This study addresses the critical issue of reliability for AI-assisted medical diagnosis. We focus on the selection prediction approach that allows the diagnosis system to abstain from providing the decision if it is not confident in the diagnosis. Such selective prediction (or abstention) approaches are usually based on the modeling predictive uncertainty of machine learning models involved. This study explores uncertainty quantification in machine learning models for medical text analysis, addressing diverse tasks across multiple datasets. We focus on binary mortality prediction from textual data in MIMIC-III, multi-label medical code prediction using ICD-10 codes from MIMIC-IV, and multi-class classification with a private outpatient visits dataset. Additionally, we analyze mental health datasets targeting depression and anxiety detection, utilizing various text-based sources, such as essays, social media posts, and clinical descriptions. In addition to comparing uncertainty methods, we introduce HUQ-2, a new state-of-the-art method for enhancing reliability in selective prediction tasks. Our results provide a detailed comparison of uncertainty quantification methods. They demonstrate the effectiveness of HUQ-2 in capturing and evaluating uncertainty, paving the way for more reliable and interpretable applications in medical text analysis.

Keywords: Trajectory prediction, Transformers, Knowledge integration, Deep learning Abstract: Predicting disease trajectories from electronic health records (EHRs) is a complex task due to major challenges such as data non-stationarity, high granularity of medical codes, and integration of multimodal data. EHRs contain both structured data, such as diagnostic codes, and unstructured data, such as clinical notes, which hold essential information often overlooked. Current models, primarily based on structured data, struggle to capture the complete medical context of patients, resulting in a loss of valuable information. To address this issue, we propose an approach that integrates unstructured clinical notes into transformer-based deep learning models for sequential disease prediction. Experiments on MIMIC-IV datasets demonstrate that the proposed approach outperforms traditional models relying solely on structured data. 1 INTRODUCTION In healthcare, the exponential growth of Electronic Health Records (EHRs) has revolutionized patient care while posing new challenges. Healthcare professionals now frequently interact with medical records spanning several decades, having to process and analyze this vast amount of information to make informed decisions about patients' future health status. This evolution has accelerated the development of automated systems to predict future diagnoses from past medical data, thus becoming a key element of personalized and proactive medicine (Figure 1). Machine learning techniques, particularly deep learning, have seen increasing growth in medicine (Egger et al., 2022), thanks to their adaptability and good results.

For a long time, the authorship of the Federalist Papers had been a subject of inquiry and debate, not only by linguists and historians but also by statisticians. In what was arguably the first Bayesian case study, Mosteller and Wallace (1963) provided the first statistical evidence for attributing all disputed papers to Madison. Our paper revisits this historical dataset but from a lens of modern language models, both small and large. We review some of the more popular Large Language Model (LLM) tools and examine them from a statistical point of view in the context of text classification. We investigate whether, without any attempt to fine-tune, the general embedding constructs can be useful for stylometry and attribution. We explain differences between various word/phrase embeddings and discuss how to aggregate them in a document. Contrary to our expectations, we exemplify that dimension expansion with word embeddings may not always be beneficial for attribution relative to dimension reduction with topic embeddings. Our experiments demonstrate that default LLM embeddings (even after manual fine-tuning) may not consistently improve authorship attribution accuracy. Instead, Bayesian analysis with topic embeddings trained on ``function words" yields superior out-of-sample classification performance. This suggests that traditional (small) statistical language models, with their interpretability and solid theoretical foundation, can offer significant advantages in authorship attribution tasks. The code used in this analysis is available at github.com/sowonjeong/slm-to-llm

In statistics, generalized linear models (GLMs) are widely used for modeling data and can expressively capture potential nonlinear dependence of the model's outcomes on its covariates. Within the broad family of GLMs, those with binary outcomes, which include logistic and probit regressions, are motivated by common tasks such as binary classification with (possibly) non-separable data. In addition, in modern machine learning and statistics, data is often high-dimensional yet has a low intrinsic dimension, making sparsity constraints in models another reasonable consideration. In this work, we propose to use and analyze an iterative hard thresholding (projected gradient descent on the ReLU loss) algorithm, called binary iterative hard thresholding (BIHT), for parameter estimation in sparse GLMs with binary outcomes. We establish that BIHT is statistically efficient and converges to the correct solution for parameter estimation in a general class of sparse binary GLMs. Unlike many other methods for learning GLMs, including maximum likelihood estimation, generalized approximate message passing, and GLM-tron (Kakade et al. 2011; Bahmani et al. 2016), BIHT does not require knowledge of the GLM's link function, offering flexibility and generality in allowing the algorithm to learn arbitrary binary GLMs. As two applications, logistic and probit regression are additionally studied. In this regard, it is shown that in logistic regression, the algorithm is in fact statistically optimal in the sense that the order-wise sample complexity matches (up to logarithmic factors) the lower bound obtained previously. To the best of our knowledge, this is the first work achieving statistical optimality for logistic regression in all noise regimes with a computationally efficient algorithm. Moreover, for probit regression, our sample complexity is on the same order as that obtained for logistic regression.

