Clinical NLP research faces a scarcity of publicly available datasets due to privacy concerns. MIMIC-III marked a significant milestone, enabling substantial progress, and now, with MIMIC-IV, the dataset has expanded significantly, offering a broader scope. In this paper, we focus on the task of predicting clinical outcomes from clinical text. This is crucial in modern healthcare, aiding in preventive care, differential diagnosis, and capacity planning. We introduce a novel clinical outcome prediction dataset derived from MIMIC-IV. Furthermore, we provide initial insights into the performance of models trained on MIMIC-III when applied to our new dataset, with specific attention to potential data drift. We investigate challenges tied to evolving documentation standards and changing codes in the International Classification of Diseases (ICD) taxonomy, such as the transition from ICD-9 to ICD-10. We also explore variations in clinical text across different hospital wards. Our study aims to probe the robustness and generalization of clinical outcome prediction models, contributing to the ongoing advancement of clinical NLP in healthcare.

Differential diagnosis (DDx) is vital for physicians and challenging due to the existence of numerous diseases and their complex symptoms. Model training for this task is generally hindered by limited data access due to privacy concerns. To address this, we present DDxGym, a specialized OpenAI Gym environment for clinical differential diagnosis. DDxGym formulates DDx as a natural-language-based reinforcement learning (RL) problem, where agents emulate medical professionals, selecting examinations and treatments for patients with randomly sampled diseases. This RL environment utilizes data labeled from online resources, evaluated by medical professionals for accuracy. Transformers, while effective for encoding text in DDxGym, are unstable in online RL. For that reason we propose a novel training method using an auxiliary masked language modeling objective for policy optimization, resulting in model stabilization and significant performance improvement over strong baselines. Following this approach, our agent effectively navigates large action spaces and identifies universally applicable actions. All data, environment details, and implementation, including experiment reproduction code, are made publicly available.

The use of deep neural models for diagnosis prediction from clinical text has shown promising results. However, in clinical practice such models must not only be accurate, but provide doctors with interpretable and helpful results. We introduce ProtoPatient, a novel method based on prototypical networks and label-wise attention with both of these abilities. ProtoPatient makes predictions based on parts of the text that are similar to prototypical patients—providing justifications that doctors understand. We evaluate the model on two publicly available clinical datasets and show that it outperforms existing baselines. Quantitative and qualitative evaluations with medical doctors further demonstrate that the model provides valuable explanations for clinical decision support.

Clinical phenotyping enables the automatic extraction of clinical conditions from patient records, which can be beneficial to doctors and clinics worldwide. However, current state-of-the-art models are mostly applicable to clinical notes written in English. We therefore investigate cross-lingual knowledge transfer strategies to execute this task for clinics that do not use the English language and have a small amount of in-domain data available. Our results reveal two strategies that outperform the state-of-the-art: Translation-based methods in combination with domain-specific encoders and cross-lingual encoders plus adapters. We find that these strategies perform especially well for classifying rare phenotypes and we advise on which method to prefer in which situation. Our results show that using multilingual data overall improves clinical phenotyping models and can compensate for data sparseness.

Outcome prediction from clinical text can prevent doctors from overlooking possible risks and help hospitals to plan capacities. We simulate patients at admission time, when decision support can be especially valuable, and contribute a novel *admission to discharge* task with four common outcome prediction targets: Diagnoses at discharge, procedures performed, in-hospital mortality and length-of-stay prediction. The ideal system should infer outcomes based on symptoms, pre-conditions and risk factors of a patient. We evaluate the effectiveness of language models to handle this scenario and propose *clinical outcome pre-training* to integrate knowledge about patient outcomes from multiple public sources. We further present a simple method to incorporate ICD code hierarchy into the models. We show that our approach improves performance on the outcome tasks against several baselines. A detailed analysis reveals further strengths of the model, including transferability, but also weaknesses such as handling of vital values and inconsistencies in the underlying data.

In order to provide high-quality care, health professionals must efficiently identify the presence, possibility, or absence of symptoms, treatments and other relevant entities in free-text clinical notes. Such is the task of assertion detection - to identify the assertion class (present, possible, absent) of an entity based on textual cues in unstructured text. We evaluate state-of-the-art medical language models on the task and show that they outperform the baselines in all three classes. As transferability is especially important in the medical domain we further study how the best performing model behaves on unseen data from two other medical datasets. For this purpose we introduce a newly annotated set of 5,000 assertions for the publicly available MIMIC-III dataset. We conclude with an error analysis that reveals situations in which the models still go wrong and points towards future research directions.

Universal embeddings, such as BERT or ELMo, are useful for a broad set of natural language processing tasks like text classification or sentiment analysis. Moreover, specialized embeddings also exist for tasks like topic modeling or named entity disambiguation. We study if we can complement these universal embeddings with specialized embeddings. We conduct an in-depth evaluation of nine well known natural language understanding tasks with SentEval. Also, we extend SentEval with two additional tasks to the medical domain. We present PubMedSection, a novel topic classification dataset focussed on the biomedical domain. Our comprehensive analysis covers 11 tasks and combinations of six embeddings. We report that combined embeddings outperform state of the art universal embeddings without any embedding fine-tuning. We observe that adding topic model based embeddings helps for most tasks and that differing pre-training tasks encode complementary features. Moreover, we present new state of the art results on the MPQA and SUBJ tasks in SentEval.