Unlocking Historical Clinical Trial Data with ALIGN: A Compositional Large Language Model System for Medical Coding

The reuse of historical clinical trial data has significant potential to accelerate medical research and drug development. However, interoperability challenges, particularly with missing medical codes, hinders effective data integration across studies. While Large Language Models (LLMs) offer a promising solution for automated coding without labeled data, current approaches face challenges on complex coding tasks. We introduce ALIGN, a novel compositional LLM-based system for automated, zero-shot medical coding. ALIGN follows a three-step process: (1) diverse candidate code generation; (2) self-evaluation of codes and (3) confidence scoring and uncertainty estimation enabling human deferral to ensure reliability. We evaluate ALIGN on harmonizing medication terms into Anatomical Therapeutic Chemical (ATC) and medical history terms into Medical Dictionary for Regulatory Activities (MedDRA) codes extracted from 22 immunology trials. ALIGN outperformed the LLM baselines, while also providing capabilities for trustworthy deployment. For MedDRA coding, ALIGN achieved high accuracy across all levels, matching RAG and excelling at the most specific levels (87-90% for HLGT). For ATC coding, ALIGN demonstrated superior performance, particularly at lower hierarchy levels (ATC Level 4), with 72-73% overall accuracy and 86-89% accuracy for common medications, outperforming baselines by 7-22%. ALIGN's uncertainty-based deferral improved accuracy by 17% to 90% accuracy with 30% deferral, notably enhancing performance on uncommon medications. ALIGN achieves this cost-efficiently at \$0.0007 and \$0.02 per code for GPT-4o-mini and GPT-4o, reducing barriers to clinical adoption. ALIGN advances automated medical coding for clinical trial data, contributing to enhanced data interoperability and reusability, positioning it as a promising tool to improve clinical research and accelerate drug development.

Matchmaker: Self-Improving Large Language Model Programs for Schema Matching

Schema matching -- the task of finding matches between attributes across disparate data sources with different tables and hierarchies -- is critical for creating interoperable machine learning (ML)-ready data. Addressing this fundamental data-centric problem has wide implications, especially in domains like healthcare, finance and e-commerce -- but also has the potential to benefit ML models more generally, by increasing the data available for ML model training. However, schema matching is a challenging ML task due to structural/hierarchical and semantic heterogeneity between different schemas. Previous ML approaches to automate schema matching have either required significant labeled data for model training, which is often unrealistic or suffer from poor zero-shot performance. To this end, we propose Matchmaker - a compositional language model program for schema matching, comprised of candidate generation, refinement and confidence scoring. Matchmaker also self-improves in a zero-shot manner without the need for labeled demonstrations via a novel optimization approach, which constructs synthetic in-context demonstrations to guide the language model's reasoning process. Empirically, we demonstrate on real-world medical schema matching benchmarks that Matchmaker outperforms previous ML-based approaches, highlighting its potential to accelerate data integration and interoperability of ML-ready data.

Context-Aware Testing: A New Paradigm for Model Testing with Large Language Models

The predominant de facto paradigm of testing ML models relies on either using only held-out data to compute aggregate evaluation metrics or by assessing the performance on different subgroups. However, such data-only testing methods operate under the restrictive assumption that the available empirical data is the sole input for testing ML models, disregarding valuable contextual information that could guide model testing. In this paper, we challenge the go-to approach of data-only testing and introduce context-aware testing (CAT) which uses context as an inductive bias to guide the search for meaningful model failures. We instantiate the first CAT system, SMART Testing, which employs large language models to hypothesize relevant and likely failures, which are evaluated on data using a self-falsification mechanism. Through empirical evaluations in diverse settings, we show that SMART automatically identifies more relevant and impactful failures than alternatives, demonstrating the potential of CAT as a testing paradigm.

