Daily Papers

We consider the task of evaluating policies of algorithmic resource allocation through randomized controlled trials (RCTs). Such policies are tasked with optimizing the utilization of limited intervention resources, with the goal of maximizing the benefits derived. Evaluation of such allocation policies through RCTs proves difficult, notwithstanding the scale of the trial, because the individuals' outcomes are inextricably interlinked through resource constraints controlling the policy decisions. Our key contribution is to present a new estimator leveraging our proposed novel concept, that involves retrospective reshuffling of participants across experimental arms at the end of an RCT. We identify conditions under which such reassignments are permissible and can be leveraged to construct counterfactual trials, whose outcomes can be accurately ascertained, for free. We prove theoretically that such an estimator is more accurate than common estimators based on sample means -- we show that it returns an unbiased estimate and simultaneously reduces variance. We demonstrate the value of our approach through empirical experiments on synthetic, semi-synthetic as well as real case study data and show improved estimation accuracy across the board.

The increasing threat of emerging infectious diseases and antimicrobial resistance requires more efficient, high-quality research. Perpetual Observational Studies (POS) nested within a clinical research network can improve planning, quality and efficiency of interventional and observational studies, although real-life benefits and challenges need to be assessed. Ecraid (European Clinical Research Alliance on Infectious Diseases) has initiated POS and will monitor the impact for five specific infectious syndromes.

Navigating certain communication situations can be challenging due to individuals' lack of skills and the interference of strong emotions. However, effective learning opportunities are rarely accessible. In this work, we conduct a human-centered study that uses language models to simulate bespoke communication training and provide just-in-time feedback to support the practice and learning of interpersonal effectiveness skills. We apply the interpersonal effectiveness framework from Dialectical Behavioral Therapy (DBT), DEAR MAN, which focuses on both conversational and emotional skills. We present IMBUE, an interactive training system that provides feedback 25% more similar to experts' feedback, compared to that generated by GPT-4. IMBUE is the first to focus on communication skills and emotion management simultaneously, incorporate experts' domain knowledge in providing feedback, and be grounded in psychology theory. Through a randomized trial of 86 participants, we find that IMBUE's simulation-only variant significantly improves participants' self-efficacy (up to 17%) and reduces negative emotions (up to 25%). With IMBUE's additional just-in-time feedback, participants demonstrate 17% improvement in skill mastery, along with greater enhancements in self-efficacy (27% more) and reduction of negative emotions (16% more) compared to simulation-only. The improvement in skill mastery is the only measure that is transferred to new and more difficult situations; situation specific training is necessary for improving self-efficacy and emotion reduction.

This study explores the relationship between textual features and Information Engagement (IE) on digital platforms. It highlights the impact of computational linguistics and analytics on user interaction. The READ model is introduced to quantify key predictors like representativeness, ease of use, affect, and distribution, which forecast engagement levels. The model's effectiveness is validated through AB testing and randomized trials, showing strong predictive performance in participation (accuracy: 0.94), perception (accuracy: 0.85), perseverance (accuracy: 0.81), and overall IE (accuracy: 0.97). While participation metrics are strong, perception and perseverance show slightly lower recall and F1-scores, indicating some challenges. The study demonstrates that modifying text based on the READ model's insights leads to significant improvements. For example, increasing representativeness and positive affect boosts selection rates by 11 percent, raises evaluation averages from 3.98 to 4.46, and improves retention rates by 11 percent. These findings highlight the importance of linguistic factors in IE, providing a framework for enhancing digital text engagement. The research offers practical strategies applicable to fields like education, health, and media.

Dynamic treatment regimes (DTRs) are personalized, adaptive, multi-stage treatment plans that adapt treatment decisions both to an individual's initial features and to intermediate outcomes and features at each subsequent stage, which are affected by decisions in prior stages. Examples include personalized first- and second-line treatments of chronic conditions like diabetes, cancer, and depression, which adapt to patient response to first-line treatment, disease progression, and individual characteristics. While existing literature mostly focuses on estimating the optimal DTR from offline data such as from sequentially randomized trials, we study the problem of developing the optimal DTR in an online manner, where the interaction with each individual affect both our cumulative reward and our data collection for future learning. We term this the DTR bandit problem. We propose a novel algorithm that, by carefully balancing exploration and exploitation, is guaranteed to achieve rate-optimal regret when the transition and reward models are linear. We demonstrate our algorithm and its benefits both in synthetic experiments and in a case study of adaptive treatment of major depressive disorder using real-world data.

Many social and environmental phenomena are associated with macroscopic changes in the built environment, captured by satellite imagery on a global scale and with daily temporal resolution. While widely used for prediction, these images and especially image sequences remain underutilized for causal inference, especially in the context of randomized controlled trials (RCTs), where causal identification is established by design. In this paper, we develop and compare a set of general tools for analyzing Conditional Average Treatment Effects (CATEs) from temporal satellite data that can be applied to any RCT where geographical identifiers are available. Through a simulation study, we analyze different modeling strategies for estimating CATE in sequences of satellite images. We find that image sequence representation models with more parameters generally yield a greater ability to detect heterogeneity. To explore the role of model and data choice in practice, we apply the approaches to two influential RCTs -- Banerjee et al. (2015), a poverty study in Cusco, Peru, and Bolsen et al. (2014), a water conservation experiment in Georgia, USA. We benchmark our image sequence models against image-only, tabular-only, and combined image-tabular data sources, summarizing practical implications for investigators in a multivariate analysis. Land cover classifications over satellite images facilitate interpretation of what image features drive heterogeneity. We also show robustness to data and model choice of satellite-based generalization of the RCT results to larger geographical areas outside the original. Overall, this paper shows how satellite sequence data can be incorporated into the analysis of RCTs, and provides evidence about the implications of data, model, and evaluation metric choice for causal analysis.

The development and popularization of large language models (LLMs) have raised concerns that they will be used to create tailor-made, convincing arguments to push false or misleading narratives online. Early work has found that language models can generate content perceived as at least on par and often more persuasive than human-written messages. However, there is still limited knowledge about LLMs' persuasive capabilities in direct conversations with human counterparts and how personalization can improve their performance. In this pre-registered study, we analyze the effect of AI-driven persuasion in a controlled, harmless setting. We create a web-based platform where participants engage in short, multiple-round debates with a live opponent. Each participant is randomly assigned to one of four treatment conditions, corresponding to a two-by-two factorial design: (1) Games are either played between two humans or between a human and an LLM; (2) Personalization might or might not be enabled, granting one of the two players access to basic sociodemographic information about their opponent. We found that participants who debated GPT-4 with access to their personal information had 81.7% (p < 0.01; N=820 unique participants) higher odds of increased agreement with their opponents compared to participants who debated humans. Without personalization, GPT-4 still outperforms humans, but the effect is lower and statistically non-significant (p=0.31). Overall, our results suggest that concerns around personalization are meaningful and have important implications for the governance of social media and the design of new online environments.

Randomized controlled trials are susceptible to imbalance on covariates predictive of the outcome. Rerandomization and deterministic treatment assignment are two proposed solutions. This paper explores the relationship between rerandomization and deterministic assignment, showing how deterministic assignment is an extreme case of rerandomization. The paper argues that in small experiments, both fully randomized and fully deterministic assignment have limitations. Instead, the researcher should consider setting the rerandomization acceptance probability based on an analysis of covariates and assumptions about the data structure to achieve an optimal alignment between randomness and balance. This allows for the calculation of minimum p-values along with valid permutation tests and fiducial intervals. The paper also introduces tools, including a new, open-source R package named fastrerandomize, to implement rerandomization and explore options for optimal rerandomization acceptance thresholds.

Randomized controlled trials (RCTs) are considered the gold standard for estimating the average treatment effect (ATE) of interventions. One use of RCTs is to study the causes of global poverty -- a subject explicitly cited in the 2019 Nobel Memorial Prize awarded to Duflo, Banerjee, and Kremer "for their experimental approach to alleviating global poverty." Because the ATE is a population summary, anti-poverty experiments often seek to unpack the effect variation around the ATE by conditioning (CATE) on tabular variables such as age and ethnicity that were measured during the RCT data collection. Although such variables are key to unpacking CATE, using only such variables may fail to capture historical, geographical, or neighborhood-specific contributors to effect variation, as tabular RCT data are often only observed near the time of the experiment. In global poverty research, when the location of the experiment units is approximately known, satellite imagery can provide a window into such factors important for understanding heterogeneity. However, there is no method that specifically enables applied researchers to analyze CATE from images. In this paper, using a deep probabilistic modeling framework, we develop such a method that estimates latent clusters of images by identifying images with similar treatment effects distributions. Our interpretable image CATE model also includes a sensitivity factor that quantifies the importance of image segments contributing to the effect cluster prediction. We compare the proposed methods against alternatives in simulation; also, we show how the model works in an actual RCT, estimating the effects of an anti-poverty intervention in northern Uganda and obtaining a posterior predictive distribution over effects for the rest of the country where no experimental data was collected. We make all models available in open-source software.

Generative AI, particularly Language Models (LMs), has the potential to transform real-world domains with societal impact, particularly where access to experts is limited. For example, in education, training novice educators with expert guidance is important for effectiveness but expensive, creating significant barriers to improving education quality at scale. This challenge disproportionately harms students from under-served communities, who stand to gain the most from high-quality education. We introduce Tutor CoPilot, a novel Human-AI approach that leverages a model of expert thinking to provide expert-like guidance to tutors as they tutor. This study is the first randomized controlled trial of a Human-AI system in live tutoring, involving 900 tutors and 1,800 K-12 students from historically under-served communities. Following a preregistered analysis plan, we find that students working with tutors that have access to Tutor CoPilot are 4 percentage points (p.p.) more likely to master topics (p<0.01). Notably, students of lower-rated tutors experienced the greatest benefit, improving mastery by 9 p.p. We find that Tutor CoPilot costs only $20 per-tutor annually. We analyze 550,000+ messages using classifiers to identify pedagogical strategies, and find that tutors with access to Tutor CoPilot are more likely to use high-quality strategies to foster student understanding (e.g., asking guiding questions) and less likely to give away the answer to the student. Tutor interviews highlight how Tutor CoPilot's guidance helps tutors to respond to student needs, though they flag issues in Tutor CoPilot, such as generating suggestions that are not grade-level appropriate. Altogether, our study of Tutor CoPilot demonstrates how Human-AI systems can scale expertise in real-world domains, bridge gaps in skills and create a future where high-quality education is accessible to all students.

We present PubMed 200k RCT, a new dataset based on PubMed for sequential sentence classification. The dataset consists of approximately 200,000 abstracts of randomized controlled trials, totaling 2.3 million sentences. Each sentence of each abstract is labeled with their role in the abstract using one of the following classes: background, objective, method, result, or conclusion. The purpose of releasing this dataset is twofold. First, the majority of datasets for sequential short-text classification (i.e., classification of short texts that appear in sequences) are small: we hope that releasing a new large dataset will help develop more accurate algorithms for this task. Second, from an application perspective, researchers need better tools to efficiently skim through the literature. Automatically classifying each sentence in an abstract would help researchers read abstracts more efficiently, especially in fields where abstracts may be long, such as the medical field.

Earth Observation (EO) data are increasingly used in policy analysis by enabling granular estimation of treatment effects. However, a challenge in EO-based causal inference lies in balancing the trade-off between capturing fine-grained individual heterogeneity and broader contextual information. This paper introduces Multi-scale Concatenation, a family of composable procedures that transform arbitrary single-scale CATE estimation algorithms into multi-scale algorithms. We benchmark the performance of Multi-scale Concatenation on a CATE estimation pipeline combining Vision Transformer (ViT) models fine-tuned on satellite images to encode images of different scales with Causal Forests to obtain the final CATE estimate. We first perform simulation studies, showing how a multi-scale approach captures multi-level dynamics that single-scale ViT models fail to capture. We then apply the multi-scale method to two randomized controlled trials (RCTs) conducted in Peru and Uganda using Landsat satellite imagery. In the RCT analysis, the Rank Average Treatment Effect Ratio (RATE Ratio) measure is employed to assess performance without ground truth individual treatment effects. Results indicate that Multi-scale Concatenation improves the performance of deep learning models in EO-based CATE estimation without the complexity of designing new multi-scale architectures for a specific use case.

Indirect experiments provide a valuable framework for estimating treatment effects in situations where conducting randomized control trials (RCTs) is impractical or unethical. Unlike RCTs, indirect experiments estimate treatment effects by leveraging (conditional) instrumental variables, enabling estimation through encouragement and recommendation rather than strict treatment assignment. However, the sample efficiency of such estimators depends not only on the inherent variability in outcomes but also on the varying compliance levels of users with the instrumental variables and the choice of estimator being used, especially when dealing with numerous instrumental variables. While adaptive experiment design has a rich literature for direct experiments, in this paper we take the initial steps towards enhancing sample efficiency for indirect experiments by adaptively designing a data collection policy over instrumental variables. Our main contribution is a practical computational procedure that utilizes influence functions to search for an optimal data collection policy, minimizing the mean-squared error of the desired (non-linear) estimator. Through experiments conducted in various domains inspired by real-world applications, we showcase how our method can significantly improve the sample efficiency of indirect experiments.

We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials. Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the `PICO' elements). These spans are further annotated at a more granular level, e.g., individual interventions within them are marked and mapped onto a structured medical vocabulary. We acquired annotations from a diverse set of workers with varying levels of expertise and cost. We describe our data collection process and the corpus itself in detail. We then outline a set of challenging NLP tasks that would aid searching of the medical literature and the practice of evidence-based medicine.

