Tree ensembles are widely recognized for their effectiveness in classification tasks, achieving state-of-the-art performance across diverse domains, including bioinformatics, finance, and medical diagnosis. With increasing emphasis on data privacy and the \textit{right to be forgotten}, several unlearning algorithms have been proposed to enable tree ensembles to forget sensitive information. However, existing methods are often tailored to a particular model or rely on the discrete tree structure, making them difficult to generalize to complex ensembles and inefficient for large-scale datasets. To address these limitations, we propose FUTURE, a novel unlearning algorithm for tree ensembles. Specifically, we formulate the problem of forgetting samples as a gradient-based optimization task. In order to accommodate non-differentiability of tree ensembles, we adopt the probabilistic model approximations within the optimization framework. This enables end-to-end unlearning in an effective and efficient manner. Extensive experiments on real-world datasets show that FUTURE yields significant and successful unlearning performance.

Human metapneumovirus (hMPV) poses serious risks to pediatric, elderly, and immunocompromised populations. Traditional antibody discovery pipelines require 10-12 months, limiting their applicability for rapid outbreak response. This project introduces ImmunoAI, a machine learning framework that accelerates antibody discovery by predicting high-affinity candidates using gradient-boosted models trained on thermodynamic, hydrodynamic, and 3D topological interface descriptors. A dataset of 213 antibody-antigen complexes was curated to extract geometric and physicochemical features, and a LightGBM regressor was trained to predict binding affinity with high precision. The model reduced the antibody candidate search space by 89%, and fine-tuning on 117 SARS-CoV-2 binding pairs further reduced Root Mean Square Error (RMSE) from 1.70 to 0.92. In the absence of an experimental structure for the hMPV A2.2 variant, AlphaFold2 was used to predict its 3D structure. The fine-tuned model identified two optimal antibodies with predicted picomolar affinities targeting key mutation sites (G42V and E96K), making them excellent candidates for experimental testing. In summary, ImmunoAI shortens design cycles and enables faster, structure-informed responses to viral outbreaks.

Model updates (new hyperparameters, kernels, depths, solvers, or data) change performance, but the \emph{reason} often remains opaque. We introduce \textbf{Delta-Attribution} (\mbox{$Δ$-Attribution}), a model-agnostic framework that explains \emph{what changed} between versions $A$ and $B$ by differencing per-feature attributions: $Δϕ(x)=ϕ_B(x)-ϕ_A(x)$. We evaluate $Δϕ$ with a \emph{$Δ$-Attribution Quality Suite} covering magnitude/sparsity (L1, Top-$k$, entropy), agreement/shift (rank-overlap@10, Jensen--Shannon divergence), behavioural alignment (Delta Conservation Error, DCE; Behaviour--Attribution Coupling, BAC; CO$Δ$F), and robustness (noise, baseline sensitivity, grouped occlusion). Instantiated via fast occlusion/clamping in standardized space with a class-anchored margin and baseline averaging, we audit 45 settings: five classical families (Logistic Regression, SVC, Random Forests, Gradient Boosting, $k$NN), three datasets (Breast Cancer, Wine, Digits), and three A/B pairs per family. \textbf{Findings.} Inductive-bias changes yield large, behaviour-aligned deltas (e.g., SVC poly$\!\rightarrow$rbf on Breast Cancer: BAC$\approx$0.998, DCE$\approx$6.6; Random Forest feature-rule swap on Digits: BAC$\approx$0.997, DCE$\approx$7.5), while ``cosmetic'' tweaks (SVC \texttt{gamma=scale} vs.\ \texttt{auto}, $k$NN search) show rank-overlap@10$=1.0$ and DCE$\approx$0. The largest redistribution appears for deeper GB on Breast Cancer (JSD$\approx$0.357). $Δ$-Attribution offers a lightweight update audit that complements accuracy by distinguishing benign changes from behaviourally meaningful or risky reliance shifts.

