwent cross-model evaluation against five criteria: correctness, code quality, security, performance, and completeness. Experimental evaluation on the VulRepair test set dataset showed statistically significant improvements in Perfect Prediction rates, with the quality-filtered synthetic dataset outperforming both baseline and real-world commit data configurations in certain scenarios. The methodology was validated through rigorous statistical testing, including ANOVA and post-hoc Tukey's Honest Significant Difference analysis. Furthermore, the best-performing configurations surpassed existing systems despite using a less computationally intensive decoding strategy. This research establishes a self-bootstrapping paradigm in which LLMs generate and evaluate their own training data, potentially transforming approaches to data scarcity across software engineering tasks and advancing the development of robust, adaptable tools for automated code maintenance.

We introduce MLE-Dojo, a Gym-style framework for systematically reinforcement learning, evaluating, and improving autonomous large language model (LLM) agents in iterative machine learning engineering (MLE) workflows. Unlike existing benchmarks that primarily rely on static datasets or single-attempt evaluations, MLE-Dojo provides an interactive environment enabling agents to iteratively experiment, debug, and refine solutions through structured feedback loops. Built upon 200+ real-world Kaggle challenges, MLE-Dojo covers diverse, open-ended MLE tasks carefully curated to reflect realistic engineering scenarios such as data processing, architecture search, hyperparameter tuning, and code debugging. Its fully executable environment supports comprehensive agent training via both supervised fine-tuning and reinforcement learning, facilitating iterative experimentation, realistic data sampling, and real-time outcome verification. Extensive evaluations of eight frontier LLMs reveal that while current models achieve meaningful iterative improvements, they still exhibit significant limitations in autonomously generating long-horizon solutions and efficiently resolving complex errors. Furthermore, MLE-Dojo's flexible and extensible architecture seamlessly integrates diverse data sources, tools, and evaluation protocols, uniquely enabling model-based agent tuning and promoting interoperability, scalability, and reproducibility. We open-source our framework and benchmarks to foster community-driven innovation towards next-generation MLE agents.

Federated Learning (FL) offers a promising framework for collaboratively training machine learning models across decentralized genomic datasets without direct data sharing. While this approach preserves data locality, it remains susceptible to sophisticated inference attacks that can compromise individual privacy. In this study, we simulate a federated learning setup using synthetic genomic data and assess its vulnerability to three key attack vectors: Membership Inference Attack (MIA), Gradient-Based Membership Inference Attack, and Label Inference Attack (LIA). Our experiments reveal that Gradient-Based MIA achieves the highest effectiveness, with a precision of 0.79 and F1-score of 0.87, underscoring the risk posed by gradient exposure in federated updates. Additionally, we visualize comparative attack performance through radar plots and quantify model leakage across clients. The findings emphasize the inadequacy of naïve FL setups in safeguarding genomic privacy and motivate the development of more robust privacy-preserving mechanisms tailored to the unique sensitivity of genomic data.

The increasing volume of healthcare textual data requires computationally efficient, yet highly accurate classification approaches able to handle the nuanced and complex nature of medical terminology. This research presents Knowledge Distillation for Healthcare Multi - Label Text Classification (KDH - MLTC), a framework leveraging model compr ession and Large Language Models (LLMs). The proposed approach addresses conventional healthcare Multi - Label Text Classification (MLTC) challenges by integrating knowledge distillation and sequential fine - tuning, subsequently optimized through Particle Swa rm Optimization (PSO) for hyperparameter tuning. KDH - MLTC transfers knowledge from a more complex teacher LLM ( i.e., BERT) to a lighter student LLM ( i.e., DistilBERT) through sequential training adapted to MLTC that preserves the teacher's learned information while significantly reducing computational requirements. As a result, the classification is enabled to be conducted locally, making it suitable for healthcare textual data characterized by sensitivity and, therefore, ensuring HIPAA compliance. The e xpe riments conducted on three medical literature datasets of different sizes, sampled from the Hallmark of Cancer (HoC) dataset, demonstrate that KDH - MLTC achieves superior performance compared to existing approaches, particularly for the largest dataset, reaching an F1 score of 82.70% 0.89%. Additionally, statistical validation and an ablation study ar e carried out, proving the robustness of KDH - MLTC. Furthermore, the PSO - based hyperparameter optimization process allow ed the identification of optimal configurations. The proposed approach contributes to healthcare text classification research, balancing efficiency requirements in resource - constrained healthcare settings with satisfactory accuracy demands.

Watermarking AI-generated text is critical for combating misuse. Yet recent theoretical work argues that any watermark can be erased via random walk attacks that perturb text while preserving quality. However, such attacks rely on two key assumptions: (1) rapid mixing (watermarks dissolve quickly under perturbations) and (2) reliable quality preservation (automated quality oracles perfectly guide edits). Through large-scale experiments and human-validated assessments, we find mixing is slow: 100% of perturbed texts retain traces of their origin after hundreds of edits, defying rapid mixing. Oracles falter, as state-of-the-art quality detectors misjudge edits (77% accuracy), compounding errors during attacks. Ultimately, attacks underperform: automated walks remove watermarks just 26% of the time -- dropping to 10% under human quality review. These findings challenge the inevitability of watermark removal. Instead, practical barriers -- slow mixing and imperfect quality control -- reveal watermarking to be far more robust than theoretical models suggest. The gap between idealized attacks and real-world feasibility underscores the need for stronger watermarking methods and more realistic attack models.

SIEM systems serve as a critical hub, employing rule-based logic to detect and respond to threats. Redundant or overlapping rules in SIEM systems lead to excessive false alerts, degrading analyst performance due to alert fatigue, and increase computational overhead and response latency for actual threats. As a result, optimizing SIEM rule sets is essential for efficient operations. Despite the importance of such optimization, research in this area is limited, with current practices relying on manual optimization methods that are both time-consuming and error-prone due to the scale and complexity of enterprise-level rule sets. To address this gap, we present RuleGenie, a novel large language model (LLM) aided recommender system designed to optimize SIEM rule sets. Our approach leverages transformer models' multi-head attention capabilities to generate SIEM rule embeddings, which are then analyzed using a similarity matching algorithm to identify the top-k most similar rules. The LLM then processes the rules identified, utilizing its information extraction, language understanding, and reasoning capabilities to analyze rule similarity, evaluate threat coverage and performance metrics, and deliver optimized recommendations for refining the rule set. By automating the rule optimization process, RuleGenie allows security teams to focus on more strategic tasks while enhancing the efficiency of SIEM systems and strengthening organizations' security posture. We evaluated RuleGenie on a comprehensive set of real-world SIEM rule formats, including Splunk, Sigma, and AQL (Ariel query language), demonstrating its platform-agnostic capabilities and adaptability across diverse security infrastructures. Our experimental results show that RuleGenie can effectively identify redundant rules, which in turn decreases false positive rates and enhances overall rule efficiency.