Plain language summarization with LLMs can be useful for improving textual accessibility of technical content. But how factual are these summaries in a high-stakes domain like medicine? This paper presents FactPICO, a factuality benchmark for plain language summarization of medical texts describing randomized controlled trials (RCTs), which are the basis of evidence-based medicine and can directly inform patient treatment. FactPICO consists of 345 plain language summaries of RCT abstracts generated from three LLMs (i.e., GPT-4, Llama-2, and Alpaca), with fine-grained evaluation and natural language rationales from experts. We assess the factuality of critical elements of RCTs in those summaries: Populations, Interventions, Comparators, Outcomes (PICO), as well as the reported findings concerning these. We also evaluate the correctness of the extra information (e.g., explanations) added by LLMs. Using FactPICO, we benchmark a range of existing factuality metrics, including the newly devised ones based on LLMs. We find that plain language summarization of medical evidence is still challenging, especially when balancing between simplicity and factuality, and that existing metrics correlate poorly with expert judgments on the instance level.

Language models (LMs) can perform complex reasoning either end-to-end, with hidden latent state, or compositionally, with transparent intermediate state. Composition offers benefits for interpretability and safety, but may need workflow support and infrastructure to remain competitive. We describe iterated decomposition, a human-in-the-loop workflow for developing and refining compositional LM programs. We improve the performance of compositions by zooming in on failing components and refining them through decomposition, additional context, chain of thought, etc. To support this workflow, we develop ICE, an open-source tool for visualizing the execution traces of LM programs. We apply iterated decomposition to three real-world tasks and improve the accuracy of LM programs over less compositional baselines: describing the placebo used in a randomized controlled trial (25% to 65%), evaluating participant adherence to a medical intervention (53% to 70%), and answering NLP questions on the Qasper dataset (38% to 69%). These applications serve as case studies for a workflow that, if automated, could keep ML systems interpretable and safe even as they scale to increasingly complex tasks.

Large language models, particularly GPT-3, are able to produce high quality summaries of general domain news articles in few- and zero-shot settings. However, it is unclear if such models are similarly capable in more specialized, high-stakes domains such as biomedicine. In this paper, we enlist domain experts (individuals with medical training) to evaluate summaries of biomedical articles generated by GPT-3, given zero supervision. We consider both single- and multi-document settings. In the former, GPT-3 is tasked with generating regular and plain-language summaries of articles describing randomized controlled trials; in the latter, we assess the degree to which GPT-3 is able to synthesize evidence reported across a collection of articles. We design an annotation scheme for evaluating model outputs, with an emphasis on assessing the factual accuracy of generated summaries. We find that while GPT-3 is able to summarize and simplify single biomedical articles faithfully, it struggles to provide accurate aggregations of findings over multiple documents. We release all data and annotations used in this work.

Nowadays the medical domain is receiving more and more attention in applications involving Artificial Intelligence. Clinicians have to deal with an enormous amount of unstructured textual data to make a conclusion about patients' health in their everyday life. Argument mining helps to provide a structure to such data by detecting argumentative components in the text and classifying the relations between them. However, as it is the case for many tasks in Natural Language Processing in general and in medical text processing in particular, the large majority of the work on computational argumentation has been done only for English. This is also the case with the only dataset available for argumentation in the medical domain, namely, the annotated medical data of abstracts of Randomized Controlled Trials (RCT) from the MEDLINE database. In order to mitigate the lack of annotated data for other languages, we empirically investigate several strategies to perform argument mining and classification in medical texts for a language for which no annotated data is available. This project shows that automatically translating and project annotations from English to a target language (Spanish) is an effective way to generate annotated data without manual intervention. Furthermore, our experiments demonstrate that the translation and projection approach outperforms zero-shot cross-lingual approaches using a large masked multilingual language model. Finally, we show how the automatically generated data in Spanish can also be used to improve results in the original English evaluation setting.

Clinical trials are fundamental in developing new drugs, medical devices, and treatments. However, they are often time-consuming and have low success rates. Although there have been initial attempts to create large language models (LLMs) for clinical trial design and patient-trial matching, these models remain task-specific and not adaptable to diverse clinical trial tasks. To address this challenge, we propose a clinical trial foundation model named Panacea, designed to handle multiple tasks, including trial search, trial summarization, trial design, and patient-trial matching. We also assemble a large-scale dataset, named TrialAlign, of 793,279 trial documents and 1,113,207 trial-related scientific papers, to infuse clinical knowledge into the model by pre-training. We further curate TrialInstruct, which has 200,866 of instruction data for fine-tuning. These resources enable Panacea to be widely applicable for a range of clinical trial tasks based on user requirements. We evaluated Panacea on a new benchmark, named TrialPanorama, which covers eight clinical trial tasks. Our method performed the best on seven of the eight tasks compared to six cutting-edge generic or medicine-specific LLMs. Specifically, Panacea showed great potential to collaborate with human experts in crafting the design of eligibility criteria, study arms, and outcome measures, in multi-round conversations. In addition, Panacea achieved 14.42% improvement in patient-trial matching, 41.78% to 52.02% improvement in trial search, and consistently ranked at the top for five aspects of trial summarization. Our approach demonstrates the effectiveness of Panacea in clinical trials and establishes a comprehensive resource, including training data, model, and benchmark, for developing clinical trial foundation models, paving the path for AI-based clinical trial development.

Understanding causality should be a core requirement of any attempt to build real impact through AI. Due to the inherent unobservability of counterfactuals, large randomised trials (RCTs) are the standard for causal inference. But large experiments are generically expensive, and randomisation carries its own costs, e.g. when suboptimal decisions are trialed. Recent work has proposed more sample-efficient alternatives to RCTs, but these are not adaptable to the downstream application for which the causal effect is sought. In this work, we develop a task-specific approach to experimental design and derive sampling strategies customised to particular downstream applications. Across a range of important tasks, real-world datasets, and sample sizes, our method outperforms other benchmarks, e.g. requiring an order-of-magnitude less data to match RCT performance on targeted marketing tasks.

Patient recruitment is challenging for clinical trials. We introduce TrialGPT, an end-to-end framework for zero-shot patient-to-trial matching with large language models. TrialGPT comprises three modules: it first performs large-scale filtering to retrieve candidate trials (TrialGPT-Retrieval); then predicts criterion-level patient eligibility (TrialGPT-Matching); and finally generates trial-level scores (TrialGPT-Ranking). We evaluate TrialGPT on three cohorts of 183 synthetic patients with over 75,000 trial annotations. TrialGPT-Retrieval can recall over 90% of relevant trials using less than 6% of the initial collection. Manual evaluations on 1,015 patient-criterion pairs show that TrialGPT-Matching achieves an accuracy of 87.3% with faithful explanations, close to the expert performance. The TrialGPT-Ranking scores are highly correlated with human judgments and outperform the best-competing models by 43.8% in ranking and excluding trials. Furthermore, our user study reveals that TrialGPT can reduce the screening time by 42.6% in patient recruitment. Overall, these results have demonstrated promising opportunities for patient-to-trial matching with TrialGPT.

We study the problem of adaptively identifying patient subpopulations that benefit from a given treatment during a confirmatory clinical trial. This type of adaptive clinical trial has been thoroughly studied in biostatistics, but has been allowed only limited adaptivity so far. Here, we aim to relax classical restrictions on such designs and investigate how to incorporate ideas from the recent machine learning literature on adaptive and online experimentation to make trials more flexible and efficient. We find that the unique characteristics of the subpopulation selection problem -- most importantly that (i) one is usually interested in finding subpopulations with any treatment benefit (and not necessarily the single subgroup with largest effect) given a limited budget and that (ii) effectiveness only has to be demonstrated across the subpopulation on average -- give rise to interesting challenges and new desiderata when designing algorithmic solutions. Building on these findings, we propose AdaGGI and AdaGCPI, two meta-algorithms for subpopulation construction. We empirically investigate their performance across a range of simulation scenarios and derive insights into their (dis)advantages across different settings.

Temporally dense single-person "small data" have become widely available thanks to mobile apps and wearable sensors. Many caregivers and self-trackers want to use these data to help a specific person change their behavior to achieve desired health outcomes. Ideally, this involves discerning possible causes from correlations using that person's own observational time series data. In this paper, we estimate within-individual average treatment effects of physical activity on sleep duration, and vice-versa. We introduce the model twin randomization (MoTR; "motor") method for analyzing an individual's intensive longitudinal data. Formally, MoTR is an application of the g-formula (i.e., standardization, back-door adjustment) under serial interference. It estimates stable recurring effects, as is done in n-of-1 trials and single case experimental designs. We compare our approach to standard methods (with possible confounding) to show how to use causal inference to make better personalized recommendations for health behavior change, and analyze 222 days of Fitbit sleep and steps data for one of the authors.

Clinical trial matching is a key process in health delivery and discovery. In practice, it is plagued by overwhelming unstructured data and unscalable manual processing. In this paper, we conduct a systematic study on scaling clinical trial matching using large language models (LLMs), with oncology as the focus area. Our study is grounded in a clinical trial matching system currently in test deployment at a large U.S. health network. Initial findings are promising: out of box, cutting-edge LLMs, such as GPT-4, can already structure elaborate eligibility criteria of clinical trials and extract complex matching logic (e.g., nested AND/OR/NOT). While still far from perfect, LLMs substantially outperform prior strong baselines and may serve as a preliminary solution to help triage patient-trial candidates with humans in the loop. Our study also reveals a few significant growth areas for applying LLMs to end-to-end clinical trial matching, such as context limitation and accuracy, especially in structuring patient information from longitudinal medical records.

Synthesizing clinical evidence largely relies on systematic reviews of clinical trials and retrospective analyses from medical literature. However, the rapid expansion of publications presents challenges in efficiently identifying, summarizing, and updating clinical evidence. Here, we introduce TrialMind, a generative artificial intelligence (AI) pipeline for facilitating human-AI collaboration in three crucial tasks for evidence synthesis: study search, screening, and data extraction. To assess its performance, we chose published systematic reviews to build the benchmark dataset, named TrialReviewBench, which contains 100 systematic reviews and the associated 2,220 clinical studies. Our results show that TrialMind excels across all three tasks. In study search, it generates diverse and comprehensive search queries to achieve high recall rates (Ours 0.711-0.834 v.s. Human baseline 0.138-0.232). For study screening, TrialMind surpasses traditional embedding-based methods by 30% to 160%. In data extraction, it outperforms a GPT-4 baseline by 29.6% to 61.5%. We further conducted user studies to confirm its practical utility. Compared to manual efforts, human-AI collaboration using TrialMind yielded a 71.4% recall lift and 44.2% time savings in study screening and a 23.5% accuracy lift and 63.4% time savings in data extraction. Additionally, when comparing synthesized clinical evidence presented in forest plots, medical experts favored TrialMind's outputs over GPT-4's outputs in 62.5% to 100% of cases. These findings show the promise of LLM-based approaches like TrialMind to accelerate clinical evidence synthesis via streamlining study search, screening, and data extraction from medical literature, with exceptional performance improvement when working with human experts.

Clinical trial matching is the task of identifying trials for which patients may be potentially eligible. Typically, this task is labor-intensive and requires detailed verification of patient electronic health records (EHRs) against the stringent inclusion and exclusion criteria of clinical trials. This process is manual, time-intensive, and challenging to scale up, resulting in many patients missing out on potential therapeutic options. Recent advancements in Large Language Models (LLMs) have made automating patient-trial matching possible, as shown in multiple concurrent research studies. However, the current approaches are confined to constrained, often synthetic datasets that do not adequately mirror the complexities encountered in real-world medical data. In this study, we present the first, end-to-end large-scale empirical evaluation of clinical trial matching using real-world EHRs. Our study showcases the capability of LLMs to accurately match patients with appropriate clinical trials. We perform experiments with proprietary LLMs, including GPT-4 and GPT-3.5, as well as our custom fine-tuned model called OncoLLM and show that OncoLLM, despite its significantly smaller size, not only outperforms GPT-3.5 but also matches the performance of qualified medical doctors. All experiments were carried out on real-world EHRs that include clinical notes and available clinical trials from a single cancer center in the United States.

How do we most effectively treat a disease or condition? Ideally, we could consult a database of evidence gleaned from clinical trials to answer such questions. Unfortunately, no such database exists; clinical trial results are instead disseminated primarily via lengthy natural language articles. Perusing all such articles would be prohibitively time-consuming for healthcare practitioners; they instead tend to depend on manually compiled systematic reviews of medical literature to inform care. NLP may speed this process up, and eventually facilitate immediate consult of published evidence. The Evidence Inference dataset was recently released to facilitate research toward this end. This task entails inferring the comparative performance of two treatments, with respect to a given outcome, from a particular article (describing a clinical trial) and identifying supporting evidence. For instance: Does this article report that chemotherapy performed better than surgery for five-year survival rates of operable cancers? In this paper, we collect additional annotations to expand the Evidence Inference dataset by 25\%, provide stronger baseline models, systematically inspect the errors that these make, and probe dataset quality. We also release an abstract only (as opposed to full-texts) version of the task for rapid model prototyping. The updated corpus, documentation, and code for new baselines and evaluations are available at http://evidence-inference.ebm-nlp.com/.

For observational studies, we study the sensitivity of causal inference when treatment assignments may depend on unobserved confounders. We develop a loss minimization approach for estimating bounds on the conditional average treatment effect (CATE) when unobserved confounders have a bounded effect on the odds ratio of treatment selection. Our approach is scalable and allows flexible use of model classes in estimation, including nonparametric and black-box machine learning methods. Based on these bounds for the CATE, we propose a sensitivity analysis for the average treatment effect (ATE). Our semi-parametric estimator extends/bounds the augmented inverse propensity weighted (AIPW) estimator for the ATE under bounded unobserved confounding. By constructing a Neyman orthogonal score, our estimator of the bound for the ATE is a regular root-n estimator so long as the nuisance parameters are estimated at the o_p(n^{-1/4}) rate. We complement our methodology with optimality results showing that our proposed bounds are tight in certain cases. We demonstrate our method on simulated and real data examples, and show accurate coverage of our confidence intervals in practical finite sample regimes with rich covariate information.