Log schema extraction is the process of deriving human-readable templates from massive volumes of log data, which is essential yet notoriously labor-intensive. Recent studies have attempted to streamline this task by leveraging Large Language Models (LLMs) for automated schema extraction. However, existing methods invariably rely on predefined regular expressions, necessitating human domain expertise and severely limiting productivity gains. To fundamentally address this limitation, we introduce SchemaCoder, the first fully automated schema extraction framework applicable to a wide range of log file formats without requiring human customization within the flow. At its core, SchemaCoder features a novel Residual Question-Tree (Q-Tree) Boosting mechanism that iteratively refines schema extraction through targeted, adaptive queries driven by LLMs. Particularly, our method partitions logs into semantic chunks via context-bounded segmentation, selects representative patterns using embedding-based sampling, and generates schema code through hierarchical Q-Tree-driven LLM queries, iteratively refined by our textual-residual evolutionary optimizer and residual boosting. Experimental validation demonstrates SchemaCoder's superiority on the widely-used LogHub-2.0 benchmark, achieving an average improvement of 21.3% over state-of-the-arts.

This thesis develops computational methods in similarity-preserving hashing, classification, and cancer genomics. Standard space partitioning-based hashing relies on Binary Search Trees (BSTs), but their exponential growth and sparsity hinder efficiency. To overcome this, we introduce Compressed BST of Inverted hash tables (ComBI), which enables fast approximate nearest-neighbor search with reduced memory. On datasets of up to one billion samples, ComBI achieves 0.90 precision with 4X-296X speed-ups over Multi-Index Hashing, and also outperforms Cellfishing.jl on single-cell RNA-seq searches with 2X-13X gains. Building on hashing structures, we propose Guided Random Forest (GRAF), a tree-based ensemble classifier that integrates global and local partitioning, bridging decision trees and boosting while reducing generalization error. Across 115 datasets, GRAF delivers competitive or superior accuracy, and its unsupervised variant (uGRAF) supports guided hashing and importance sampling. We show that GRAF and ComBI can be used to estimate per-sample classifiability, which enables scalable prediction of cancer patient survival. To address challenges in interpreting mutations, we introduce Continuous Representation of Codon Switches (CRCS), a deep learning framework that embeds genetic changes into numerical vectors. CRCS allows identification of somatic mutations without matched normals, discovery of driver genes, and scoring of tumor mutations, with survival prediction validated in bladder, liver, and brain cancers. Together, these methods provide efficient, scalable, and interpretable tools for large-scale data analysis and biomedical applications.

Time-series forecasting underpins critical decisions across aviation, energy, retail and health. Classical autoregressive integrated moving average (ARIMA) models offer interpretability via coefficients but struggle with nonlinearities, whereas tree-based machine-learning models such as XGBoost deliver high accuracy but are often opaque. This paper presents a unified framework for interpreting time-series forecasts using local interpretable model-agnostic explanations (LIME) and SHapley additive exPlanations (SHAP). We convert a univariate series into a leakage-free supervised learning problem, train a gradient-boosted tree alongside an ARIMA baseline and apply post-hoc explainability. Using the Air Passengers dataset as a case study, we show that a small set of lagged features -- particularly the twelve-month lag -- and seasonal encodings explain most forecast variance. We contribute: (i) a methodology for applying LIME and SHAP to time series without violating chronology; (ii) theoretical exposition of the underlying algorithms; (iii) empirical evaluation with extensive analysis; and (iv) guidelines for practitioners.

Variations in complex traits are influenced by multiple genetic variants, environmental risk factors, and their interactions. Though substantial progress has been made in identifying single genetic variants associated with complex traits, detecting the gene-gene and gene-environment interactions remains a great challenge. When a large number of genetic variants and environmental risk factors are involved, searching for interactions is limited to pair-wise interactions due to the exponentially increased feature space and computational intensity. Alternatively, recursive partitioning approaches, such as random forests, have gained popularity in high-dimensional genetic association studies. In this article, we propose a U-Statistic-based random forest approach, referred to as Forest U-Test, for genetic association studies with quantitative traits. Through simulation studies, we showed that the Forest U-Test outperformed existing methods. The proposed method was also applied to study Cannabis Dependence CD, using three independent datasets from the Study of Addiction: Genetics and Environment. A significant joint association was detected with an empirical p-value less than 0.001. The finding was also replicated in two independent datasets with p-values of 5.93e-19 and 4.70e-17, respectively.

Boosting is one of the most successful ideas in machine learning.

Approximate nearest neighbor (ANN) search is a fundamental algorithmic problem.