Modern machine learning systems have outgrown their origins as isolated predictive constructs, evolving into complex socio-technical architectures that actively mediate human opportunity. As algorithms increasingly determine access to economic and social opportunities, it has become widely recognized that these systems are deeply embedded with the structural inequalities and prejudices of their environments. The field of algorithmic fairness emerged in response to the growing recognition that models optimized for predictive accuracy can systematically disadvantage marginalized groups. Early mitigation strategies, however, rested on fragile simplifications that limited their effectiveness in complex sociotechnical environments. This thesis identifies and addresses two fundamental limitations of contemporary fairness paradigms: the reliance on deterministic point estimates for auditing and the treatment of individuals as isolated entities devoid of structural context. First, the diagnosis of algorithmic unfairness has traditionally depended on scalar metrics that fail to capture the nuances of real-world deployment. This deterministic approach ignores the high statistical variance inherent in small, intersectional groups, often leading to false alarms or missed detections of bias. Furthermore, standard auditing struggles with the opacity of black-box models, frequently conflating unjustifiable bias with the influence of legitimate features.

Uncertainty estimates in machine learning are typically evaluated using generic metrics such as the negative log-likelihood and expected calibration error, yet good performance on such metrics does not necessarily imply high utility in downstream decisions. We introduce decision-alignment, a criterion that reveals which evaluation metrics meaningfully align with downstream utilities. Applying this framework, we show that many widely used uncertainty metrics are either misaligned with common decision problems or encode pathological prior beliefs about the downstream task. We then propose prior-weighted utility metrics, a special class of proper scoring rules that provides decision-aligned uncertainty evaluation. Across benchmark experiments and real-world case studies, our metrics consistently align with realized decision utility, while conventional metrics do not. Our results surface flaws in the current UQ evaluation protocol and offer a principled extension of existing metrics toward decision-relevant UQ evaluation.

Synthetic data augmentation is widely used to mitigate class imbalance, but its theoretical effects on score-based classification remain poorly understood. This paper develops a framework for characterizing when synthetic minority augmentation can improve threshold-integrated and threshold-optimized metrics, including AUROC, AUPRC, best-threshold balanced accuracy, and best-threshold \(\F_1\) score. We separate the effect of augmentation into two components: a change in effective class weighting and a discrepancy between the synthetic and true minority distributions. Under well-specified score models, the raw estimator already targets the likelihood-ratio ordering, which is population-optimal for the metrics considered. Consequently, augmentation cannot provide a fundamental population-level improvement beyond possible finite-sample variance reduction, and may introduce additional bias through synthetic distributional error. We further establish minimax lower bounds showing that the raw estimator already achieves the optimal metric-regret rate in the well-specified regime. Under misspecification, however, augmentation can play a qualitatively different role: by changing the effective class balance, it can alter the restricted-class projection and correct ranking errors induced by the raw imbalanced objective. We provide explicit improvement bounds quantifying the roles of approximation error, finite-sample estimation error, and synthetic distributional error. Simulation studies corroborate the theory, demonstrating limited gains under well-specification and nontrivial but nonmonotone improvements under misspecification.

Large vision-language models (LVLMs) derive their capabilities from extensive training on vast corpora of visual and textual data.

We examine hypothesis testing within a principal-agent framework, where a strategic agent, holding private beliefs about the effectiveness of a product, submits data to a principal who decides on approval. The principal employs a hypothesis testing rule, aiming to pick a p-value threshold that balances false positives and false negatives while anticipating the agent's incentive to maximize expected profitability. Building on prior work, we develop a game-theoretic model that captures how the agent's participation and reporting behavior respond to the principal's statistical decision rule. Despite the complexity of the interaction, we show that the principal's errors exhibit clear monotonic behavior when segmented by an efficiently computable critical p-value threshold, leading to an interpretable characterization of their optimal p-value threshold.

Firms' algorithm development practices are often homogeneous. Whether firms train algorithms on similar data or rely on similar pre-trained models, the result is correlated predictions. In the context of personalized pricing, correlated algorithms can be viewed as a means to collude among competing firms, but whether or not this conduct is legal depends on the mechanisms of achieving collusion. We investigate the precise mechanisms through a formal game-theoretic model. Indeed, we find that (1) higher correlation diminishes consumer welfare and (2) as consumers become more price sensitive, firms are increasingly incentivized to compromise on the accuracy of their predictions in exchange for coordination. We demonstrate our theoretical results in a stylized empirical study where two firms compete using personalized pricing algorithms. Our results demonstrate a new mechanism for achieving collusion through correlation, which allows us to analyze its legal implications. Correlation through algorithms is a new frontier of anti-competitive behavior that is largely unconsidered by US antitrust law.

Imaging systems have traditionally been designed to mimic the human eye and produce visually interpretable measurements.

We present a theoretical framework showing that popular LLM alignment methods--including RLHF and its variants--can be understood as divergence estimators between aligned (safe or preferred) and unaligned (harmful or less-preferred) distributions. This perspective explains the emergence of separation in the latent space between safe and harmful prompts after alignment. As an application of our general divergence framework, we propose KLDO, a novel KL divergence-based alignment method, and empirically validate its effectiveness. We further show that using compliance-refusal datasets, rather than standard preference-based datasets, leads to stronger separation and improved safety alignment. Finally, to quantify the separation effect, we propose a distance-based metric in the prompt representation space, which also acts as a statistically significant indicator for model safety.

Deep learning systems deployed in real-world applications often encounter data that is different from their in-distribution (ID).

The advent of single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) offers an innovative perspective for deciphering regulatory mechanisms by assembling a vast repository of single-cell chromatin accessibility data. While foundation models have achieved significant success in single-cell transcriptomics, there is currently no foundation model for scATAC-seq that supports zero-shot high-quality cell identification and comprehensive multi-omics analysis simultaneously. Key challenges lie in the high dimensionality and sparsity of scATAC-seq data, as well as the lack of a standardized schema for representing open chromatin regions (OCRs). Here, we present ChromFound, a foundation model tailored for scATAC-seq. ChromFound utilizes a hybrid architecture and genome-aware tokenization to effectively capture genome-wide long contexts and regulatory signals from dynamic chromatin landscapes. Pretrained on 1.97 million cells from 30 tissues and 6 disease conditions, ChromFound demonstrates broad applicability across 6 diverse tasks. Notably, it achieves robust zero-shot performance in generating universal cell representations and exhibits excellent transferability in cell type annotation and cross-omics prediction. By uncovering enhancer-gene links undetected by existing computational methods, ChromFound offers a promising framework for understanding disease risk variants in the noncoding genome.