To effectively optimize and personalize treatments, it is necessary to investigate the heterogeneity of treatment effects. With the wide range of users being treated over many online controlled experiments, the typical approach of manually investigating each dimension of heterogeneity becomes overly cumbersome and prone to subjective human biases. We need an efficient way to search through thousands of experiments with hundreds of target covariates and hundreds of breakdown dimensions. In this paper, we propose a systematic paradigm for detecting, surfacing and characterizing heterogeneous treatment effects. First, we detect if treatment effect variation is present in an experiment, prior to specifying any breakdowns. Second, we surface the most relevant dimensions for heterogeneity. Finally, we characterize the heterogeneity beyond just the conditional average treatment effects (CATE) by studying the conditional distributions of the estimated individual treatment effects. We show the effectiveness of our methods using simulated data and empirical studies.

We explore algorithms to select actions in the causal bandit setting where the learner can choose to intervene on a set of random variables related by a causal graph, and the learner sequentially chooses interventions and observes a sample from the interventional distribution. The learner's goal is to quickly find the intervention, among all interventions on observable variables, that maximizes the expectation of an outcome variable. We depart from previous literature by assuming no knowledge of the causal graph except that latent confounders between the outcome and its ancestors are not present. We first show that the unknown graph problem can be exponentially hard in the parents of the outcome. To remedy this, we adopt an additional additive assumption on the outcome which allows us to solve the problem by casting it as an additive combinatorial linear bandit problem with full-bandit feedback. We propose a novel action-elimination algorithm for this setting, show how to apply this algorithm to the causal bandit problem, provide sample complexity bounds, and empirically validate our findings on a suite of randomly generated causal models, effectively showing that one does not need to explicitly learn the parents of the outcome to identify the best intervention.

The fastrerandomize R package provides hardware-accelerated tools for performing rerandomization and randomization testing in experimental research. Using a JAX backend, the package enables exact rerandomization inference even for large experiments with hundreds of billions of possible randomizations. Key functionalities include generating pools of acceptable rerandomizations based on covariate balance, conducting exact randomization tests, and performing pre-analysis evaluations to determine optimal rerandomization acceptance thresholds. Through batched processing and GPU acceleration, fastrerandomize achieves substantial performance gains compared to existing implementations, making previously intractable designs computationally feasible. The package therefore extends the randomization-based inference toolkit in R, allowing researchers to efficiently implement more stringent rerandomization designs and conduct valid inference even with large sample sizes or in high-dimensional settings.

Large Language Models (LLMs) and multi-agent systems have shown impressive capabilities in natural language tasks but face challenges in clinical trial applications, primarily due to limited access to external knowledge. Recognizing the potential of advanced clinical trial tools that aggregate and predict based on the latest medical data, we propose an integrated solution to enhance their accessibility and utility. We introduce Clinical Agent System (ClinicalAgent), a clinical multi-agent system designed for clinical trial tasks, leveraging GPT-4, multi-agent architectures, LEAST-TO-MOST, and ReAct reasoning technology. This integration not only boosts LLM performance in clinical contexts but also introduces novel functionalities. The proposed method achieves competitive predictive performance in clinical trial outcome prediction (0.7908 PR-AUC), obtaining a 0.3326 improvement over the standard prompt Method. Publicly available code can be found at https://anonymous.4open.science/r/ClinicalAgent-6671.

We advance the study of incentivized bandit exploration, in which arm choices are viewed as recommendations and are required to be Bayesian incentive compatible. Recent work has shown under certain independence assumptions that after collecting enough initial samples, the popular Thompson sampling algorithm becomes incentive compatible. We give an analog of this result for linear bandits, where the independence of the prior is replaced by a natural convexity condition. This opens up the possibility of efficient and regret-optimal incentivized exploration in high-dimensional action spaces. In the semibandit model, we also improve the sample complexity for the pre-Thompson sampling phase of initial data collection.

Machine learning (ML) holds great potential for accurately forecasting treatment outcomes over time, which could ultimately enable the adoption of more individualized treatment strategies in many practical applications. However, a significant challenge that has been largely overlooked by the ML literature on this topic is the presence of informative sampling in observational data. When instances are observed irregularly over time, sampling times are typically not random, but rather informative -- depending on the instance's characteristics, past outcomes, and administered treatments. In this work, we formalize informative sampling as a covariate shift problem and show that it can prohibit accurate estimation of treatment outcomes if not properly accounted for. To overcome this challenge, we present a general framework for learning treatment outcomes in the presence of informative sampling using inverse intensity-weighting, and propose a novel method, TESAR-CDE, that instantiates this framework using Neural CDEs. Using a simulation environment based on a clinical use case, we demonstrate the effectiveness of our approach in learning under informative sampling.

The global cost of drug discovery and development exceeds $200 billion annually. The main results of drug discovery and development are the outcomes of clinical trials, which directly influence the regulatory approval of new drug candidates and ultimately affect patient outcomes. Despite their significance, large-scale, high-quality clinical trial outcome data are not readily available to the public. Suppose a large clinical trial outcome dataset is provided; machine learning researchers can potentially develop accurate prediction models using past trials and outcome labels, which could help prioritize and optimize therapeutic programs, ultimately benefiting patients. This paper introduces Clinical Trial Outcome (CTO) dataset, the largest trial outcome dataset with around 479K clinical trials, aggregating outcomes from multiple sources of weakly supervised labels, minimizing the noise from individual sources, and eliminating the need for human annotation. These sources include large language model (LLM) decisions on trial-related documents, news headline sentiments, stock prices of trial sponsors, trial linkages across phases, and other signals such as patient dropout rates and adverse events. CTO's labels show unprecedented agreement with supervised clinical trial outcome labels from test split of the supervised TOP dataset, with a 91 F1.

Instrumental variable (IV) methods are used to estimate causal effects in settings with unobserved confounding, where we cannot directly experiment on the treatment variable. Instruments are variables which only affect the outcome indirectly via the treatment variable(s). Most IV applications focus on low-dimensional treatments and crucially require at least as many instruments as treatments. This assumption is restrictive: in the natural sciences we often seek to infer causal effects of high-dimensional treatments (e.g., the effect of gene expressions or microbiota on health and disease), but can only run few experiments with a limited number of instruments (e.g., drugs or antibiotics). In such underspecified problems, the full treatment effect is not identifiable in a single experiment even in the linear case. We show that one can still reliably recover the projection of the treatment effect onto the instrumented subspace and develop techniques to consistently combine such partial estimates from different sets of instruments. We then leverage our combined estimators in an algorithm that iteratively proposes the most informative instruments at each round of experimentation to maximize the overall information about the full causal effect.

Researchers and developers increasingly rely on toxicity scoring to moderate generative language model outputs, in settings such as customer service, information retrieval, and content generation. However, toxicity scoring may render pertinent information inaccessible, rigidify or "value-lock" cultural norms, and prevent language reclamation processes, particularly for marginalized people. In this work, we extend the concept of algorithmic recourse to generative language models: we provide users a novel mechanism to achieve their desired prediction by dynamically setting thresholds for toxicity filtering. Users thereby exercise increased agency relative to interactions with the baseline system. A pilot study (n = 30) supports the potential of our proposed recourse mechanism, indicating improvements in usability compared to fixed-threshold toxicity-filtering of model outputs. Future work should explore the intersection of toxicity scoring, model controllability, user agency, and language reclamation processes -- particularly with regard to the bias that many communities encounter when interacting with generative language models.

The evaluation of machine learning models using human-labeled validation data can be expensive and time-consuming. AI-labeled synthetic data can be used to decrease the number of human annotations required for this purpose in a process called autoevaluation. We suggest efficient and statistically principled algorithms for this purpose that improve sample efficiency while remaining unbiased. These algorithms increase the effective human-labeled sample size by up to 50% on experiments with GPT-4.

Large participatory biomedical studies, studies that recruit individuals to join a dataset, are gaining popularity and investment, especially for analysis by modern AI methods. Because they purposively recruit participants, these studies are uniquely able to address a lack of historical representation, an issue that has affected many biomedical datasets. In this work, we define representativeness as the similarity to a target population distribution of a set of attributes and our goal is to mirror the U.S. population across distributions of age, gender, race, and ethnicity. Many participatory studies recruit at several institutions, so we introduce a computational approach to adaptively allocate recruitment resources among sites to improve representativeness. In simulated recruitment of 10,000-participant cohorts from medical centers in the STAR Clinical Research Network, we show that our approach yields a more representative cohort than existing baselines. Thus, we highlight the value of computational modeling in guiding recruitment efforts.

The recommendation of medication is a vital aspect of intelligent healthcare systems, as it involves prescribing the most suitable drugs based on a patient's specific health needs. Unfortunately, many sophisticated models currently in use tend to overlook the nuanced semantics of medical data, while only relying heavily on identities. Furthermore, these models face significant challenges in handling cases involving patients who are visiting the hospital for the first time, as they lack prior prescription histories to draw upon. To tackle these issues, we harness the powerful semantic comprehension and input-agnostic characteristics of Large Language Models (LLMs). Our research aims to transform existing medication recommendation methodologies using LLMs. In this paper, we introduce a novel approach called Large Language Model Distilling Medication Recommendation (LEADER). We begin by creating appropriate prompt templates that enable LLMs to suggest medications effectively. However, the straightforward integration of LLMs into recommender systems leads to an out-of-corpus issue specific to drugs. We handle it by adapting the LLMs with a novel output layer and a refined tuning loss function. Although LLM-based models exhibit remarkable capabilities, they are plagued by high computational costs during inference, which is impractical for the healthcare sector. To mitigate this, we have developed a feature-level knowledge distillation technique, which transfers the LLM's proficiency to a more compact model. Extensive experiments conducted on two real-world datasets, MIMIC-III and MIMIC-IV, demonstrate that our proposed model not only delivers effective results but also is efficient. To ease the reproducibility of our experiments, we release the implementation code online.

Gaussian process upper confidence bound (GP-UCB) is a theoretically promising approach for black-box optimization; however, the confidence parameter beta is considerably large in the theorem and chosen heuristically in practice. Then, randomized GP-UCB (RGP-UCB) uses a randomized confidence parameter, which follows the Gamma distribution, to mitigate the impact of manually specifying beta. This study first generalizes the regret analysis of RGP-UCB to a wider class of distributions, including the Gamma distribution. Furthermore, we propose improved RGP-UCB (IRGP-UCB) based on a two-parameter exponential distribution, which achieves tighter Bayesian regret bounds. IRGP-UCB does not require an increase in the confidence parameter in terms of the number of iterations, which avoids over-exploration in the later iterations. Finally, we demonstrate the effectiveness of IRGP-UCB through extensive experiments.

Systematic literature review is essential for evidence-based medicine, requiring comprehensive analysis of clinical trial publications. However, the application of artificial intelligence (AI) models for medical literature mining has been limited by insufficient training and evaluation across broad therapeutic areas and diverse tasks. Here, we present LEADS, an AI foundation model for study search, screening, and data extraction from medical literature. The model is trained on 633,759 instruction data points in LEADSInstruct, curated from 21,335 systematic reviews, 453,625 clinical trial publications, and 27,015 clinical trial registries. We showed that LEADS demonstrates consistent improvements over four cutting-edge generic large language models (LLMs) on six tasks. Furthermore, LEADS enhances expert workflows by providing supportive references following expert requests, streamlining processes while maintaining high-quality results. A study with 16 clinicians and medical researchers from 14 different institutions revealed that experts collaborating with LEADS achieved a recall of 0.81 compared to 0.77 experts working alone in study selection, with a time savings of 22.6%. In data extraction tasks, experts using LEADS achieved an accuracy of 0.85 versus 0.80 without using LEADS, alongside a 26.9% time savings. These findings highlight the potential of specialized medical literature foundation models to outperform generic models, delivering significant quality and efficiency benefits when integrated into expert workflows for medical literature mining.

We introduce a general, flexible, parametric survival modelling framework which encompasses key shapes of hazard function (constant, increasing, decreasing, up-then-down, down-then-up), various common survival distributions (log-logistic, Burr type XII, Weibull, Gompertz), and includes defective distributions (i.e., cure models). This generality is achieved using four basic distributional parameters: two scale-type parameters and two shape parameters. Generalising to covariate dependence, the scale-type regression components correspond to accelerated failure time (AFT) and proportional hazards (PH) models. Therefore, this general formulation unifies the most popular survival models which allows us to consider the practical value of possible modelling choices for survival data. Furthermore, in line with our proposed flexible baseline distribution, we advocate the use of multi-parameter regression in which more than one distributional parameter depends on covariates - rather than the usual convention of having a single covariate-dependent (scale) parameter. While many choices are available, we suggest introducing covariates through just one or other of the two scale parameters, which covers AFT and PH models, in combination with a `power' shape parameter, which allows for more complex non-AFT/non-PH effects, while the other shape parameter remains covariate-independent, and handles automatic selection of the baseline distribution. We explore inferential issues in simulations, both with and without a covariate, with particular focus on evidence concerning the need, or otherwise, to include both AFT and PH parameters. We illustrate the efficacy of our modelling framework by investigating differences between treatment groups using data from a lung cancer study and a melanoma study. Censoring is accommodated throughout.

