Tom Hope


2022

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Literature-Augmented Clinical Outcome Prediction
Aakanksha Naik | Sravanthi Parasa | Sergey Feldman | Lucy Lu Wang | Tom Hope
Findings of the Association for Computational Linguistics: NAACL 2022

We present BEEP (Biomedical Evidence-Enhanced Predictions), a novel approach for clinical outcome prediction that retrieves patient-specific medical literature and incorporates it into predictive models. Based on each individual patient’s clinical notes, we train language models (LMs) to find relevant papers and fuse them with information from notes to predict outcomes such as in-hospital mortality. We develop methods to retrieve literature based on noisy, information-dense patient notes, and to augment existing outcome prediction models with retrieved papers in a manner that maximizes predictive accuracy. Our approach boosts predictive performance on three important clinical tasks in comparison to strong recent LM baselines, increasing F1 by up to 5 points and precision@Top-K by a large margin of over 25%.

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A Dataset for N-ary Relation Extraction of Drug Combinations
Aryeh Tiktinsky | Vijay Viswanathan | Danna Niezni | Dana Meron Azagury | Yosi Shamay | Hillel Taub-Tabib | Tom Hope | Yoav Goldberg
Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies

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 (https://huggingface.co/datasets/allenai/drug-combo-extraction), code (https://github.com/allenai/drug-combo-extraction) and baseline models (https://huggingface.co/allenai/drug-combo-classifier-pubmedbert-dapt) publicly to encourage the NLP community to participate in this task.

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Multi-Vector Models with Textual Guidance for Fine-Grained Scientific Document Similarity
Sheshera Mysore | Arman Cohan | Tom Hope
Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies

We present a new scientific document similarity model based on matching fine-grained aspects of texts. To train our model, we exploit a naturally-occurring source of supervision: sentences in the full-text of papers that cite multiple papers together (co-citations). Such co-citations not only reflect close paper relatedness, but also provide textual descriptions of how the co-cited papers are related. This novel form of textual supervision is used for learning to match aspects across papers. We develop multi-vector representations where vectors correspond to sentence-level aspects of documents, and present two methods for aspect matching: (1) A fast method that only matches single aspects, and (2) a method that makes sparse multiple matches with an Optimal Transport mechanism that computes an Earth Mover’s Distance between aspects. Our approach improves performance on document similarity tasks in four datasets. Further, our fast single-match method achieves competitive results, paving the way for applying fine-grained similarity to large scientific corpora.

2021

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Extracting a Knowledge Base of Mechanisms from COVID-19 Papers
Tom Hope | Aida Amini | David Wadden | Madeleine van Zuylen | Sravanthi Parasa | Eric Horvitz | Daniel Weld | Roy Schwartz | Hannaneh Hajishirzi
Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies

The COVID-19 pandemic has spawned a diverse body of scientific literature that is challenging to navigate, stimulating interest in automated tools to help find useful knowledge. We pursue the construction of a knowledge base (KB) of mechanisms—a fundamental concept across the sciences, which encompasses activities, functions and causal relations, ranging from cellular processes to economic impacts. We extract this information from the natural language of scientific papers by developing a broad, unified schema that strikes a balance between relevance and breadth. We annotate a dataset of mechanisms with our schema and train a model to extract mechanism relations from papers. Our experiments demonstrate the utility of our KB in supporting interdisciplinary scientific search over COVID-19 literature, outperforming the prominent PubMed search in a study with clinical experts. Our search engine, dataset and code are publicly available.

2020

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Language (Re)modelling: Towards Embodied Language Understanding
Ronen Tamari | Chen Shani | Tom Hope | Miriam R L Petruck | Omri Abend | Dafna Shahaf
Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics

While natural language understanding (NLU) is advancing rapidly, today’s technology differs from human-like language understanding in fundamental ways, notably in its inferior efficiency, interpretability, and generalization. This work proposes an approach to representation and learning based on the tenets of embodied cognitive linguistics (ECL). According to ECL, natural language is inherently executable (like programming languages), driven by mental simulation and metaphoric mappings over hierarchical compositions of structures and schemata learned through embodied interaction. This position paper argues that the use of grounding by metaphoric reasoning and simulation will greatly benefit NLU systems, and proposes a system architecture along with a roadmap towards realizing this vision.

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SciSight: Combining faceted navigation and research group detection for COVID-19 exploratory scientific search
Tom Hope | Jason Portenoy | Kishore Vasan | Jonathan Borchardt | Eric Horvitz | Daniel Weld | Marti Hearst | Jevin West
Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing: System Demonstrations

The COVID-19 pandemic has sparked unprecedented mobilization of scientists, generating a deluge of papers that makes it hard for researchers to keep track and explore new directions. Search engines are designed for targeted queries, not for discovery of connections across a corpus. In this paper, we present SciSight, a system for exploratory search of COVID-19 research integrating two key capabilities: first, exploring associations between biomedical facets automatically extracted from papers (e.g., genes, drugs, diseases, patient outcomes); second, combining textual and network information to search and visualize groups of researchers and their ties. SciSight has so far served over 15K users with over 42K page views and 13% returns.