BioDEX: Large-Scale Biomedical Adverse Drug Event Extraction for Real-World Pharmacovigilance

Timely and accurate extraction of Adverse Drug Events (ADE) from biomedical literature is paramount for public safety, but involves slow and costly manual labor. We set out to improve drug safety monitoring (pharmacovigilance, PV) through the use of Natural Language Processing (NLP). We introduce BioDEX, a large-scale resource for Biomedical adverse Drug Event Extraction, rooted in the historical output of drug safety reporting in the U.S. BioDEX consists of 65k abstracts and 19k full-text biomedical papers with 256k associated document-level safety reports created by medical experts. The core features of these reports include the reported weight, age, and biological sex of a patient, a set of drugs taken by the patient, the drug dosages, the reactions experienced, and whether the reaction was life threatening. In this work, we consider the task of predicting the core information of the report given its originating paper. We estimate human performance to be 72.0% F1, whereas our best model achieves 62.3% F1, indicating significant headroom on this task. We also begin to explore ways in which these models could help professional PV reviewers. Our code and data are available: https://github.com/KarelDO/BioDEX.

Interpretability at Scale: Identifying Causal Mechanisms in Alpaca

Obtaining human-interpretable explanations of large, general-purpose language models is an urgent goal for AI safety. However, it is just as important that our interpretability methods are faithful to the causal dynamics underlying model behavior and able to robustly generalize to unseen inputs. Distributed Alignment Search (DAS) is a powerful gradient descent method grounded in a theory of causal abstraction that uncovered perfect alignments between interpretable symbolic algorithms and small deep learning models fine-tuned for specific tasks. In the present paper, we scale DAS significantly by replacing the remaining brute-force search steps with learned parameters -- an approach we call DAS. This enables us to efficiently search for interpretable causal structure in large language models while they follow instructions. We apply DAS to the Alpaca model (7B parameters), which, off the shelf, solves a simple numerical reasoning problem. With DAS, we discover that Alpaca does this by implementing a causal model with two interpretable boolean variables. Furthermore, we find that the alignment of neural representations with these variables is robust to changes in inputs and instructions. These findings mark a first step toward deeply understanding the inner-workings of our largest and most widely deployed language models.

ReCOGS: How Incidental Details of a Logical Form Overshadow an Evaluation of Semantic Interpretation

Compositional generalization benchmarks seek to assess whether models can accurately compute meanings for novel sentences, but operationalize this in terms of logical form (LF) prediction. This raises the concern that semantically irrelevant details of the chosen LFs could shape model performance. We argue that this concern is realized for the COGS benchmark (Kim and Linzen, 2020). COGS poses generalization splits that appear impossible for present-day models, which could be taken as an indictment of those models. However, we show that the negative results trace to incidental features of COGS LFs. Converting these LFs to semantically equivalent ones and factoring out capabilities unrelated to semantic interpretation, we find that even baseline models get traction. A recent variable-free translation of COGS LFs suggests similar conclusions, but we observe this format is not semantically equivalent; it is incapable of accurately representing some COGS meanings. These findings inform our proposal for ReCOGS, a modified version of COGS that comes closer to assessing the target semantic capabilities while remaining very challenging. Overall, our results reaffirm the importance of compositional generalization and careful benchmark task design.

Finding Alignments Between Interpretable Causal Variables and Distributed Neural Representations

Causal abstraction is a promising theoretical framework for explainable artificial intelligence that defines when an interpretable high-level causal model is a faithful simplification of a low-level deep learning system. However, existing causal abstraction methods have two major limitations: they require a brute-force search over alignments between the high-level model and the low-level one, and they presuppose that variables in the high-level model will align with disjoint sets of neurons in the low-level one. In this paper, we present distributed alignment search (DAS), which overcomes these limitations. In DAS, we find the alignment between high-level and low-level models using gradient descent rather than conducting a brute-force search, and we allow individual neurons to play multiple distinct roles by analyzing representations in non-standard bases-distributed representations. Our experiments show that DAS can discover internal structure that prior approaches miss. Overall, DAS removes previous obstacles to conducting causal abstraction analyses and allows us to find conceptual structure in trained neural nets.

UDAPDR: Unsupervised Domain Adaptation via LLM Prompting and Distillation of Rerankers

Many information retrieval tasks require large labeled datasets for fine-tuning. However, such datasets are often unavailable, and their utility for real-world applications can diminish quickly due to domain shifts. To address this challenge, we develop and motivate a method for using large language models (LLMs) to generate large numbers of synthetic queries cheaply. The method begins by generating a small number of synthetic queries using an expensive LLM. After that, a much less expensive one is used to create large numbers of synthetic queries, which are used to fine-tune a family of reranker models. These rerankers are then distilled into a single efficient retriever for use in the target domain. We show that this technique boosts zero-shot accuracy in long-tail domains, even where only 2K synthetic queries are used for fine-tuning, and that it achieves substantially lower latency than standard reranking methods. We make our end-to-end approach, including our synthetic datasets and replication code, publicly available on Github.