With an increasing number of replication studies performed in psychological science, the question of how to evaluate the outcome of a replication attempt deserves careful consideration. Bayesian approaches allow to incorporate uncertainty and prior information into the analysis of the replication attempt by their design. The Replication Bayes Factor, introduced by Verhagen & Wagenmakers (2014), provides quantitative, relative evidence in favor or against a successful replication. In previous work by Verhagen & Wagenmakers (2014) it was limited to the case of t-tests. In this paper, the Replication Bayes Factor is extended to F-tests in multi-group, fixed-effect ANOVA designs. Simulations and examples are presented to facilitate the understanding and to demonstrate the usefulness of this approach. Finally, the Replication Bayes Factor is compared to other Bayesian and frequentist approaches and discussed in the context of replication attempts. R code to calculate Replication Bayes factors and to reproduce the examples in the paper is available at https://osf.io/jv39h/.

Experience replay is a key component in reinforcement learning for stabilizing learning and improving sample efficiency. Its typical implementation samples transitions with replacement from a replay buffer. In contrast, in supervised learning with a fixed dataset, it is a common practice to shuffle the dataset every epoch and consume data sequentially, which is called random reshuffling (RR). RR enjoys theoretically better convergence properties and has been shown to outperform with-replacement sampling empirically. To leverage the benefits of RR in reinforcement learning, we propose sampling methods that extend RR to experience replay, both in uniform and prioritized settings. We evaluate our sampling methods on Atari benchmarks, demonstrating their effectiveness in deep reinforcement learning.

In modern recommendation systems, the standard pipeline involves training machine learning models on historical data to predict user behaviors and improve recommendations continuously. However, these data training loops can introduce interference in A/B tests, where data generated by control and treatment algorithms, potentially with different distributions, are combined. To address these challenges, we introduce a novel approach called weighted training. This approach entails training a model to predict the probability of each data point appearing in either the treatment or control data and subsequently applying weighted losses during model training. We demonstrate that this approach achieves the least variance among all estimators without causing shifts in the training distributions. Through simulation studies, we demonstrate the lower bias and variance of our approach compared to other methods.

Literature-Based Discovery (LBD) aims to discover new scientific knowledge by mining papers and generating hypotheses. Standard LBD is limited to predicting pairwise relations between discrete concepts (e.g., drug-disease links), and ignores critical contexts like experimental settings (e.g., a specific patient population where a drug is evaluated) and background motivations (e.g., to find drugs without specific side effects). We address these limitations with a novel formulation of contextualized-LBD (C-LBD): generating scientific hypotheses in natural language, while grounding them in a context that controls the hypothesis search space. We present a modeling framework using retrieval of ``inspirations'' from past scientific papers. Our evaluations reveal that GPT-4 tends to generate ideas with overall low technical depth and novelty, while our inspiration prompting approaches partially mitigate this issue. Our work represents a first step toward building language models that generate new ideas derived from scientific literature.

Predicting how different interventions will causally affect a specific individual is important in a variety of domains such as personalized medicine, public policy, and online marketing. There are a large number of methods to predict the effect of an existing intervention based on historical data from individuals who received it. However, in many settings it is important to predict the effects of novel interventions (e.g., a newly invented drug), which these methods do not address. Here, we consider zero-shot causal learning: predicting the personalized effects of a novel intervention. We propose CaML, a causal meta-learning framework which formulates the personalized prediction of each intervention's effect as a task. CaML trains a single meta-model across thousands of tasks, each constructed by sampling an intervention, along with its recipients and nonrecipients. By leveraging both intervention information (e.g., a drug's attributes) and individual features~(e.g., a patient's history), CaML is able to predict the personalized effects of novel interventions that do not exist at the time of training. Experimental results on real world datasets in large-scale medical claims and cell-line perturbations demonstrate the effectiveness of our approach. Most strikingly, CaML's zero-shot predictions outperform even strong baselines trained directly on data from the test interventions.

Mediation analysis learns the causal effect transmitted via mediator variables between treatments and outcomes and receives increasing attention in various scientific domains to elucidate causal relations. Most existing works focus on point-exposure studies where each subject only receives one treatment at a single time point. However, there are a number of applications (e.g., mobile health) where the treatments are sequentially assigned over time and the dynamic mediation effects are of primary interest. Proposing a reinforcement learning (RL) framework, we are the first to evaluate dynamic mediation effects in settings with infinite horizons. We decompose the average treatment effect into an immediate direct effect, an immediate mediation effect, a delayed direct effect, and a delayed mediation effect. Upon the identification of each effect component, we further develop robust and semi-parametrically efficient estimators under the RL framework to infer these causal effects. The superior performance of the proposed method is demonstrated through extensive numerical studies, theoretical results, and an analysis of a mobile health dataset.

We present a generic framework for creating differentially private versions of any hypothesis test in a black-box way. We analyze the resulting tests analytically and experimentally. Most crucially, we show good practical performance for small data sets, showing that at epsilon = 1 we only need 5-6 times as much data as in the fully public setting. We compare our work to the one existing framework of this type, as well as to several individually-designed private hypothesis tests. Our framework is higher power than other generic solutions and at least competitive with (and often better than) individually-designed tests.

This work derives methods for performing nonparametric, nonasymptotic statistical inference for population means under the constraint of local differential privacy (LDP). Given bounded observations (X_1, dots, X_n) with mean mu^star that are privatized into (Z_1, dots, Z_n), we present confidence intervals (CI) and time-uniform confidence sequences (CS) for mu^star when only given access to the privatized data. To achieve this, we introduce a nonparametric and sequentially interactive generalization of Warner's famous ``randomized response'' mechanism, satisfying LDP for arbitrary bounded random variables, and then provide CIs and CSs for their means given access to the resulting privatized observations. For example, our results yield private analogues of Hoeffding's inequality in both fixed-time and time-uniform regimes. We extend these Hoeffding-type CSs to capture time-varying (non-stationary) means, and conclude by illustrating how these methods can be used to conduct private online A/B tests.

Given the dominance of dense retrievers that do not generalize well beyond their training dataset distributions, domain-specific test sets are essential in evaluating retrieval. There are few test datasets for retrieval systems intended for use by healthcare providers in a point-of-care setting. To fill this gap we have collaborated with medical professionals to create CURE, an ad-hoc retrieval test dataset for passage ranking with 2000 queries spanning 10 medical domains with a monolingual (English) and two cross-lingual (French/Spanish -> English) conditions. In this paper, we describe how CURE was constructed and provide baseline results to showcase its effectiveness as an evaluation tool. CURE is published with a Creative Commons Attribution Non Commercial 4.0 license and can be accessed on Hugging Face.

We study contextual combinatorial bandits with probabilistically triggered arms (C^2MAB-T) under a variety of smoothness conditions that capture a wide range of applications, such as contextual cascading bandits and contextual influence maximization bandits. Under the triggering probability modulated (TPM) condition, we devise the C^2-UCB-T algorithm and propose a novel analysis that achieves an O(dKT) regret bound, removing a potentially exponentially large factor O(1/p_{min}), where d is the dimension of contexts, p_{min} is the minimum positive probability that any arm can be triggered, and batch-size K is the maximum number of arms that can be triggered per round. Under the variance modulated (VM) or triggering probability and variance modulated (TPVM) conditions, we propose a new variance-adaptive algorithm VAC^2-UCB and derive a regret bound O(dT), which is independent of the batch-size K. As a valuable by-product, our analysis technique and variance-adaptive algorithm can be applied to the CMAB-T and C^2MAB setting, improving existing results there as well. We also include experiments that demonstrate the improved performance of our algorithms compared with benchmark algorithms on synthetic and real-world datasets.

Motivated by concerns about making online decisions that incur undue amount of risk at each time step, in this paper, we formulate the probably anytime-safe stochastic combinatorial semi-bandits problem. In this problem, the agent is given the option to select a subset of size at most K from a set of L ground items. Each item is associated to a certain mean reward as well as a variance that represents its risk. To mitigate the risk that the agent incurs, we require that with probability at least 1-delta, over the entire horizon of time T, each of the choices that the agent makes should contain items whose sum of variances does not exceed a certain variance budget. We call this probably anytime-safe constraint. Under this constraint, we design and analyze an algorithm {\sc PASCombUCB} that minimizes the regret over the horizon of time T. By developing accompanying information-theoretic lower bounds, we show that under both the problem-dependent and problem-independent paradigms, {\sc PASCombUCB} is almost asymptotically optimal. Experiments are conducted to corroborate our theoretical findings. Our problem setup, the proposed {\sc PASCombUCB} algorithm, and novel analyses are applicable to domains such as recommendation systems and transportation in which an agent is allowed to choose multiple items at a single time step and wishes to control the risk over the whole time horizon.

The automation of scientific discovery has been a long-standing goal within the research community, driven by the potential to accelerate knowledge creation. While significant progress has been made using commercial large language models (LLMs) as research assistants or idea generators, the possibility of automating the entire research process with open-source LLMs remains largely unexplored. This paper explores the feasibility of using open-source post-trained LLMs as autonomous agents capable of performing the full cycle of automated research and review, from literature review and manuscript preparation to peer review and paper revision. Our iterative preference training framework consists of CycleResearcher, which conducts research tasks, and CycleReviewer, which simulates the peer review process, providing iterative feedback via reinforcement learning. To train these models, we develop two new datasets, Review-5k and Research-14k, reflecting real-world machine learning research and peer review dynamics. Our results demonstrate that CycleReviewer achieves a 26.89\% improvement in mean absolute error (MAE) over individual human reviewers in predicting paper scores, indicating that LLMs can surpass expert-level performance in research evaluation. In research, the papers generated by the CycleResearcher model achieved a score of 5.36 in simulated peer reviews, surpassing the preprint level of 5.24 from human experts and approaching the accepted paper level of 5.69. This work represents a significant step toward fully automated scientific inquiry, providing ethical safeguards and advancing AI-driven research capabilities. The code, dataset and model weight are released at http://github/minjun-zhu/Researcher.

Conditional Average Treatment Effects (CATE) estimation is one of the main challenges in causal inference with observational data. In addition to Machine Learning based-models, nonparametric estimators called meta-learners have been developed to estimate the CATE with the main advantage of not restraining the estimation to a specific supervised learning method. This task becomes, however, more complicated when the treatment is not binary as some limitations of the naive extensions emerge. This paper looks into meta-learners for estimating the heterogeneous effects of multi-valued treatments. We consider different meta-learners, and we carry out a theoretical analysis of their error upper bounds as functions of important parameters such as the number of treatment levels, showing that the naive extensions do not always provide satisfactory results. We introduce and discuss meta-learners that perform well as the number of treatments increases. We empirically confirm the strengths and weaknesses of those methods with synthetic and semi-synthetic datasets.

In this work, we initiate the idea of using denoising diffusion models to learn priors for online decision making problems. Our special focus is on the meta-learning for bandit framework, with the goal of learning a strategy that performs well across bandit tasks of a same class. To this end, we train a diffusion model that learns the underlying task distribution and combine Thompson sampling with the learned prior to deal with new tasks at test time. Our posterior sampling algorithm is designed to carefully balance between the learned prior and the noisy observations that come from the learner's interaction with the environment. To capture realistic bandit scenarios, we also propose a novel diffusion model training procedure that trains even from incomplete and/or noisy data, which could be of independent interest. Finally, our extensive experimental evaluations clearly demonstrate the potential of the proposed approach.

We consider a resource-aware variant of the classical multi-armed bandit problem: In each round, the learner selects an arm and determines a resource limit. It then observes a corresponding (random) reward, provided the (random) amount of consumed resources remains below the limit. Otherwise, the observation is censored, i.e., no reward is obtained. For this problem setting, we introduce a measure of regret, which incorporates the actual amount of allocated resources of each learning round as well as the optimality of realizable rewards. Thus, to minimize regret, the learner needs to set a resource limit and choose an arm in such a way that the chance to realize a high reward within the predefined resource limit is high, while the resource limit itself should be kept as low as possible. We propose a UCB-inspired online learning algorithm, which we analyze theoretically in terms of its regret upper bound. In a simulation study, we show that our learning algorithm outperforms straightforward extensions of standard multi-armed bandit algorithms.

Medical systematic reviews can be very costly and resource intensive. We explore how Large Language Models (LLMs) can support and be trained to perform literature screening when provided with a detailed set of selection criteria. Specifically, we instruction tune LLaMA and Guanaco models to perform abstract screening for medical systematic reviews. Our best model, Bio-SIEVE, outperforms both ChatGPT and trained traditional approaches, and generalises better across medical domains. However, there remains the challenge of adapting the model to safety-first scenarios. We also explore the impact of multi-task training with Bio-SIEVE-Multi, including tasks such as PICO extraction and exclusion reasoning, but find that it is unable to match single-task Bio-SIEVE's performance. We see Bio-SIEVE as an important step towards specialising LLMs for the biomedical systematic review process and explore its future developmental opportunities. We release our models, code and a list of DOIs to reconstruct our dataset for reproducibility.

This study investigates GPT-4's assessment of its performance in healthcare applications. A simple prompting technique was used to prompt the LLM with questions taken from the United States Medical Licensing Examination (USMLE) questionnaire and it was tasked to evaluate its confidence score before posing the question and after asking the question. The questionnaire was categorized into two groups-questions with feedback (WF) and questions with no feedback(NF) post-question. The model was asked to provide absolute and relative confidence scores before and after each question. The experimental findings were analyzed using statistical tools to study the variability of confidence in WF and NF groups. Additionally, a sequential analysis was conducted to observe the performance variation for the WF and NF groups. Results indicate that feedback influences relative confidence but doesn't consistently increase or decrease it. Understanding the performance of LLM is paramount in exploring its utility in sensitive areas like healthcare. This study contributes to the ongoing discourse on the reliability of AI, particularly of LLMs like GPT-4, within healthcare, offering insights into how feedback mechanisms might be optimized to enhance AI-assisted medical education and decision support.