The label ranking problem is a supervised learning scenario in which the learner predicts a total order of the class labels for a given input instance. Recently, research has increasingly focused on the partial label ranking problem, a generalization of the label ranking problem that allows ties in the predicted orders. So far, most existing learning approaches for the partial label ranking problem rely on approximation algorithms for rank aggregation in the final prediction step. This paper explores several alternative aggregation methods for this critical step, including scoring-based and probabilistic-based rank aggregation approaches. To enhance their suitability for the more general partial label ranking problem, the investigated methods are extended to increase the likelihood of producing ties. Experimental evaluations on standard benchmarks demonstrate that scoring-based variants consistently outperform the current state-of-the-art method in handling incomplete information. In contrast, probabilistic-based variants fail to achieve competitive performance.

The aim of this thesis is to extend the applications of the Quantile Regression Forest (QRF) algorithm to handle mixed-frequency and longitudinal data. To this end, standard statistical approaches have been exploited to build two novel algorithms: the Mixed- Frequency Quantile Regression Forest (MIDAS-QRF) and the Finite Mixture Quantile Regression Forest (FM-QRF). The MIDAS-QRF combines the flexibility of QRF with the Mixed Data Sampling (MIDAS) approach, enabling non-parametric quantile estimation with variables observed at different frequencies. FM-QRF, on the other hand, extends random effects machine learning algorithms to a QR framework, allowing for conditional quantile estimation in a longitudinal data setting. The contributions of this dissertation lie both methodologically and empirically. Methodologically, the MIDAS-QRF and the FM-QRF represent two novel approaches for handling mixed-frequency and longitudinal data in QR machine learning framework. Empirically, the application of the proposed models in financial risk management and climate-change impact evaluation demonstrates their validity as accurate and flexible models to be applied in complex empirical settings.

This paper introduces a novel framework for graph sparsification that preserves the essential learning attributes of original graphs, improving computational efficiency and reducing complexity in learning algorithms. We refer to these sparse graphs as "learning backbones". Our approach leverages the zero-forcing (ZF) phenomenon, a dynamic process on graphs with applications in network control. The key idea is to generate a tree from the original graph that retains critical dynamical properties. By correlating these properties with learning attributes, we construct effective learning backbones. We evaluate the performance of our ZF-based backbones in graph classification tasks across eight datasets and six baseline models. The results demonstrate that our method outperforms existing techniques. Additionally, we explore extensions using node distance metrics to further enhance the framework's utility.

Modeling disease progression through multiple stages is critical for clinical decision-making for chronic diseases, e.g., cancer, diabetes, chronic kidney diseases, and so on. Existing approaches often model the disease progression as a uniform trajectory pattern at the population level. However, chronic diseases are highly heterogeneous and often have multiple progression patterns depending on a patient's individual genetics and environmental effects due to lifestyles. We propose a personalized disease progression model to jointly learn the heterogeneous progression patterns and groups of genetic profiles. In particular, an end-to-end pipeline is designed to simultaneously infer the characteristics of patients from genetic markers using a variational autoencoder and how it drives the disease progressions using an RNN-based state-space model based on clinical observations. Our proposed model shows improvement on real-world and synthetic clinical data.

Fairness constraints applied to machine learning (ML) models in static contexts have been shown to potentially produce adverse outcomes among demographic groups over time. To address this issue, emerging research focuses on creating fair solutions that persist over time. While many approaches treat this as a single-agent decision-making problem, real-world systems often consist of multiple interacting entities that influence outcomes. Explicitly modeling these entities as agents enables more flexible analysis of their interventions and the effects they have on a system's underlying dynamics. A significant challenge in conducting research on multi-agent systems is the lack of realistic environments that leverage the limited real-world data available for analysis. To address this gap, we introduce the concept of a Multi-Agent Fair Environment (MAFE) and present and analyze three MAFEs that model distinct social systems. Experimental results demonstrate the utility of our MAFEs as testbeds for developing multi-agent fair algorithms.

Recent advancements in software engineering (SWE) agents have largely followed a $\textit{tool-based paradigm}$, where agents interact with hand-engineered tool APIs to perform specific tasks. While effective for specialized tasks, these methods fundamentally lack generalization, as they require predefined tools for each task and do not scale across programming languages and domains. We introduce $\texttt{Programming with Pixels}$ (PwP), an agent environment that unifies software development tasks by enabling $\textit{computer-use agents}$-agents that operate directly within an IDE through visual perception, typing, and clicking, rather than relying on predefined tool APIs. To systematically evaluate these agents, we propose $\texttt{PwP-Bench}$, a benchmark that unifies existing SWE benchmarks spanning tasks across multiple programming languages, modalities, and domains under a task-agnostic state and action space. Our experiments demonstrate that general-purpose computer-use agents can approach or even surpass specialized tool-based agents on a variety of SWE tasks without the need for hand-engineered tools. However, our analysis shows that current models suffer from limited visual grounding and fail to exploit many IDE tools that could simplify their tasks. When agents can directly access IDE tools, without visual interaction, they show significant performance improvements, highlighting the untapped potential of leveraging built-in IDE capabilities. Our results establish PwP as a scalable testbed for building and evaluating the next wave of software engineering agents. We release code and data at https://programmingwithpixels.com