Demonstrate-Search-Predict: Composing retrieval and language models for knowledge-intensive NLP

Retrieval-augmented in-context learning has emerged as a powerful approach for addressing knowledge-intensive tasks using frozen language models (LM) and retrieval models (RM). Existing work has combined these in simple "retrieve-then-read" pipelines in which the RM retrieves passages that are inserted into the LM prompt. To begin to fully realize the potential of frozen LMs and RMs, we propose Demonstrate-Search-Predict (DSP), a framework that relies on passing natural language texts in sophisticated pipelines between an LM and an RM. DSP can express high-level programs that bootstrap pipeline-aware demonstrations, search for relevant passages, and generate grounded predictions, systematically breaking down problems into small transformations that the LM and RM can handle more reliably. We have written novel DSP programs for answering questions in open-domain, multi-hop, and conversational settings, establishing in early evaluations new state-of-the-art in-context learning results and delivering 37-200%, 8-40%, and 80-290% relative gains against vanilla LMs, a standard retrieve-then-read pipeline, and a contemporaneous self-ask pipeline, respectively.

Detecting Contradictory COVID-19 Drug Efficacy Claims from Biomedical Literature

The COVID-19 pandemic created a deluge of questionable and contradictory scientific claims about drug efficacy -- an "infodemic" with lasting consequences for science and society. In this work, we argue that NLP models can help domain experts distill and understand the literature in this complex, high-stakes area. Our task is to automatically identify contradictory claims about COVID-19 drug efficacy. We frame this as a natural language inference problem and offer a new NLI dataset created by domain experts. The NLI framing allows us to create curricula combining existing datasets and our own. The resulting models are useful investigative tools. We provide a case study of how these models help a domain expert summarize and assess evidence concerning remdisivir and hydroxychloroquine.

Inducing Character-level Structure in Subword-based Language Models with Type-level Interchange Intervention Training

Language tasks involving character-level manipulations (e.g., spelling correction, many word games) are challenging for models based in subword tokenization. To address this, we adapt the interchange intervention training method of Geiger et al. (2021) to operate on type-level variables over characters. This allows us to encode robust, position-independent character-level information in the internal representations of subword-based models. We additionally introduce a suite of character-level tasks that systematically vary in their dependence on meaning and sequence-level context. While simple character-level tokenization approaches still perform best on purely form-based tasks like string reversal, our method is superior for more complex tasks that blend form, meaning, and context, such as spelling correction in context and word search games. Our approach also leads to subword-based models with human-intepretable internal representations of characters.

Moving Beyond Downstream Task Accuracy for Information Retrieval Benchmarking

Neural information retrieval (IR) systems have progressed rapidly in recent years, in large part due to the release of publicly available benchmarking tasks. Unfortunately, some dimensions of this progress are illusory: the majority of the popular IR benchmarks today focus exclusively on downstream task accuracy and thus conceal the costs incurred by systems that trade away efficiency for quality. Latency, hardware cost, and other efficiency considerations are paramount to the deployment of IR systems in user-facing settings. We propose that IR benchmarks structure their evaluation methodology to include not only metrics of accuracy, but also efficiency considerations such as a query latency and the corresponding cost budget for a reproducible hardware setting. For the popular IR benchmarks MS MARCO and XOR-TyDi, we show how the best choice of IR system varies according to how these efficiency considerations are chosen and weighed. We hope that future benchmarks will adopt these guidelines toward more holistic IR evaluation.

Systematicity in GPT-3's Interpretation of Novel English Noun Compounds

Levin et al. (2019) show experimentally that the interpretations of novel English noun compounds (e.g., stew skillet), while not fully compositional, are highly predictable based on whether the modifier and head refer to artifacts or natural kinds. Is the large language model GPT-3 governed by the same interpretive principles? To address this question, we first compare Levin et al.'s experimental data with GPT-3 generations, finding a high degree of similarity. However, this evidence is consistent with GPT3 reasoning only about specific lexical items rather than the more abstract conceptual categories of Levin et al.'s theory. To probe more deeply, we construct prompts that require the relevant kind of conceptual reasoning. Here, we fail to find convincing evidence that GPT-3 is reasoning about more than just individual lexical items. These results highlight the importance of controlling for low-level distributional regularities when assessing whether a large language model latently encodes a deeper theory.