Epidemiologists often wish to estimate quantities that are easy to communicate and correspond to the results of realistic public health scenarios. Methods from causal inference can answer these questions. We adopt the language of potential outcomes under Rubin's original Bayesian framework and show that the parametric g-formula is easily amenable to a Bayesian approach. We show that the frequentist properties of the Bayesian g-formula suggest it improves the accuracy of estimates of causal effects in small samples or when data may be sparse. We demonstrate our approach to estimate the effect of environmental tobacco smoke on body mass index z-scores among children aged 4-9 years who were enrolled in a longitudinal birth cohort in New York, USA. We give a general algorithm and supply SAS and Stan code that can be adopted to implement our computational approach in both time-fixed and longitudinal data.

In recommender system or crowdsourcing applications of online learning, a human's preferences or abilities are often a function of the algorithm's recent actions. Motivated by this, a significant line of work has formalized settings where an action's loss is a function of the number of times that action was recently played in the prior m timesteps, where m corresponds to a bound on human memory capacity. To more faithfully capture decay of human memory with time, we introduce the Weighted Tallying Bandit (WTB), which generalizes this setting by requiring that an action's loss is a function of a weighted summation of the number of times that arm was played in the last m timesteps. This WTB setting is intractable without further assumption. So we study it under Repeated Exposure Optimality (REO), a condition motivated by the literature on human physiology, which requires the existence of an action that when repetitively played will eventually yield smaller loss than any other sequence of actions. We study the minimization of the complete policy regret (CPR), which is the strongest notion of regret, in WTB under REO. Since m is typically unknown, we assume we only have access to an upper bound M on m. We show that for problems with K actions and horizon T, a simple modification of the successive elimination algorithm has O left( KT + (m+M)K right) CPR. Interestingly, upto an additive (in lieu of mutliplicative) factor in (m+M)K, this recovers the classical guarantee for the simpler stochastic multi-armed bandit with traditional regret. We additionally show that in our setting, any algorithm will suffer additive CPR of Omega left( mK + M right), demonstrating our result is nearly optimal. Our algorithm is computationally efficient, and we experimentally demonstrate its practicality and superiority over natural baselines.

With COVID-19 having emerged as the most widespread human pandemic disease in a century, the need to control its spread to avoid massive loss of life became more than necessary, and extremely fast. Several vaccines were developed and the task of policy makers was suddenly to convince the reluctant population to be vaccinated by various means. While some countries have chosen a policy of mandatory vaccination or punitive incentives, many states in the United States have adopted various incentives to try to increase vaccination coverage. A study we conducted in recent months quantified the effect of these measures on the proportion of the population vaccinated, using the synthetic control method, by simulating what would have happened without these measures. The aim now is to generalize this study to smaller scales, to improve the results of our previous study, to quantify their robustness and to provide a tool that can be used by policy makers to adapt their behavior in light of the results obtained.

We consider the problem of performing Bayesian inference in probabilistic models where observations are accompanied by uncertainty, referred to as "uncertain evidence." We explore how to interpret uncertain evidence, and by extension the importance of proper interpretation as it pertains to inference about latent variables. We consider a recently-proposed method "distributional evidence" as well as revisit two older methods: Jeffrey's rule and virtual evidence. We devise guidelines on how to account for uncertain evidence and we provide new insights, particularly regarding consistency. To showcase the impact of different interpretations of the same uncertain evidence, we carry out experiments in which one interpretation is defined as "correct." We then compare inference results from each different interpretation illustrating the importance of careful consideration of uncertain evidence.

In this report, we survey Bayesian Optimization methods focussed on the Multi-Armed Bandit Problem. We take the help of the paper "Portfolio Allocation for Bayesian Optimization". We report a small literature survey on the acquisition functions and the types of portfolio strategies used in papers discussing Bayesian Optimization. We also replicate the experiments and report our findings and compare them to the results in the paper. Code link: https://colab.research.google.com/drive/1GZ14klEDoe3dcBeZKo5l8qqrKf_GmBDn?usp=sharing#scrollTo=XgIBau3O45_V.

In their recent Nature Human Behaviour paper, "Emergent analogical reasoning in large language models," (Webb, Holyoak, and Lu, 2023) the authors argue that "large language models such as GPT-3 have acquired an emergent ability to find zero-shot solutions to a broad range of analogy problems." In this response, we provide counterexamples of the letter string analogies. In our tests, GPT-3 fails to solve even the easiest variants of the problems presented in the original paper. Zero-shot reasoning is an extraordinary claim that requires extraordinary evidence. We do not see that evidence in our experiments. To strengthen claims of humanlike reasoning such as zero-shot reasoning, it is important that the field develop approaches that rule out data memorization.

We test whether Large Language Models (LLMs) can be used to simulate human participants in social-science studies. To do this, we run replications of 14 studies from the Many Labs 2 replication project with OpenAI's text-davinci-003 model, colloquially known as GPT3.5. Based on our pre-registered analyses, we find that among the eight studies we could analyse, our GPT sample replicated 37.5% of the original results and 37.5% of the Many Labs 2 results. However, we were unable to analyse the remaining six studies due to an unexpected phenomenon we call the "correct answer" effect. Different runs of GPT3.5 answered nuanced questions probing political orientation, economic preference, judgement, and moral philosophy with zero or near-zero variation in responses: with the supposedly "correct answer." In one exploratory follow-up study, we found that a "correct answer" was robust to changing the demographic details that precede the prompt. In another, we found that most but not all "correct answers" were robust to changing the order of answer choices. One of our most striking findings occurred in our replication of the Moral Foundations Theory survey results, where we found GPT3.5 identifying as a political conservative in 99.6% of the cases, and as a liberal in 99.3% of the cases in the reverse-order condition. However, both self-reported 'GPT conservatives' and 'GPT liberals' showed right-leaning moral foundations. Our results cast doubts on the validity of using LLMs as a general replacement for human participants in the social sciences. Our results also raise concerns that a hypothetical AI-led future may be subject to a diminished diversity-of-thought.

Recent work has shown promising results in causal discovery by leveraging interventional data with gradient-based methods, even when the intervened variables are unknown. However, previous work assumes that the correspondence between samples and interventions is known, which is often unrealistic. We envision a scenario with an extensive dataset sampled from multiple intervention distributions and one observation distribution, but where we do not know which distribution originated each sample and how the intervention affected the system, i.e., interventions are entirely latent. We propose a method based on neural networks and variational inference that addresses this scenario by framing it as learning a shared causal graph among an infinite mixture (under a Dirichlet process prior) of intervention structural causal models. Experiments with synthetic and real data show that our approach and its semi-supervised variant are able to discover causal relations in this challenging scenario.

We study a distributed stochastic multi-armed bandit where a client supplies the learner with communication-constrained feedback based on the rewards for the corresponding arm pulls. In our setup, the client must encode the rewards such that the second moment of the encoded rewards is no more than P, and this encoded reward is further corrupted by additive Gaussian noise of variance sigma^2; the learner only has access to this corrupted reward. For this setting, we derive an information-theoretic lower bound of Omegaleft(frac{KT{SNR wedge1}} right) on the minimax regret of any scheme, where SNR := P{sigma^2}, and K and T are the number of arms and time horizon, respectively. Furthermore, we propose a multi-phase bandit algorithm, UEtext{-UCB++}, which matches this lower bound to a minor additive factor. UEtext{-UCB++} performs uniform exploration in its initial phases and then utilizes the {\em upper confidence bound }(UCB) bandit algorithm in its final phase. An interesting feature of UEtext{-UCB++} is that the coarser estimates of the mean rewards formed during a uniform exploration phase help to refine the encoding protocol in the next phase, leading to more accurate mean estimates of the rewards in the subsequent phase. This positive reinforcement cycle is critical to reducing the number of uniform exploration rounds and closely matching our lower bound.

Most bandit algorithms assume that the reward variances or their upper bounds are known, and that they are the same for all arms. This naturally leads to suboptimal performance and higher regret due to variance overestimation. On the other hand, underestimated reward variances may lead to linear regret due to committing early to a suboptimal arm. This motivated prior works on variance-adaptive frequentist algorithms, which have strong instance-dependent regret bounds but cannot incorporate prior knowledge on reward variances. We lay foundations for the Bayesian setting, which incorporates prior knowledge. This results in lower regret in practice, due to using the prior in the algorithm design, and also improved regret guarantees. Specifically, we study Gaussian bandits with {unknown heterogeneous reward variances}, and develop a Thompson sampling algorithm with prior-dependent Bayes regret bounds. We achieve lower regret with lower reward variances and more informative priors on them, which is precisely why we pay only for what is uncertain. This is the first result of its kind. Finally, we corroborate our theory with extensive experiments, which show the superiority of our variance-adaptive Bayesian algorithm over prior frequentist approaches. We also show that our approach is robust to model misspecification and can be applied with estimated priors.

Scientific experimentation, a cornerstone of human progress, demands rigor in reliability, methodical control, and interpretability to yield meaningful results. Despite the growing capabilities of large language models (LLMs) in automating different aspects of the scientific process, automating rigorous experimentation remains a significant challenge. To address this gap, we propose Curie, an AI agent framework designed to embed rigor into the experimentation process through three key components: an intra-agent rigor module to enhance reliability, an inter-agent rigor module to maintain methodical control, and an experiment knowledge module to enhance interpretability. To evaluate Curie, we design a novel experimental benchmark composed of 46 questions across four computer science domains, derived from influential research papers, and widely adopted open-source projects. Compared to the strongest baseline tested, we achieve a 3.4times improvement in correctly answering experimental questions.Curie is open-sourced at https://github.com/Just-Curieous/Curie.

While the evaluation of explanations is an important step towards trustworthy models, it needs to be done carefully, and the employed metrics need to be well-understood. Specifically model randomization testing is often overestimated and regarded as a sole criterion for selecting or discarding certain explanation methods. To address shortcomings of this test, we start by observing an experimental gap in the ranking of explanation methods between randomization-based sanity checks [1] and model output faithfulness measures (e.g. [25]). We identify limitations of model-randomization-based sanity checks for the purpose of evaluating explanations. Firstly, we show that uninformative attribution maps created with zero pixel-wise covariance easily achieve high scores in this type of checks. Secondly, we show that top-down model randomization preserves scales of forward pass activations with high probability. That is, channels with large activations have a high probility to contribute strongly to the output, even after randomization of the network on top of them. Hence, explanations after randomization can only be expected to differ to a certain extent. This explains the observed experimental gap. In summary, these results demonstrate the inadequacy of model-randomization-based sanity checks as a criterion to rank attribution methods.

We introduce a new type of test, called a Turing Experiment (TE), for evaluating how well a language model, such as GPT-3, can simulate different aspects of human behavior. Unlike the Turing Test, which involves simulating a single arbitrary individual, a TE requires simulating a representative sample of participants in human subject research. We give TEs that attempt to replicate well-established findings in prior studies. We design a methodology for simulating TEs and illustrate its use to compare how well different language models are able to reproduce classic economic, psycholinguistic, and social psychology experiments: Ultimatum Game, Garden Path Sentences, Milgram Shock Experiment, and Wisdom of Crowds. In the first three TEs, the existing findings were replicated using recent models, while the last TE reveals a "hyper-accuracy distortion" present in some language models.

We consider the stochastic linear contextual bandit problem with high-dimensional features. We analyze the Thompson sampling algorithm using special classes of sparsity-inducing priors (e.g., spike-and-slab) to model the unknown parameter and provide a nearly optimal upper bound on the expected cumulative regret. To the best of our knowledge, this is the first work that provides theoretical guarantees of Thompson sampling in high-dimensional and sparse contextual bandits. For faster computation, we use variational inference instead of Markov Chain Monte Carlo (MCMC) to approximate the posterior distribution. Extensive simulations demonstrate the improved performance of our proposed algorithm over existing ones.

Objective: The reading level of health educational materials significantly influences the understandability and accessibility of the information, particularly for minoritized populations. Many patient educational resources surpass the reading level and complexity of widely accepted standards. There is a critical need for high-performing text simplification models in health information to enhance dissemination and literacy. This need is particularly acute in cancer education, where effective prevention and screening education can substantially reduce morbidity and mortality. Methods: We introduce Simplified Digestive Cancer (SimpleDC), a parallel corpus of cancer education materials tailored for health text simplification research, comprising educational content from the American Cancer Society, Centers for Disease Control and Prevention, and National Cancer Institute. Utilizing SimpleDC alongside the existing Med-EASi corpus, we explore Large Language Model (LLM)-based simplification methods, including fine-tuning, reinforcement learning (RL), reinforcement learning with human feedback (RLHF), domain adaptation, and prompt-based approaches. Our experimentation encompasses Llama 2 and GPT-4. A novel RLHF reward function is introduced, featuring a lightweight model adept at distinguishing between original and simplified texts, thereby enhancing the model's effectiveness with unlabeled data. Results: Fine-tuned Llama 2 models demonstrated high performance across various metrics. Our innovative RLHF reward function surpassed existing RL text simplification reward functions in effectiveness. The results underscore that RL/RLHF can augment fine-tuning, facilitating model training on unlabeled text and improving performance.

