Predicting phenotypes with complex genetic bases based on a small, interpretable set of variant features remains a challenging task. Conventionally, data-driven approaches are utilized for this task, yet the high dimensional nature of genotype data makes the analysis and prediction difficult. Motivated by the extensive knowledge encoded in pre-trained LLMs and their success in processing complex biomedical concepts, we set to examine the ability of LLMs in feature selection and engineering for tabular genotype data, with a novel knowledge-driven framework. We develop FREEFORM, Free-flow Reasoning and Ensembling for Enhanced Feature Output and Robust Modeling, designed with chain-of-thought and ensembling principles, to select and engineer features with the intrinsic knowledge of LLMs. Evaluated on two distinct genotype-phenotype datasets, genetic ancestry and hereditary hearing loss, we find this framework outperforms several data-driven methods, particularly on low-shot regimes. FREEFORM is available as open-source framework at GitHub: https://github.com/PennShenLab/FREEFORM.

Retrieval-Augmented Generation (RAG) has been shown to enhance the factual accuracy of Large Language Models (LLMs), but existing methods often suffer from limited reasoning capabilities in effectively using the retrieved evidence, particularly when using open-source LLMs. To mitigate this gap, we introduce a novel framework, Open-RAG, designed to enhance reasoning capabilities in RAG with open-source LLMs. Our framework transforms an arbitrary dense LLM into a parameter-efficient sparse mixture of experts (MoE) model capable of handling complex reasoning tasks, including both single- and multi-hop queries. Open-RAG uniquely trains the model to navigate challenging distractors that appear relevant but are misleading. As a result, Open-RAG leverages latent learning, dynamically selecting relevant experts and integrating external knowledge effectively for more accurate and contextually relevant responses. In addition, we propose a hybrid adaptive retrieval method to determine retrieval necessity and balance the trade-off between performance gain and inference speed. Experimental results show that the Llama2-7B-based Open-RAG outperforms state-of-the-art LLMs and RAG models such as ChatGPT, Self-RAG, and Command R+ in various knowledge-intensive tasks. We open-source our code and models at https://openragmoe.github.io/

Despite often being perceived as morally objectionable, stereotypes are a common feature of social groups, a phenomenon that has often been attributed to biased motivations or limits on the ability to process information. We argue that one reason for this continued prevalence is that pre-existing expectations about how others will behave, in the context of social coordination, can change the behaviors of one's social partners, creating the very stereotype one expected to see, even in the absence of other potential sources of stereotyping. We use a computational model of dynamic social coordination to illustrate how this "feedback loop" can emerge, engendering and entrenching stereotypic behavior, and then show that human behavior on the task generates a comparable feedback loop. Notably, people's choices on the task are not related to social dominance or system justification, suggesting biased motivations are not necessary to maintain these stereotypes.

We study the depth of grade-school math (GSM) problem-solving capabilities of LLMs. To this end, we evaluate their performance on pairs of existing math word problems together so that the answer to the second problem depends on correctly answering the first problem. Our findings reveal a significant reasoning gap in most LLMs, that is performance difference between solving the compositional pairs and solving each question independently. This gap is more pronounced in smaller, more cost-efficient, and math-specialized models. Moreover, instruction-tuning recipes and code generation have varying effects across LLM sizes, while finetuning on GSM can lead to task overfitting. Our analysis indicates that large reasoning gaps are not because of test-set leakage, but due to distraction from additional context and poor second-hop reasoning. Overall, LLMs exhibit systematic differences in their reasoning abilities, despite what their performance on standard benchmarks indicates.

Recently, retrieval-based language models (RLMs) have received much attention. However, most of them leverage a pre-trained retriever with fixed parameters, which may not adapt well to causal language models. In this work, we propose Grouped Cross-Attention, a novel module enabling joint pre-training of the retriever and causal LM, and apply it to long-context modeling. For a given input sequence, we split it into chunks and use the current chunk to retrieve past chunks for subsequent text generation. Our innovation allows the retriever to learn how to retrieve past chunks that better minimize the auto-regressive loss of subsequent tokens in an end-to-end manner. By integrating top-$k$ retrieval, our model can be pre-trained efficiently from scratch with context lengths up to 64K tokens. Our experiments show our model, compared with long-range LM baselines, can achieve lower perplexity with comparable or lower pre-training and inference costs.

