In recent years, machine learning for clinical decision support has gained more and more attention. In order to introduce such applications into clinical practice, a good performance might be essential, however, the aspect of trust should not be underestimated. For the treating physician using such a system and being (legally) responsible for the decision made, it is particularly important to understand the system’s recommendation. To provide insights into a model’s decision, various techniques from the field of explainability (XAI) have been proposed whose output is often enough not targeted to the domain experts that want to use the model. To close this gap, in this work, we explore how explanations could possibly look like in future. To this end, this work presents a dataset of textual explanations in context of decision support. Within a reader study, human physicians estimated the likelihood of possible negative patient outcomes in the near future and justified each decision with a few sentences. Using those sentences, we created a novel corpus, annotated with different semantic layers. Moreover, we provide an analysis of how those explanations are constructed, and how they change depending on physician, on the estimated risk and also in comparison to an automatic clinical decision support system with feature importance.
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.
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 this work we present a fine-grained annotation schema to detect named entities in German clinical data of chronically ill patients with kidney diseases. The annotation schema is driven by the needs of our clinical partners and the linguistic aspects of German language. In order to generate annotations within a short period, the work also presents a semi-automatic annotation which uses additional sources of knowledge such as UMLS, to pre-annotate concepts in advance. The presented schema will be used to apply novel techniques from natural language processing and machine learning to support doctors treating their patients by improved information access from unstructured German texts.
An important subtask in clinical text mining tries to identify whether a clinical finding is expressed as present, absent or unsure in a text. This work presents a system for detecting mentions of clinical findings that are negated or just speculated. The system has been applied to two different types of German clinical texts: clinical notes and discharge summaries. Our approach is built on top of NegEx, a well known algorithm for identifying non-factive mentions of medical findings. In this work, we adjust a previous adaptation of NegEx to German and evaluate the system on our data to detect negation and speculation. The results are compared to a baseline algorithm and are analyzed for both types of clinical documents. Our system achieves an F1-Score above 0.9 on both types of reports.