We propose a novel hierarchical Bayesian model for learning with a large (possibly infinite) number of tasks/episodes, which suits well the few-shot meta learning problem. We consider episode-wise random variables to model episode-specific target generative processes, where these local random variables are governed by a higher-level global random variate. The global variable helps memorize the important information from historic episodes while controlling how much the model needs to be adapted to new episodes in a principled Bayesian manner. Within our model framework, the prediction on a novel episode/task can be seen as a Bayesian inference problem. However, a main obstacle in learning with a large/infinite number of local random variables in online nature, is that one is not allowed to store the posterior distribution of the current local random variable for frequent future updates, typical in conventional variational inference. We need to be able to treat each local variable as a one-time iterate in the optimization. We propose a Normal-Inverse-Wishart model, for which we show that this one-time iterate optimization becomes feasible due to the approximate closed-form solutions for the local posterior distributions. The resulting algorithm is more attractive than the MAML in that it is not required to maintain computational graphs for the whole gradient optimization steps per episode. Our approach is also different from existing Bayesian meta learning methods in that unlike dealing with a single random variable for the whole episodes, our approach has a hierarchical structure that allows one-time episodic optimization, desirable for principled Bayesian learning with many/infinite tasks. The code is available at https://github.com/minyoungkim21/niwmeta.

To generate evidence regarding the safety and efficacy of artificial intelligence (AI) enabled medical devices, AI models need to be evaluated on a diverse population of patient cases, some of which may not be readily available. We propose an evaluation approach for testing medical imaging AI models that relies on in silico imaging pipelines in which stochastic digital models of human anatomy (in object space) with and without pathology are imaged using a digital replica imaging acquisition system to generate realistic synthetic image datasets. Here, we release M-SYNTH, a dataset of cohorts with four breast fibroglandular density distributions imaged at different exposure levels using Monte Carlo x-ray simulations with the publicly available Virtual Imaging Clinical Trial for Regulatory Evaluation (VICTRE) toolkit. We utilize the synthetic dataset to analyze AI model performance and find that model performance decreases with increasing breast density and increases with higher mass density, as expected. As exposure levels decrease, AI model performance drops with the highest performance achieved at exposure levels lower than the nominal recommended dose for the breast type.

In causal inference, estimating heterogeneous treatment effects (HTE) is critical for identifying how different subgroups respond to interventions, with broad applications in fields such as precision medicine and personalized advertising. Although HTE estimation methods aim to improve accuracy, how to provide explicit subgroup descriptions remains unclear, hindering data interpretation and strategic intervention management. In this paper, we propose CURLS, a novel rule learning method leveraging HTE, which can effectively describe subgroups with significant treatment effects. Specifically, we frame causal rule learning as a discrete optimization problem, finely balancing treatment effect with variance and considering the rule interpretability. We design an iterative procedure based on the minorize-maximization algorithm and solve a submodular lower bound as an approximation for the original. Quantitative experiments and qualitative case studies verify that compared with state-of-the-art methods, CURLS can find subgroups where the estimated and true effects are 16.1% and 13.8% higher and the variance is 12.0% smaller, while maintaining similar or better estimation accuracy and rule interpretability. Code is available at https://osf.io/zwp2k/.

We study the problem of designing mechanisms for information acquisition scenarios. This setting models strategic interactions between an uniformed receiver and a set of informed senders. In our model the senders receive information about the underlying state of nature and communicate their observation (either truthfully or not) to the receiver, which, based on this information, selects an action. Our goal is to design mechanisms maximizing the receiver's utility while incentivizing the senders to report truthfully their information. First, we provide an algorithm that efficiently computes an optimal incentive compatible (IC) mechanism. Then, we focus on the online problem in which the receiver sequentially interacts in an unknown game, with the objective of minimizing the cumulative regret w.r.t. the optimal IC mechanism, and the cumulative violation of the incentive compatibility constraints. We investigate two different online scenarios, i.e., the full and bandit feedback settings. For the full feedback problem, we propose an algorithm that guarantees mathcal O(sqrt T) regret and violation, while for the bandit feedback setting we present an algorithm that attains mathcal O(T^{alpha}) regret and mathcal O(T^{1-alpha/2}) violation for any alphain[1/2, 1]. Finally, we complement our results providing a tight lower bound.

The approval success rate of drug candidates is very low with the majority of failure due to safety and efficacy. Increasingly available high dimensional information on targets, drug molecules and indications provides an opportunity for ML methods to integrate multiple data modalities and better predict clinically promising drug targets. Notably, drug targets with human genetics evidence are shown to have better odds to succeed. However, a recent tensor factorization-based approach found that additional information on targets and indications might not necessarily improve the predictive accuracy. Here we revisit this approach by integrating different types of human genetics evidence collated from publicly available sources to support each target-indication pair. We use Bayesian tensor factorization to show that models incorporating all available human genetics evidence (rare disease, gene burden, common disease) modestly improves the clinical outcome prediction over models using single line of genetics evidence. We provide additional insight into the relative predictive power of different types of human genetics evidence for predicting the success of clinical outcomes.

Combination therapies have become the standard of care for diseases such as cancer, tuberculosis, malaria and HIV. However, the combinatorial set of available multi-drug treatments creates a challenge in identifying effective combination therapies available in a situation. To assist medical professionals in identifying beneficial drug-combinations, we construct an expert-annotated dataset for extracting information about the efficacy of drug combinations from the scientific literature. Beyond its practical utility, the dataset also presents a unique NLP challenge, as the first relation extraction dataset consisting of variable-length relations. Furthermore, the relations in this dataset predominantly require language understanding beyond the sentence level, adding to the challenge of this task. We provide a promising baseline model and identify clear areas for further improvement. We release our dataset, code, and baseline models publicly to encourage the NLP community to participate in this task.

The third ML4H symposium was held in person on December 10, 2023, in New Orleans, Louisiana, USA. The symposium included research roundtable sessions to foster discussions between participants and senior researchers on timely and relevant topics for the ML4H community. Encouraged by the successful virtual roundtables in the previous year, we organized eleven in-person roundtables and four virtual roundtables at ML4H 2022. The organization of the research roundtables at the conference involved 17 Senior Chairs and 19 Junior Chairs across 11 tables. Each roundtable session included invited senior chairs (with substantial experience in the field), junior chairs (responsible for facilitating the discussion), and attendees from diverse backgrounds with interest in the session's topic. Herein we detail the organization process and compile takeaways from these roundtable discussions, including recent advances, applications, and open challenges for each topic. We conclude with a summary and lessons learned across all roundtables. This document serves as a comprehensive review paper, summarizing the recent advancements in machine learning for healthcare as contributed by foremost researchers in the field.

The increased capabilities of generative AI have dramatically expanded its possible use cases in medicine. We provide a comprehensive overview of generative AI use cases for clinicians, patients, clinical trial organizers, researchers, and trainees. We then discuss the many challenges -- including maintaining privacy and security, improving transparency and interpretability, upholding equity, and rigorously evaluating models -- which must be overcome to realize this potential, and the open research directions they give rise to.

Instrumental variable methods have been widely used to identify causal effects in the presence of unmeasured confounding. A key identification condition known as the exclusion restriction states that the instrument cannot have a direct effect on the outcome which is not mediated by the exposure in view. In the health and social sciences, such an assumption is often not credible. To address this concern, we consider identification conditions of the population average treatment effect with an invalid instrumental variable which does not satisfy the exclusion restriction, and derive the efficient influence function targeting the identifying functional under a nonparametric observed data model. We propose a novel multiply robust locally efficient estimator of the average treatment effect that is consistent in the union of multiple parametric nuisance models, as well as a multiply debiased machine learning estimator for which the nuisance parameters are estimated using generic machine learning methods, that effectively exploit various forms of linear or nonlinear structured sparsity in the nuisance parameter space. When one cannot be confident that any of these machine learners is consistent at sufficiently fast rates to ensure n-consistency for the average treatment effect, we introduce a new criteria for selective machine learning which leverages the multiple robustness property in order to ensure small bias. The proposed methods are illustrated through extensive simulations and a data analysis evaluating the causal effect of 401(k) participation on savings.

We investigate the extent to which offline demonstration data can improve online learning. It is natural to expect some improvement, but the question is how, and by how much? We show that the degree of improvement must depend on the quality of the demonstration data. To generate portable insights, we focus on Thompson sampling (TS) applied to a multi-armed bandit as a prototypical online learning algorithm and model. The demonstration data is generated by an expert with a given competence level, a notion we introduce. We propose an informed TS algorithm that utilizes the demonstration data in a coherent way through Bayes' rule and derive a prior-dependent Bayesian regret bound. This offers insight into how pretraining can greatly improve online performance and how the degree of improvement increases with the expert's competence level. We also develop a practical, approximate informed TS algorithm through Bayesian bootstrapping and show substantial empirical regret reduction through experiments.

Observational studies require adjustment for confounding factors that are correlated with both the treatment and outcome. In the setting where the observed variables are tabular quantities such as average income in a neighborhood, tools have been developed for addressing such confounding. However, in many parts of the developing world, features about local communities may be scarce. In this context, satellite imagery can play an important role, serving as a proxy for the confounding variables otherwise unobserved. In this paper, we study confounder adjustment in this non-tabular setting, where patterns or objects found in satellite images contribute to the confounder bias. Using the evaluation of anti-poverty aid programs in Africa as our running example, we formalize the challenge of performing causal adjustment with such unstructured data -- what conditions are sufficient to identify causal effects, how to perform estimation, and how to quantify the ways in which certain aspects of the unstructured image object are most predictive of the treatment decision. Via simulation, we also explore the sensitivity of satellite image-based observational inference to image resolution and to misspecification of the image-associated confounder. Finally, we apply these tools in estimating the effect of anti-poverty interventions in African communities from satellite imagery.

Weighting methods in causal inference have been widely used to achieve a desirable level of covariate balancing. However, the existing weighting methods have desirable theoretical properties only when a certain model, either the propensity score or outcome regression model, is correctly specified. In addition, the corresponding estimators do not behave well for finite samples due to large variance even when the model is correctly specified. In this paper, we consider to use the integral probability metric (IPM), which is a metric between two probability measures, for covariate balancing. Optimal weights are determined so that weighted empirical distributions for the treated and control groups have the smallest IPM value for a given set of discriminators. We prove that the corresponding estimator can be consistent without correctly specifying any model (neither the propensity score nor the outcome regression model). In addition, we empirically show that our proposed method outperforms existing weighting methods with large margins for finite samples.

Large-language models have recently demonstrated impressive zero-shot capabilities in a variety of natural language tasks such as summarization, dialogue generation, and question-answering. Despite many promising applications in clinical medicine, adoption of these models in real-world settings has been largely limited by their tendency to generate incorrect and sometimes even toxic statements. In this study, we develop Almanac, a large language model framework augmented with retrieval capabilities for medical guideline and treatment recommendations. Performance on a novel dataset of clinical scenarios (n = 130) evaluated by a panel of 5 board-certified and resident physicians demonstrates significant increases in factuality (mean of 18% at p-value < 0.05) across all specialties, with improvements in completeness and safety. Our results demonstrate the potential for large language models to be effective tools in the clinical decision-making process, while also emphasizing the importance of careful testing and deployment to mitigate their shortcomings.

Commonsense causality reasoning (CCR) aims at identifying plausible causes and effects in natural language descriptions that are deemed reasonable by an average person. Although being of great academic and practical interest, this problem is still shadowed by the lack of a well-posed theoretical framework; existing work usually relies on deep language models wholeheartedly, and is potentially susceptible to confounding co-occurrences. Motivated by classical causal principles, we articulate the central question of CCR and draw parallels between human subjects in observational studies and natural languages to adopt CCR to the potential-outcomes framework, which is the first such attempt for commonsense tasks. We propose a novel framework, ROCK, to Reason O(A)bout Commonsense K(C)ausality, which utilizes temporal signals as incidental supervision, and balances confounding effects using temporal propensities that are analogous to propensity scores. The ROCK implementation is modular and zero-shot, and demonstrates good CCR capabilities.

Simple regret is a natural and parameter-free performance criterion for pure exploration in multi-armed bandits yet is less popular than the probability of missing the best arm or an epsilon-good arm, perhaps due to lack of easy ways to characterize it. In this paper, we make significant progress on minimizing simple regret in both data-rich (Tge n) and data-poor regime (T le n) where n is the number of arms, and T is the number of samples. At its heart is our improved instance-dependent analysis of the well-known Sequential Halving (SH) algorithm, where we bound the probability of returning an arm whose mean reward is not within epsilon from the best (i.e., not epsilon-good) for any choice of epsilon>0, although epsilon is not an input to SH. Our bound not only leads to an optimal worst-case simple regret bound of n/T up to logarithmic factors but also essentially matches the instance-dependent lower bound for returning an epsilon-good arm reported by Katz-Samuels and Jamieson (2020). For the more challenging data-poor regime, we propose Bracketing SH (BSH) that enjoys the same improvement even without sampling each arm at least once. Our empirical study shows that BSH outperforms existing methods on real-world tasks.

We propose a new test to measure a text model's multitask accuracy. The test covers 57 tasks including elementary mathematics, US history, computer science, law, and more. To attain high accuracy on this test, models must possess extensive world knowledge and problem solving ability. We find that while most recent models have near random-chance accuracy, the very largest GPT-3 model improves over random chance by almost 20 percentage points on average. However, on every one of the 57 tasks, the best models still need substantial improvements before they can reach expert-level accuracy. Models also have lopsided performance and frequently do not know when they are wrong. Worse, they still have near-random accuracy on some socially important subjects such as morality and law. By comprehensively evaluating the breadth and depth of a model's academic and professional understanding, our test can be used to analyze models across many tasks and to identify important shortcomings.