In Query-driven Travel Recommender Systems (RSs), it is crucial to understand the user intent behind challenging natural language (NL) destination queries such as the broadly worded "youth-friendly activities" or the indirect description "a high school graduation trip". Such queries are challenging due to the wide scope and subtlety of potential user intents that confound the ability of retrieval methods to infer relevant destinations from available textual descriptions such as WikiVoyage. While query reformulation (QR) has proven effective in enhancing retrieval by addressing user intent, existing QR methods tend to focus only on expanding the range of potentially matching query subtopics (breadth) or elaborating on the potential meaning of a query (depth), but not both. In this paper, we introduce Elaborative Subtopic Query Reformulation (EQR), a large language model-based QR method that combines both breadth and depth by generating potential query subtopics with information-rich elaborations. We also release TravelDest, a novel dataset for query-driven travel destination RSs. Experiments on TravelDest show that EQR achieves significant improvements in recall and precision over existing state-of-the-art QR methods.

The widespread use of machine learning models in high-stakes domains can have a major negative impact, especially on individuals who receive undesirable outcomes. Algorithmic recourse provides such individuals with suggestions of minimum-cost improvements they can make to achieve a desirable outcome in the future. However, machine learning models often get updated over time and this can cause a recourse to become invalid (i.e., not lead to the desirable outcome). The robust recourse literature aims to choose recourses that are less sensitive, even against adversarial model changes, but this comes at a higher cost. To overcome this obstacle, we initiate the study of algorithmic recourse through the learning-augmented framework and evaluate the extent to which a designer equipped with a prediction regarding future model changes can reduce the cost of recourse when the prediction is accurate (consistency) while also limiting the cost even when the prediction is inaccurate (robustness). We propose a novel algorithm for this problem, study the robustness-consistency trade-off, and analyze how prediction accuracy affects performance.

Artificial intelligence (AI) and large language models (LLMs) in healthcare require advanced clinical skills (CS), yet current benchmarks fail to evaluate these comprehensively. We introduce MedQA-CS, an AI-SCE framework inspired by medical education's Objective Structured Clinical Examinations (OSCEs), to address this gap. MedQA-CS evaluates LLMs through two instruction-following tasks, LLM-as-medical-student and LLM-as-CS-examiner, designed to reflect real clinical scenarios. Our contributions include developing MedQA-CS, a comprehensive evaluation framework with publicly available data and expert annotations, and providing the quantitative and qualitative assessment of LLMs as reliable judges in CS evaluation. Our experiments show that MedQA-CS is a more challenging benchmark for evaluating clinical skills than traditional multiple-choice QA benchmarks (e.g., MedQA). Combined with existing benchmarks, MedQA-CS enables a more comprehensive evaluation of LLMs' clinical capabilities for both open- and closed-source LLMs.

Machine unlearning (MU) aims to remove the influence of particular data points from the learnable parameters of a trained machine learning model. This is a crucial capability in light of data privacy requirements, trustworthiness, and safety in deployed models. MU is particularly challenging for deep neural networks (DNNs), such as convolutional nets or vision transformers, as such DNNs tend to memorize a notable portion of their training dataset. Nevertheless, the community lacks a rigorous and multifaceted study that looks into the success of MU methods for DNNs. In this paper, we investigate 18 state-of-the-art MU methods across various benchmark datasets and models, with each evaluation conducted over 10 different initializations, a comprehensive evaluation involving MU over 100K models. We show that, with the proper hyperparameters, Masked Small Gradients (MSG) and Convolution Transpose (CT), consistently perform better in terms of model accuracy and run-time efficiency across different models, datasets, and initializations, assessed by population-based membership inference attacks (MIA) and per-sample unlearning likelihood ratio attacks (U-LiRA). Furthermore, our benchmark highlights the fact that comparing a MU method only with commonly used baselines, such as Gradient Ascent (GA) or Successive Random Relabeling (SRL), is inadequate, and we need better baselines like Negative Gradient Plus (NG+) with proper hyperparameter selection.

In medical settings, it is critical that all who are in need of care are correctly heard and understood. When this is not the case due to prejudices a listener has, the speaker is experiencing \emph{testimonial injustice}, which, building upon recent work, we quantify by the presence of several categories of unjust vocabulary in medical notes. In this paper, we use FCI, a causal discovery method, to study the degree to which certain demographic features could lead to marginalization (e.g., age, gender, and race) by way of contributing to testimonial injustice. To achieve this, we review physicians' notes for each patient, where we identify occurrences of unjust vocabulary, along with the demographic features present, and use causal discovery to build a Structural Causal Model (SCM) relating those demographic features to testimonial injustice. We analyze and discuss the resulting SCMs to show the interaction of these factors and how they influence the experience of injustice. Despite the potential presence of some confounding variables, we observe how one contributing feature can make a person more prone to experiencing another contributor of testimonial injustice. There is no single root of injustice and thus intersectionality cannot be ignored. These results call for considering more than singular or equalized attributes of who a person is when analyzing and improving their experiences of bias and injustice. This work is thus a first foray at using causal discovery to understand the nuanced experiences of patients in medical settings, and its insights could be used to guide design principles throughout healthcare, to build trust and promote better patient care.