Itay Laish
Itay Laish is a SWE in Israel's Google Research group, focusing on understanding of medical notes.
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LLMs Accelerate Annotation for Medical Information Extraction
Akshay Goel
Almog Gueta
Omry Gilon
Chang Liu
Xiaohong Hao
Bolous Jaber
Shashir Reddy
Rupesh Kartha
Jean Steiner
Machine Learning for Health (ML4H), PMLR (2023)
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The unstructured nature of clinical notes within electronic health records often conceals vital patient-related information, making it challenging to access or interpret. To uncover this hidden information, specialized Natural Language Processing (NLP) models are required. However, training these models necessitates large amounts of labeled data, a process that is both time-consuming and costly when relying solely on human experts for annotation. In this paper, we propose an approach that combines Large Language Models (LLMs) with human expertise to create an efficient method for generating ground truth labels for medical text annotation. By utilizing LLMs in conjunction with human annotators, we significantly reduce the human annotation burden, enabling the rapid creation of labeled datasets. We rigorously evaluate our method on a medical information extraction task, demonstrating that our approach not only substantially cuts down on human intervention but also maintains high accuracy. The results highlight the potential of using LLMs to improve the utilization of unstructured clinical data, allowing for the swift deployment of tailored NLP solutions in healthcare.
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Building a Clinically-Focused Problem List From Medical Notes
Birju Patel
Cathy Cheung
Liwen Xu
Peter Clardy
Rachana Fellinger
LOUHI 2022: The 13th International Workshop on Health Text Mining and Information Analysis (2022)
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Clinical notes often contain vital information not observed in other structured data, but their unstructured nature can lead to critical patient-related information being lost. To make sure this valuable information is utilized for patient care, algorithms that summarize notes into a problem list are often proposed. Focusing on identifying medically-relevant entities in the free-form text, these solutions are often detached from a canonical ontology and do not allow downstream use of the detected text-spans. As a solution, we present here a system for generating a canonical problem list from medical notes, consisting of two major stages. At the first stage, annotation, we use a transformer model to detect all clinical conditions which are mentioned in a single note. These clinical conditions are then grounded to a predefined ontology, and are linked to spans in the text. At the second stage, summarization, we aggregate over the set of clinical conditions detected on all of the patient's note, and produce a concise patient summary that organizes their important conditions.
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Section Classification in Clinical Notes with Multi-task Transformers
Fan Zhang
LOUHI 2022: The 13th International Workshop on Health Text Mining and Information Analysis (2022)
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Clinical notes are the backbone of electronic health records, often containing vital information not observed in other structured data. Unfortunately, the unstructured nature of clinical notes can lead to critical patient-related information being lost. Algorithms that organize clinical notes into distinct sections are often proposed in order to allow medical professionals to better access information in a given note. These algorithms, however, often assume a given partition over the note, and only classify section types given this information. In this paper, we propose a multi-task solution for note sectioning, where one model can identify context changes and label each section with its medically-relevant title. Results on in-distribution (MIMIC-III) and out-of-distribution (private held-out) datasets reveal that our multi-task approach can successfully identify note sections across different hospital systems.
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Useful Confidence Measures: Beyond the Max Score
NeurIPS 2022 Workshop on Distribution Shifts (DistShift) (2022) (to appear)
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An important component in deploying machine learning (ML) in safety-critic applications is having a reliable measure of confidence in the ML's predictions. For a classifier $f$ producing a probability vector $f(x)$ over the candidate classes, the confidence is typically taken to be $\max_i f(x)_i$. This approach is potentially limited, as it disregards the rest of the probability vector. In this work, we derive several confidence measures that depend on information beyond the maximum score, such as margin-based and entropy-based measures, and empirically evaluate their usefulness. We focus on NLP tasks and Transformer-based models. We show that in the "out of the box" regime (where the scores of $f$ are used as is), using only the maximum score to inform the confidence measure is highly suboptimal. In the post-processing regime (where the scores of $f$ can be improved using additional held-out data), this remains true (though the differences are less pronounced), with entropy-based confidence emerging as a surprisingly useful measure.
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Learning and Evaluating a Differentially Private Pre-trained Language Model
Shlomo Hoory
Avichai Tendler
Findings of the Association for Computational Linguistics: EMNLP 2021, Association for Computational Linguistics, Punta Cana, Dominican Republic, pp. 1178-1189
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Contextual language models have led to significantly better results on a plethora of language understanding tasks, especially when pre-trained on the same data as the downstream task. While this additional pre-training usually improves performance, it often leads to information leakage and therefore risks the privacy of individuals mentioned in the training data. One method to guarantee the privacy of such individuals is to train a differentially private model, but this usually comes at the expense of model performance. Moreover, it is hard to tell given a privacy parameter $\epsilon$ what was the effect on the trained representation and whether it maintained relevant information while improving privacy. To improve privacy and guide future practitioners and researchers, we demonstrate here how to train a differentially private pre-trained language model (i.e., BERT) with a privacy guarantee of $\epsilon=0.5$ with only a small degradation in performance. We experiment on a dataset of clinical notes with a model trained on an entity extraction (EE) task on and compare it to a similar model trained without differential privacy. Finally, we present a series of experiments showing how to interpret the differentially private representation and understand the information lost and maintained in this process.
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Customization Scenarios for De-identification of Clinical Notes
Danny Vainstein
Gavin Edward Bee
Jack Po
Jutta Williams
Kat Chou
Ronit Yael Slyper
Rony Amira
Shlomo Hoory
Tzvika Hartman
BMC Medical Informatics and Decision Making (2020)
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Background: Automated machine-learning systems are able to de-identify electronic medical records, including free-text clinical notes. Use of such systems would greatly boost the amount of data available to researchers, yet their deployment has been limited due to uncertainty about their performance when applied to new datasets.
Objective: We present practical options for clinical note de-identification, assessing performance of machine learning systems ranging from off-the-shelf to fully customized.
Methods: We implement a state-of-the-art machine learning de-identification system, training and testing on pairs of datasets that match the deployment scenarios. We use clinical notes from two i2b2 competition corpora, the Physionet Gold Standard corpus, and parts of the MIMIC-III dataset.
Results: Fully customized systems remove 97-99% of personally identifying information. Performance of off-the-shelf systems varies by dataset, with performance mostly above 90%. Providing a small labeled dataset or large unlabeled dataset allows for fine-tuning that improves performance over off-the-shelf systems.
Conclusion: Health organizations should be aware of the levels of customization available when selecting a de-identification deployment solution, in order to choose the one that best matches their resources and target performance level.
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Audio De-identification: A New Entity Recognition Task
Tzvika Hartman
NAACL (2019)
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Named Entity Recognition (NER) has been mostly studied in the context of written text. Specifically, NER is an important step in de-identification (de-ID) of medical records, many of which are recorded conversations between a patient and a doctor. In such recordings, audio spans with personal information should be redacted, similar to the redaction of sensitive character spans in de-ID for written text. The application of NER in the context of audio de-identification has yet to be fully investigated. To this end, we define the task of audio de-ID, in which audio spans with entity mentions should be detected. We then present our pipeline for this task, which involves Automatic Speech Recognition (ASR), NER on the transcript text, and text-to-audio alignment. Finally, we introduce a novel metric for audio de-ID and a new evaluation benchmark consisting of a large labeled segment of the Switchboard and Fisher audio datasets and detail our pipeline's results on it.
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