Relation extraction (RE) is a well-known NLP application often treated as a sentence or document-level task. However, a handful of recent efforts explore it across documents or in the cross-document setting (CrossDocRE). This is distinct from the single document case because different documents often focus on disparate themes, while text within a document tends to have a single goal.Current CrossDocRE efforts do not consider domain knowledge, which are often assumed to be known to the reader when documents are authored. Here, we propose a novel approach, KXDocRE, that embed domain knowledge of entities with input text for cross-document RE. Our proposed framework has three main benefits over baselines: 1) it incorporates domain knowledge of entities along with documents’ text; 2) it offers interpretability by producing explanatory text for predicted relations between entities 3) it improves performance over the prior methods. Code and models are available at https://github.com/kracr/cross-doc-relation-extraction.

We describe the methods and results of our submission to the 9th Social Media Mining for Health Research and Applications (SMM4H) 2024 shared tasks 4 and 5. Task 4 involved extracting the clinical and social impacts of non-medical substance use and task 5 focused on the binary classification of tweets reporting children’s medical disorders. We employed encoder language models and their ensembles, achieving the top score on task 4 and a high score for task 5.

Information retrieval (IR) for precision medicine (PM) often involves looking for multiple pieces of evidence that characterize a patient case. This typically includes at least the name of a condition and a genetic variation that applies to the patient. Other factors such as demographic attributes, comorbidities, and social determinants may also be pertinent. As such, the retrieval problem is often formulated as ad hoc search but with multiple facets (e.g., disease, mutation) that may need to be incorporated. In this paper, we present a document reranking approach that combines neural query-document matching and text summarization toward such retrieval scenarios. Our architecture builds on the basic BERT model with three specific components for reranking: (a). document-query matching (b). keyword extraction and (c). facet-conditioned abstractive summarization. The outcomes of (b) and (c) are used to essentially transform a candidate document into a concise summary that can be compared with the query at hand to compute a relevance score. Component (a) directly generates a matching score of a candidate document for a query. The full architecture benefits from the complementary potential of document-query matching and the novel document transformation approach based on summarization along PM facets. Evaluations using NIST’s TREC-PM track datasets (2017–2019) show that our model achieves state-of-the-art performance. To foster reproducibility, our code is made available here: https://github.com/bionlproc/text-summ-for-doc-retrieval.

Coding EMRs with diagnosis and procedure codes is an indispensable task for billing, secondary data analyses, and monitoring health trends. Both speed and accuracy of coding are critical. While coding errors could lead to more patient-side financial burden and misinterpretation of a patient’s well-being, timely coding is also needed to avoid backlogs and additional costs for the healthcare facility. In this paper, we present a new neural network architecture that combines ideas from few-shot learning matching networks, multi-label loss functions, and convolutional neural networks for text classification to significantly outperform other state-of-the-art models. Our evaluations are conducted using a well known de-identified EMR dataset (MIMIC) with a variety of multi-label performance measures.

This paper describes the systems we developed for tasks A and B of the 2018 CLPsych shared task. The first task (task A) focuses on predicting behavioral health scores at age 11 using childhood essays. The second task (task B) asks participants to predict future psychological distress at ages 23, 33, 42, and 50 using the age 11 essays. We propose two convolutional neural network based methods that map each task to a regression problem. Among seven teams we ranked third on task A with disattenuated Pearson correlation (DPC) score of 0.5587. Likewise, we ranked third on task B with an average DPC score of 0.3062.

Large multi-label datasets contain labels that occur thousands of times (frequent group), those that occur only a few times (few-shot group), and labels that never appear in the training dataset (zero-shot group). Multi-label few- and zero-shot label prediction is mostly unexplored on datasets with large label spaces, especially for text classification. In this paper, we perform a fine-grained evaluation to understand how state-of-the-art methods perform on infrequent labels. Furthermore, we develop few- and zero-shot methods for multi-label text classification when there is a known structure over the label space, and evaluate them on two publicly available medical text datasets: MIMIC II and MIMIC III. For few-shot labels we achieve improvements of 6.2% and 4.8% in R@10 for MIMIC II and MIMIC III, respectively, over prior efforts; the corresponding R@10 improvements for zero-shot labels are 17.3% and 19%.