A prominent challenge of offline reinforcement learning (RL) is the issue of hidden confounding: unobserved variables may influence both the actions taken by the agent and the observed outcomes. Hidden confounding can compromise the validity of any causal conclusion drawn from data and presents a major obstacle to effective offline RL. In the present paper, we tackle the problem of hidden confounding in the nonidentifiable setting. We propose a definition of uncertainty due to hidden confounding bias, termed delphic uncertainty, which uses variation over world models compatible with the observations, and differentiate it from the well-known epistemic and aleatoric uncertainties. We derive a practical method for estimating the three types of uncertainties, and construct a pessimistic offline RL algorithm to account for them. Our method does not assume identifiability of the unobserved confounders, and attempts to reduce the amount of confounding bias. We demonstrate through extensive experiments and ablations the efficacy of our approach on a sepsis management benchmark, as well as on electronic health records. Our results suggest that nonidentifiable hidden confounding bias can be mitigated to improve offline RL solutions in practice.

Large language models (LLMs) hold great promise in summarizing medical evidence. Most recent studies focus on the application of proprietary LLMs. Using proprietary LLMs introduces multiple risk factors, including a lack of transparency and vendor dependency. While open-source LLMs allow better transparency and customization, their performance falls short compared to proprietary ones. In this study, we investigated to what extent fine-tuning open-source LLMs can further improve their performance in summarizing medical evidence. Utilizing a benchmark dataset, MedReview, consisting of 8,161 pairs of systematic reviews and summaries, we fine-tuned three broadly-used, open-sourced LLMs, namely PRIMERA, LongT5, and Llama-2. Overall, the fine-tuned LLMs obtained an increase of 9.89 in ROUGE-L (95% confidence interval: 8.94-10.81), 13.21 in METEOR score (95% confidence interval: 12.05-14.37), and 15.82 in CHRF score (95% confidence interval: 13.89-16.44). The performance of fine-tuned LongT5 is close to GPT-3.5 with zero-shot settings. Furthermore, smaller fine-tuned models sometimes even demonstrated superior performance compared to larger zero-shot models. The above trends of improvement were also manifested in both human and GPT4-simulated evaluations. Our results can be applied to guide model selection for tasks demanding particular domain knowledge, such as medical evidence summarization.

With the introduction of ChatGPT, Large Language Models (LLMs) have received enormous attention in healthcare. Despite their potential benefits, researchers have underscored various ethical implications. While individual instances have drawn much attention, the debate lacks a systematic overview of practical applications currently researched and ethical issues connected to them. Against this background, this work aims to map the ethical landscape surrounding the current stage of deployment of LLMs in medicine and healthcare. Electronic databases and preprint servers were queried using a comprehensive search strategy. Studies were screened and extracted following a modified rapid review approach. Methodological quality was assessed using a hybrid approach. For 53 records, a meta-aggregative synthesis was performed. Four fields of applications emerged and testify to a vivid exploration phase. Advantages of using LLMs are attributed to their capacity in data analysis, personalized information provisioning, support in decision-making, mitigating information loss and enhancing information accessibility. However, we also identifies recurrent ethical concerns connected to fairness, bias, non-maleficence, transparency, and privacy. A distinctive concern is the tendency to produce harmful misinformation or convincingly but inaccurate content. A recurrent plea for ethical guidance and human oversight is evident. Given the variety of use cases, it is suggested that the ethical guidance debate be reframed to focus on defining what constitutes acceptable human oversight across the spectrum of applications. This involves considering diverse settings, varying potentials for harm, and different acceptable thresholds for performance and certainty in healthcare. In addition, a critical inquiry is necessary to determine the extent to which the current experimental use of LLMs is necessary and justified.

In the pharmaceutical industry, the use of artificial intelligence (AI) has seen consistent growth over the past decade. This rise is attributed to major advancements in statistical machine learning methodologies, computational capabilities and the increased availability of large datasets. AI techniques are applied throughout different stages of drug development, ranging from drug discovery to post-marketing benefit-risk assessment. Kolluri et al. provided a review of several case studies that span these stages, featuring key applications such as protein structure prediction, success probability estimation, subgroup identification, and AI-assisted clinical trial monitoring. From a regulatory standpoint, there was a notable uptick in submissions incorporating AI components in 2021. The most prevalent therapeutic areas leveraging AI were oncology (27%), psychiatry (15%), gastroenterology (12%), and neurology (11%). The paradigm of personalized or precision medicine has gained significant traction in recent research, partly due to advancements in AI techniques hamburg2010path. This shift has had a transformative impact on the pharmaceutical industry. Departing from the traditional "one-size-fits-all" model, personalized medicine incorporates various individual factors, such as environmental conditions, lifestyle choices, and health histories, to formulate customized treatment plans. By utilizing sophisticated machine learning algorithms, clinicians and researchers are better equipped to make informed decisions in areas such as disease prevention, diagnosis, and treatment selection, thereby optimizing health outcomes for each individual.

In this paper, the causal bandit problem is investigated, in which the objective is to select an optimal sequence of interventions on nodes in a causal graph. It is assumed that the graph is governed by linear structural equations; it is further assumed that both the causal topology and the distribution of interventions are unknown. By exploiting the causal relationships between the nodes whose signals contribute to the reward, interventions are optimized. First, based on the difference between the two types of graph identification errors (false positives and negatives), a causal graph learning method is proposed, which strongly reduces sample complexity relative to the prior art by learning sub-graphs. Under the assumption of Gaussian exogenous inputs and minimum-mean squared error weight estimation, a new uncertainty bound tailored to the causal bandit problem is derived. This uncertainty bound drives an upper confidence bound based intervention selection to optimize the reward. To cope with non-stationary bandits, a sub-graph change detection mechanism is proposed, with high sample efficiency. Numerical results compare the new methodology to existing schemes and show a substantial performance improvement in both stationary and non-stationary settings. Compared to existing approaches, the proposed scheme takes 67% fewer samples to learn the causal structure and achieves an average reward gain of 85%.

Despite the potential of Large Language Models (LLMs) in medicine, they may generate responses lacking supporting evidence or based on hallucinated evidence. While Retrieval Augment Generation (RAG) is popular to address this issue, few studies implemented and evaluated RAG in downstream domain-specific applications. We developed a RAG pipeline with 70,000 ophthalmology-specific documents that retrieve relevant documents to augment LLMs during inference time. In a case study on long-form consumer health questions, we systematically evaluated the responses including over 500 references of LLMs with and without RAG on 100 questions with 10 healthcare professionals. The evaluation focuses on factuality of evidence, selection and ranking of evidence, attribution of evidence, and answer accuracy and completeness. LLMs without RAG provided 252 references in total. Of which, 45.3% hallucinated, 34.1% consisted of minor errors, and 20.6% were correct. In contrast, LLMs with RAG significantly improved accuracy (54.5% being correct) and reduced error rates (18.8% with minor hallucinations and 26.7% with errors). 62.5% of the top 10 documents retrieved by RAG were selected as the top references in the LLM response, with an average ranking of 4.9. The use of RAG also improved evidence attribution (increasing from 1.85 to 2.49 on a 5-point scale, P<0.001), albeit with slight decreases in accuracy (from 3.52 to 3.23, P=0.03) and completeness (from 3.47 to 3.27, P=0.17). The results demonstrate that LLMs frequently exhibited hallucinated and erroneous evidence in the responses, raising concerns for downstream applications in the medical domain. RAG substantially reduced the proportion of such evidence but encountered challenges.

Recovering causal relationships from data is an important problem. Using observational data, one can typically only recover causal graphs up to a Markov equivalence class and additional assumptions or interventional data are needed for complete recovery. In this work, under some standard assumptions, we study causal graph discovery via adaptive interventions with node-dependent interventional costs. For this setting, we show that no algorithm can achieve an approximation guarantee that is asymptotically better than linear in the number of vertices with respect to the verification number; a well-established benchmark for adaptive search algorithms. Motivated by this negative result, we define a new benchmark that captures the worst-case interventional cost for any search algorithm. Furthermore, with respect to this new benchmark, we provide adaptive search algorithms that achieve logarithmic approximations under various settings: atomic, bounded size interventions and generalized cost objectives.

Chest X-Ray (CXR) report generation is a promising approach to improving the efficiency of CXR interpretation. However, a significant increase in diagnostic accuracy is required before that can be realised. Motivated by this, we propose a framework that is more inline with a radiologist's workflow by considering longitudinal data. Here, the decoder is additionally conditioned on the report from the subject's previous imaging study via a prompt. We also propose a new reward for reinforcement learning based on CXR-BERT, which computes the similarity between reports. We conduct experiments on the MIMIC-CXR dataset. The results indicate that longitudinal data improves CXR report generation. CXR-BERT is also shown to be a promising alternative to the current state-of-the-art reward based on RadGraph. This investigation indicates that longitudinal CXR report generation can offer a substantial increase in diagnostic accuracy. Our Hugging Face model is available at: https://huggingface.co/aehrc/cxrmate and code is available at: https://github.com/aehrc/cxrmate.

As machine learning and algorithmic decision making systems are increasingly being leveraged in high-stakes human-in-the-loop settings, there is a pressing need to understand the rationale of their predictions. Researchers have responded to this need with explainable AI (XAI), but often proclaim interpretability axiomatically without evaluation. When these systems are evaluated, they are often tested through offline simulations with proxy metrics of interpretability (such as model complexity). We empirically evaluate the veracity of three common interpretability assumptions through a large scale human-subjects experiment with a simple "placebo explanation" control. We find that feature attribution explanations provide marginal utility in our task for a human decision maker and in certain cases result in worse decisions due to cognitive and contextual confounders. This result challenges the assumed universal benefit of applying these methods and we hope this work will underscore the importance of human evaluation in XAI research. Supplemental materials -- including anonymized data from the experiment, code to replicate the study, an interactive demo of the experiment, and the models used in the analysis -- can be found at: https://doi.pizza/challenging-xai.

Extracting causal relationships from observed correlations is a growing area in probabilistic reasoning, originating with the seminal work of Pearl and others from the early 1990s. This paper develops a new, categorically oriented view based on a clear distinction between syntax (string diagrams) and semantics (stochastic matrices), connected via interpretations as structure-preserving functors. A key notion in the identification of causal effects is that of an intervention, whereby a variable is forcefully set to a particular value independent of any prior propensities. We represent the effect of such an intervention as an endofunctor which performs `string diagram surgery' within the syntactic category of string diagrams. This diagram surgery in turn yields a new, interventional distribution via the interpretation functor. While in general there is no way to compute interventional distributions purely from observed data, we show that this is possible in certain special cases using a calculational tool called comb disintegration. We demonstrate the use of this technique on a well-known toy example, where we predict the causal effect of smoking on cancer in the presence of a confounding common cause. After developing this specific example, we show this technique provides simple sufficient conditions for computing interventions which apply to a wide variety of situations considered in the causal inference literature.

Background: Rapid advancements in natural language processing have led to the development of large language models with the potential to revolutionize mental health care. These models have shown promise in assisting clinicians and providing support to individuals experiencing various psychological challenges. Objective: This study aims to compare the performance of two large language models, GPT-4 and Chat-GPT, in responding to a set of 18 psychological prompts, to assess their potential applicability in mental health care settings. Methods: A blind methodology was employed, with a clinical psychologist evaluating the models' responses without knowledge of their origins. The prompts encompassed a diverse range of mental health topics, including depression, anxiety, and trauma, to ensure a comprehensive assessment. Results: The results demonstrated a significant difference in performance between the two models (p > 0.05). GPT-4 achieved an average rating of 8.29 out of 10, while Chat-GPT received an average rating of 6.52. The clinical psychologist's evaluation suggested that GPT-4 was more effective at generating clinically relevant and empathetic responses, thereby providing better support and guidance to potential users. Conclusions: This study contributes to the growing body of literature on the applicability of large language models in mental health care settings. The findings underscore the importance of continued research and development in the field to optimize these models for clinical use. Further investigation is necessary to understand the specific factors underlying the performance differences between the two models and to explore their generalizability across various populations and mental health conditions.

Alzheimer's disease (AD) is a degenerative brain disease impairing a person's ability to perform day to day activities. The clinical manifestations of Alzheimer's disease are characterized by heterogeneity in age, disease span, progression rate, impairment of memory and cognitive abilities. Due to these variabilities, personalized care and treatment planning, as well as patient counseling about their individual progression is limited. Recent developments in machine learning to detect hidden patterns in complex, multi-dimensional datasets provides significant opportunities to address this critical need. In this work, we use unsupervised and supervised machine learning approaches for subtype identification and prediction. We apply machine learning methods to the extensive clinical observations available at the Alzheimer's Disease Neuroimaging Initiative (ADNI) data set to identify patient subtypes and to predict disease progression. Our analysis depicts the progression space for the Alzheimer's disease into low, moderate and high disease progression zones. The proposed work will enable early detection and characterization of distinct disease subtypes based on clinical heterogeneity. We anticipate that our models will enable patient counseling, clinical trial design, and ultimately individualized clinical care.

There is a practically unlimited amount of natural language data available. Still, recent work in text comprehension has focused on datasets which are small relative to current computing possibilities. This article is making a case for the community to move to larger data and as a step in that direction it is proposing the BookTest, a new dataset similar to the popular Children's Book Test (CBT), however more than 60 times larger. We show that training on the new data improves the accuracy of our Attention-Sum Reader model on the original CBT test data by a much larger margin than many recent attempts to improve the model architecture. On one version of the dataset our ensemble even exceeds the human baseline provided by Facebook. We then show in our own human study that there is still space for further improvement.

Inspired by the principle of deliberate practice in human learning, we propose Deliberate Practice for Synthetic Data Generation (DP), a novel framework that improves sample efficiency through dynamic synthetic data generation. Prior work has shown that scaling synthetic data is inherently challenging, as naively adding new data leads to diminishing returns. To address this, pruning has been identified as a key mechanism for improving scaling, enabling models to focus on the most informative synthetic samples. Rather than generating a large dataset and pruning it afterward, DP efficiently approximates the direct generation of informative samples. We theoretically show how training on challenging, informative examples improves scaling laws and empirically validate that DP achieves better scaling performance with significantly fewer training samples and iterations. On ImageNet-100, DP generates 3.4x fewer samples and requires six times fewer iterations, while on ImageNet-1k, it generates 8x fewer samples with a 30 percent reduction in iterations, all while achieving superior performance compared to prior work.

