The 2024 Shared Task on Chemotherapy Treatment Timeline Extraction aims to advance the state of the art of clinical event timeline extraction from the Electronic Health Records (EHRs). Specifically, this edition focuses on chemotherapy event timelines from EHRs of patients with breast, ovarian and skin cancers. These patient-level timelines present a novel challenge which involves tasks such as the extraction of relevant events, time expressions and temporal relations from each document and then summarizing over the documents. De-identified EHRs for 57,530 patients with breast and ovarian cancer spanning 2004-2020, and approximately 15,946 patients with melanoma spanning 2010-2020 were made available to participants after executing a Data Use Agreement. A subset of patients is annotated for gold entities, time expressions, temporal relations and patient-level timelines. The rest is considered unlabeled data. In Subtask1, gold chemotherapy event mentions and time expressions are provided (along with the EHR notes). Participants are asked to build the patient-level timelines using gold annotations as input. Thus, the subtask seeks to explore the topics of temporal relations extraction and timeline creation if event and time expression input is perfect. In Subtask2, which is the realistic real-world setting, only EHR notes are provided. Thus, the subtask aims at developing an end-to-end system for chemotherapy treatment timeline extraction from patient’s EHR notes. There were 18 submissions for Subtask 1 and 9 submissions for Subtask 2. The organizers provided a baseline system. The teams employed a variety of methods including Logistic Regression, TF-IDF, n-grams, transformer models, zero-shot prompting with Large Language Models (LLMs), and instruction tuning. The gap in performance between prompting LLMs and finetuning smaller-sized LMs indicates that for a challenging task such as patient-level chemotherapy timeline extraction, more sophisticated LLMs or prompting techniques are necessary in order to achieve optimal results as finetuing smaller-sized LMs outperforms by a wide margin.

In order to assist the drug discovery/development process, pharmaceutical companies often apply biomedical NER and linking techniques over internal and public corpora. Decades of study of the field of BioNLP has produced a plethora of algorithms, systems and datasets. However, our experience has been that no single open source system meets all the requirements of a modern pharmaceutical company. In this work, we describe these requirements according to our experience of the industry, and present Kazu, a highly extensible, scalable open source framework designed to support BioNLP for the pharmaceutical sector. Kazu is a built around a computationally efficient version of the BERN2 NER model (TinyBERN2), and subsequently wraps several other BioNLP technologies into one coherent system.

This paper describes our system developed for the Social Media Mining for Health (SMM4H) 2022 SocialDisNER task. We used several types of pre-trained language models, which are trained on Spanish biomedical literature or Spanish Tweets. We showed the difference in performance depending on the quality of the tokenization as well as introducing silver standard annotations when training the model. Our model obtained a strict F1 of 80.3% on the test set, which is an improvement of +12.8% F1 (24.6 std) over the average results across all submissions to the SocialDisNER challenge.

The recent outbreak of the novel coronavirus is wreaking havoc on the world and researchers are struggling to effectively combat it. One reason why the fight is difficult is due to the lack of information and knowledge. In this work, we outline our effort to contribute to shrinking this knowledge vacuum by creating covidAsk, a question answering (QA) system that combines biomedical text mining and QA techniques to provide answers to questions in real-time. Our system also leverages information retrieval (IR) approaches to provide entity-level answers that are complementary to QA models. Evaluation of covidAsk is carried out by using a manually created dataset called COVID-19 Questions which is based on information from various sources, including the CDC and the WHO. We hope our system will be able to aid researchers in their search for knowledge and information not only for COVID-19, but for future pandemics as well.