Self-Healing Machine Learning: A Framework for Autonomous Adaptation in Real-World Environments

Real-world machine learning systems often encounter model performance degradation due to distributional shifts in the underlying data generating process (DGP). Existing approaches to addressing shifts, such as concept drift adaptation, are limited by their reason-agnostic nature. By choosing from a pre-defined set of actions, such methods implicitly assume that the causes of model degradation are irrelevant to what actions should be taken, limiting their ability to select appropriate adaptations. In this paper, we propose an alternative paradigm to overcome these limitations, called self-healing machine learning (SHML). Contrary to previous approaches, SHML autonomously diagnoses the reason for degradation and proposes diagnosis-based corrective actions. We formalize SHML as an optimization problem over a space of adaptation actions to minimize the expected risk under the shifted DGP. We introduce a theoretical framework for self-healing systems and build an agentic self-healing solution H-LLM which uses large language models to perform self-diagnosis by reasoning about the structure underlying the DGP, and self-adaptation by proposing and evaluating corrective actions. Empirically, we analyze different components of H-LLM to understand why and when it works, demonstrating the potential of self-healing ML.

You can't handle the truth: Data-centric insights improve pseudo-labeling

Pseudo-labeling is a popular semi-supervised learning technique to leverage unlabeled data when labeled samples are scarce. The generation and selection of pseudo-labels heavily rely on labeled data. Existing approaches implicitly assume that the labeled data is gold standard and 'perfect'. However, this can be violated in reality with issues such as mislabeling or ambiguity. We address this overlooked aspect and show the importance of investigating labeled data quality to improve any pseudo-labeling method. Specifically, we introduce a novel data characterization and selection framework called DIPS to extend pseudo-labeling. We select useful labeled and pseudo-labeled samples via analysis of learning dynamics. We demonstrate the applicability and impact of DIPS for various pseudo-labeling methods across an extensive range of real-world tabular and image datasets. Additionally, DIPS improves data efficiency and reduces the performance distinctions between different pseudo-labelers. Overall, we highlight the significant benefits of a data-centric rethinking of pseudo-labeling in real-world settings.

Relaxed Quantile Regression: Prediction Intervals for Asymmetric Noise

Constructing valid prediction intervals rather than point estimates is a well-established approach for uncertainty quantification in the regression setting. Models equipped with this capacity output an interval of values in which the ground truth target will fall with some prespecified probability. This is an essential requirement in many real-world applications where simple point predictions' inability to convey the magnitude and frequency of errors renders them insufficient for high-stakes decisions. Quantile regression is a leading approach for obtaining such intervals via the empirical estimation of quantiles in the (non-parametric) distribution of outputs. This method is simple, computationally inexpensive, interpretable, assumption-free, and effective. However, it does require that the specific quantiles being learned are chosen a priori. This results in (a) intervals that are arbitrarily symmetric around the median which is sub-optimal for realistic skewed distributions, or (b) learning an excessive number of intervals. In this work, we propose Relaxed Quantile Regression (RQR), a direct alternative to quantile regression based interval construction that removes this arbitrary constraint whilst maintaining its strengths. We demonstrate that this added flexibility results in intervals with an improvement in desirable qualities (e.g. mean width) whilst retaining the essential coverage guarantees of quantile regression.

Dissecting Sample Hardness: A Fine-Grained Analysis of Hardness Characterization Methods for Data-Centric AI

Characterizing samples that are difficult to learn from is crucial to developing highly performant ML models. This has led to numerous Hardness Characterization Methods (HCMs) that aim to identify "hard" samples. However, there is a lack of consensus regarding the definition and evaluation of "hardness". Unfortunately, current HCMs have only been evaluated on specific types of hardness and often only qualitatively or with respect to downstream performance, overlooking the fundamental quantitative identification task. We address this gap by presenting a fine-grained taxonomy of hardness types. Additionally, we propose the Hardness Characterization Analysis Toolkit (H-CAT), which supports comprehensive and quantitative benchmarking of HCMs across the hardness taxonomy and can easily be extended to new HCMs, hardness types, and datasets. We use H-CAT to evaluate 13 different HCMs across 8 hardness types. This comprehensive evaluation encompassing over 14K setups uncovers strengths and weaknesses of different HCMs, leading to practical tips to guide HCM selection and future development. Our findings highlight the need for more comprehensive HCM evaluation, while we hope our hardness taxonomy and toolkit will advance the principled evaluation and uptake of data-centric AI methods.