We study a strategic variant of the multi-armed bandit problem, which we coin the strategic click-bandit. This model is motivated by applications in online recommendation where the choice of recommended items depends on both the click-through rates and the post-click rewards. Like in classical bandits, rewards follow a fixed unknown distribution. However, we assume that the click-rate of each arm is chosen strategically by the arm (e.g., a host on Airbnb) in order to maximize the number of times it gets clicked. The algorithm designer does not know the post-click rewards nor the arms' actions (i.e., strategically chosen click-rates) in advance, and must learn both values over time. To solve this problem, we design an incentive-aware learning algorithm, UCB-S, which achieves two goals simultaneously: (a) incentivizing desirable arm behavior under uncertainty; (b) minimizing regret by learning unknown parameters. We characterize all approximate Nash equilibria among arms under UCB-S and show a mathcal{O} (KT) regret bound uniformly in every equilibrium. We also show that incentive-unaware algorithms generally fail to achieve low regret in the strategic click-bandit. Finally, we support our theoretical results by simulations of strategic arm behavior which confirm the effectiveness and robustness of our proposed incentive design.

In the stochastic multi-armed bandit problem, a randomized probability matching policy called Thompson sampling (TS) has shown excellent performance in various reward models. In addition to the empirical performance, TS has been shown to achieve asymptotic problem-dependent lower bounds in several models. However, its optimality has been mainly addressed under light-tailed or one-parameter models that belong to exponential families. In this paper, we consider the optimality of TS for the Pareto model that has a heavy tail and is parameterized by two unknown parameters. Specifically, we discuss the optimality of TS with probability matching priors that include the Jeffreys prior and the reference priors. We first prove that TS with certain probability matching priors can achieve the optimal regret bound. Then, we show the suboptimality of TS with other priors, including the Jeffreys and the reference priors. Nevertheless, we find that TS with the Jeffreys and reference priors can achieve the asymptotic lower bound if one uses a truncation procedure. These results suggest carefully choosing noninformative priors to avoid suboptimality and show the effectiveness of truncation procedures in TS-based policies.

Previous works on Treatment Effect Estimation (TEE) are not in widespread use because they are predominantly theoretical, where strong parametric assumptions are made but untractable for practical application. Recent work uses multilayer perceptron (MLP) for modeling casual relationships, however, MLPs lag far behind recent advances in ML methodology, which limits their applicability and generalizability. To extend beyond the single domain formulation and towards more realistic learning scenarios, we explore model design spaces beyond MLPs, i.e., transformer backbones, which provide flexibility where attention layers govern interactions among treatments and covariates to exploit structural similarities of potential outcomes for confounding control. Through careful model design, Transformers as Treatment Effect Estimators (TransTEE) is proposed. We show empirically that TransTEE can: (1) serve as a general purpose treatment effect estimator that significantly outperforms competitive baselines in a variety of challenging TEE problems (e.g., discrete, continuous, structured, or dosage-associated treatments) and is applicable to both when covariates are tabular and when they consist of structural data (e.g., texts, graphs); (2) yield multiple advantages: compatibility with propensity score modeling, parameter efficiency, robustness to continuous treatment value distribution shifts, explainable in covariate adjustment, and real-world utility in auditing pre-trained language models

Researchers are usually interested in examining the impact of covariates when separating heterogeneous samples into latent classes that are more homogeneous. The majority of theoretical and empirical studies with such aims have focused on identifying covariates as predictors of class membership in the structural equation modeling framework. In other words, the covariates only indirectly affect the sample heterogeneity. However, the covariates' influence on between-individual differences can also be direct. This article presents a mixture model that investigates covariates to explain within-cluster and between-cluster heterogeneity simultaneously, known as a mixture-of-experts (MoE) model. This study aims to extend the MoE framework to investigate heterogeneity in nonlinear trajectories: to identify latent classes, covariates as predictors to clusters, and covariates that explain within-cluster differences in change patterns over time. Our simulation studies demonstrate that the proposed model generally estimates the parameters unbiasedly, precisely and exhibits appropriate empirical coverage for a nominal 95% confidence interval. This study also proposes implementing structural equation model forests to shrink the covariate space of the proposed mixture model. We illustrate how to select covariates and construct the proposed model with longitudinal mathematics achievement data. Additionally, we demonstrate that the proposed mixture model can be further extended in the structural equation modeling framework by allowing the covariates that have direct effects to be time-varying.

To assess the effectiveness of any medical intervention, researchers must conduct a time-intensive and highly manual literature review. NLP systems can help to automate or assist in parts of this expensive process. In support of this goal, we release MS^2 (Multi-Document Summarization of Medical Studies), a dataset of over 470k documents and 20k summaries derived from the scientific literature. This dataset facilitates the development of systems that can assess and aggregate contradictory evidence across multiple studies, and is the first large-scale, publicly available multi-document summarization dataset in the biomedical domain. We experiment with a summarization system based on BART, with promising early results. We formulate our summarization inputs and targets in both free text and structured forms and modify a recently proposed metric to assess the quality of our system's generated summaries. Data and models are available at https://github.com/allenai/ms2

The online knapsack problem is a classic problem in the field of online algorithms. Its canonical version asks how to pack items of different values and weights arriving online into a capacity-limited knapsack so as to maximize the total value of the admitted items. Although optimal competitive algorithms are known for this problem, they may be fundamentally unfair, i.e., individual items may be treated inequitably in different ways. Inspired by recent attention to fairness in online settings, we develop a natural and practically-relevant notion of time fairness for the online knapsack problem, and show that the existing optimal algorithms perform poorly under this metric. We propose a parameterized deterministic algorithm where the parameter precisely captures the Pareto-optimal trade-off between fairness and competitiveness. We show that randomization is theoretically powerful enough to be simultaneously competitive and fair; however, it does not work well in practice, using trace-driven experiments. To further improve the trade-off between fairness and competitiveness, we develop a fair, robust (competitive), and consistent learning-augmented algorithm with substantial performance improvement in trace-driven experiments.

Personalized treatment effect estimates are often of interest in high-stakes applications -- thus, before deploying a model estimating such effects in practice, one needs to be sure that the best candidate from the ever-growing machine learning toolbox for this task was chosen. Unfortunately, due to the absence of counterfactual information in practice, it is usually not possible to rely on standard validation metrics for doing so, leading to a well-known model selection dilemma in the treatment effect estimation literature. While some solutions have recently been investigated, systematic understanding of the strengths and weaknesses of different model selection criteria is still lacking. In this paper, instead of attempting to declare a global `winner', we therefore empirically investigate success- and failure modes of different selection criteria. We highlight that there is a complex interplay between selection strategies, candidate estimators and the data used for comparing them, and provide interesting insights into the relative (dis)advantages of different criteria alongside desiderata for the design of further illuminating empirical studies in this context.

Advances in large language models (LLMs) have empowered a variety of applications. However, there is still a significant gap in research when it comes to understanding and enhancing the capabilities of LLMs in the field of mental health. In this work, we present the first comprehensive evaluation of multiple LLMs, including Alpaca, Alpaca-LoRA, FLAN-T5, GPT-3.5, and GPT-4, on various mental health prediction tasks via online text data. We conduct a broad range of experiments, covering zero-shot prompting, few-shot prompting, and instruction fine-tuning. The results indicate a promising yet limited performance of LLMs with zero-shot and few-shot prompt designs for the mental health tasks. More importantly, our experiments show that instruction finetuning can significantly boost the performance of LLMs for all tasks simultaneously. Our best-finetuned models, Mental-Alpaca and Mental-FLAN-T5, outperform the best prompt design of GPT-3.5 (25 and 15 times bigger) by 10.9% on balanced accuracy and the best of GPT-4 (250 and 150 times bigger) by 4.8%. They further perform on par with the state-of-the-art task-specific language model. We also conduct an exploratory case study on LLMs' capability on the mental health reasoning tasks, illustrating the promising capability of certain models such as GPT-4. We summarize our findings into a set of action guidelines for potential methods to enhance LLMs' capability for mental health tasks. Meanwhile, we also emphasize the important limitations before achieving deployability in real-world mental health settings, such as known racial and gender bias. We highlight the important ethical risks accompanying this line of research.

Beam search is the default decoding strategy for many sequence generation tasks in NLP. The set of approximate K-best items returned by the algorithm is a useful summary of the distribution for many applications; however, the candidates typically exhibit high overlap and may give a highly biased estimate for expectations under our model. These problems can be addressed by instead using stochastic decoding strategies. In this work, we propose a new method for turning beam search into a stochastic process: Conditional Poisson stochastic beam search. Rather than taking the maximizing set at each iteration, we sample K candidates without replacement according to the conditional Poisson sampling design. We view this as a more natural alternative to Kool et. al. 2019's stochastic beam search (SBS). Furthermore, we show how samples generated under the CPSBS design can be used to build consistent estimators and sample diverse sets from sequence models. In our experiments, we observe CPSBS produces lower variance and more efficient estimators than SBS, even showing improvements in high entropy settings.

The rapid growth of biomedical knowledge has outpaced our ability to efficiently extract insights and generate novel hypotheses. Large language models (LLMs) have emerged as a promising tool to revolutionize knowledge interaction and potentially accelerate biomedical discovery. In this paper, we present a comprehensive evaluation of LLMs as biomedical hypothesis generators. We construct a dataset of background-hypothesis pairs from biomedical literature, carefully partitioned into training, seen, and unseen test sets based on publication date to mitigate data contamination. Using this dataset, we assess the hypothesis generation capabilities of top-tier instructed models in zero-shot, few-shot, and fine-tuning settings. To enhance the exploration of uncertainty, a crucial aspect of scientific discovery, we incorporate tool use and multi-agent interactions in our evaluation framework. Furthermore, we propose four novel metrics grounded in extensive literature review to evaluate the quality of generated hypotheses, considering both LLM-based and human assessments. Our experiments yield two key findings: 1) LLMs can generate novel and validated hypotheses, even when tested on literature unseen during training, and 2) Increasing uncertainty through multi-agent interactions and tool use can facilitate diverse candidate generation and improve zero-shot hypothesis generation performance. However, we also observe that the integration of additional knowledge through few-shot learning and tool use may not always lead to performance gains, highlighting the need for careful consideration of the type and scope of external knowledge incorporated. These findings underscore the potential of LLMs as powerful aids in biomedical hypothesis generation and provide valuable insights to guide further research in this area.

We consider a combinatorial multi-armed bandit problem for maximum value reward function under maximum value and index feedback. This is a new feedback structure that lies in between commonly studied semi-bandit and full-bandit feedback structures. We propose an algorithm and provide a regret bound for problem instances with stochastic arm outcomes according to arbitrary distributions with finite supports. The regret analysis rests on considering an extended set of arms, associated with values and probabilities of arm outcomes, and applying a smoothness condition. Our algorithm achieves a O((k/Delta)log(T)) distribution-dependent and a O(T) distribution-independent regret where k is the number of arms selected in each round, Delta is a distribution-dependent reward gap and T is the horizon time. Perhaps surprisingly, the regret bound is comparable to previously-known bound under more informative semi-bandit feedback. We demonstrate the effectiveness of our algorithm through experimental results.

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

We introduce a gradient-based approach for the problem of Bayesian optimal experimental design to learn causal models in a batch setting -- a critical component for causal discovery from finite data where interventions can be costly or risky. Existing methods rely on greedy approximations to construct a batch of experiments while using black-box methods to optimize over a single target-state pair to intervene with. In this work, we completely dispose of the black-box optimization techniques and greedy heuristics and instead propose a conceptually simple end-to-end gradient-based optimization procedure to acquire a set of optimal intervention target-state pairs. Such a procedure enables parameterization of the design space to efficiently optimize over a batch of multi-target-state interventions, a setting which has hitherto not been explored due to its complexity. We demonstrate that our proposed method outperforms baselines and existing acquisition strategies in both single-target and multi-target settings across a number of synthetic datasets.

In this work we propose a blackbox intervention method for visual dialog models, with the aim of assessing the contribution of individual linguistic or visual components. Concretely, we conduct structured or randomized interventions that aim to impair an individual component of the model, and observe changes in task performance. We reproduce a state-of-the-art visual dialog model and demonstrate that our methodology yields surprising insights, namely that both dialog and image information have minimal contributions to task performance. The intervention method presented here can be applied as a sanity check for the strength and robustness of each component in visual dialog systems.

In this work, we study the issue of reward hacking on the response length, a challenge emerging in Reinforcement Learning from Human Feedback (RLHF) on LLMs. A well-formatted, verbose but less helpful response from the LLMs can often deceive LLMs or even human evaluators to achieve high scores. The same issue also holds for some reward models in RL. To address the challenges in both training and evaluation, we establish a more reliable evaluation protocol for comparing different training configurations, which inspects the trade-off between LLM evaluation score and response length obtained by varying training hyperparameters. Based on this evaluation, we conduct large-scale studies, where the results shed insights into the efficacy of hyperparameters and tricks used in RL on mitigating length bias. We further propose to improve the reward model by jointly training two linear heads on shared feature representations to predict the rewards, one trained to correlate with length, and the other trained to decorrelate with length and therefore focus more on the actual content. We then discard the length head in RL to prevent reward hacking on length. Experiments demonstrate that our approach almost eliminates the reward correlation with length, and improves the obtained policy by a significant margin.