DAGnosis: Localized Identification of Data Inconsistencies using Structures

Identification and appropriate handling of inconsistencies in data at deployment time is crucial to reliably use machine learning models. While recent data-centric methods are able to identify such inconsistencies with respect to the training set, they suffer from two key limitations: (1) suboptimality in settings where features exhibit statistical independencies, due to their usage of compressive representations and (2) lack of localization to pin-point why a sample might be flagged as inconsistent, which is important to guide future data collection. We solve these two fundamental limitations using directed acyclic graphs (DAGs) to encode the training set's features probability distribution and independencies as a structure. Our method, called DAGnosis, leverages these structural interactions to bring valuable and insightful data-centric conclusions. DAGnosis unlocks the localization of the causes of inconsistencies on a DAG, an aspect overlooked by previous approaches. Moreover, we show empirically that leveraging these interactions (1) leads to more accurate conclusions in detecting inconsistencies, as well as (2) provides more detailed insights into why some samples are flagged.

Large Language Models to Enhance Bayesian Optimization

Bayesian optimization (BO) is a powerful approach for optimizing complex and expensive-to-evaluate black-box functions. Its importance is underscored in many applications, notably including hyperparameter tuning, but its efficacy depends on efficiently balancing exploration and exploitation. While there has been substantial progress in BO methods, striking this balance still remains a delicate process. In this light, we present \texttt{LLAMBO}, a novel approach that integrates the capabilities of large language models (LLM) within BO. At a high level, we frame the BO problem in natural language terms, enabling LLMs to iteratively propose promising solutions conditioned on historical evaluations. More specifically, we explore how combining contextual understanding, few-shot learning proficiency, and domain knowledge of LLMs can enhance various components of model-based BO. Our findings illustrate that \texttt{LLAMBO} is effective at zero-shot warmstarting, and improves surrogate modeling and candidate sampling, especially in the early stages of search when observations are sparse. Our approach is performed in context and does not require LLM finetuning. Additionally, it is modular by design, allowing individual components to be integrated into existing BO frameworks, or function cohesively as an end-to-end method. We empirically validate \texttt{LLAMBO}'s efficacy on the problem of hyperparameter tuning, highlighting strong empirical performance across a range of diverse benchmarks, proprietary, and synthetic tasks.

Curated LLM: Synergy of LLMs and Data Curation for tabular augmentation in ultra low-data regimes

Machine Learning (ML) in low-data settings remains an underappreciated yet crucial problem. This challenge is pronounced in low-to-middle income countries where access to large datasets is often limited or even absent. Hence, data augmentation methods to increase the sample size of datasets needed for ML are key to unlocking the transformative potential of ML in data-deprived regions and domains. Unfortunately, the limited training set constrains traditional tabular synthetic data generators in their ability to generate a large and diverse augmented dataset needed for ML tasks. To address this technical challenge, we introduce CLLM, which leverages the prior knowledge of Large Language Models (LLMs) for data augmentation in the low-data regime. While diverse, not all the data generated by LLMs will help increase utility for a downstream task, as for any generative model. Consequently, we introduce a principled curation process, leveraging learning dynamics, coupled with confidence and uncertainty metrics, to obtain a high-quality dataset. Empirically, on multiple real-world datasets, we demonstrate the superior performance of LLMs in the low-data regime compared to conventional generators. We further show our curation mechanism improves the downstream performance for all generators, including LLMs. Additionally, we provide insights and understanding into the LLM generation and curation mechanism, shedding light on the features that enable them to output high-quality augmented datasets. CLLM paves the way for wider usage of ML in data scarce domains and regions, by allying the strengths of LLMs with a robust data-centric approach.