scholarly journals Patient representation learning and interpretable evaluation using clinical notes

2018 ◽  
Vol 84 ◽  
pp. 103-113 ◽  
Author(s):  
Madhumita Sushil ◽  
Simon Šuster ◽  
Kim Luyckx ◽  
Walter Daelemans
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Xudong Zhu ◽  
Joseph M. Plasek ◽  
Chunlei Tang ◽  
Wasim Al-Assad ◽  
Zhikun Zhang ◽  
...  

Abstract Objective Our goal was to research and develop exploratory analysis tools for clinical notes, which now are underrepresented to limit the diversity of data insights on medically relevant applications. Results We characterize how exploratory analysis can affect representation learning on clinical narratives and present several self-developed tools to explore sepsis. Our experiments focus on patients with sepsis in the MIMIC-III Clinical Database or in our institution’s research patient data repository. We found that global embeddings assist in learning local representations of clinical notes. Second, aligning at any specific time facilitates the use of learning models by pooling more available clinical notes to form a training set. Furthermore, reconstruction of the timeline enhances downstream-processing techniques by emphasizing temporal expressions and temporal relationships in clinical documentation. We demonstrate that clustering helps plot various types of clinical notes against a scale, which conveys a sense of the range or spread of the data and is useful for understanding data correlations. Appropriate exploratory analysis tools provide keen insights into preprocessing clinical notes, thereby further enhancing downstream analysis capabilities, making data driven medicine possible. Our examples can help generate better data representation of clinical documentation for models with improved performance and interpretability.


1972 ◽  
Vol 37 (2) ◽  
pp. 177-186 ◽  
Author(s):  
Oliver Bloodstein ◽  
Roberta Levy Shogan

Stutterers sometimes report that by exerting articulatory pressure they can force themselves to have “real” blocks. A procedure was devised for instructing subjects to force stuttering under various conditions and for recording their introspections. Most subjects were able to force at least a few blocks which they regarded as real. Most of the words on which the attempts were said to succeed were feared or difficult words, and at times subjects assisted the process by “telling” themselves that they would not be able to say the word. Fewer subjects were able to force blocks on isolated sounds than on words, and almost none claimed to succeed on mere articulatory contacts. Subjects repeatedly characterized “real” stuttering as involving feelings of physical tension and loss of control over speech. The nature of the forced block is discussed with reference to a concept of stuttering as a struggle reaction which has acquired a high degree of automaticity.


2020 ◽  
Vol 15 (7) ◽  
pp. 750-757
Author(s):  
Jihong Wang ◽  
Yue Shi ◽  
Xiaodan Wang ◽  
Huiyou Chang

Background: At present, using computer methods to predict drug-target interactions (DTIs) is a very important step in the discovery of new drugs and drug relocation processes. The potential DTIs identified by machine learning methods can provide guidance in biochemical or clinical experiments. Objective: The goal of this article is to combine the latest network representation learning methods for drug-target prediction research, improve model prediction capabilities, and promote new drug development. Methods: We use large-scale information network embedding (LINE) method to extract network topology features of drugs, targets, diseases, etc., integrate features obtained from heterogeneous networks, construct binary classification samples, and use random forest (RF) method to predict DTIs. Results: The experiments in this paper compare the common classifiers of RF, LR, and SVM, as well as the typical network representation learning methods of LINE, Node2Vec, and DeepWalk. It can be seen that the combined method LINE-RF achieves the best results, reaching an AUC of 0.9349 and an AUPR of 0.9016. Conclusion: The learning method based on LINE network can effectively learn drugs, targets, diseases and other hidden features from the network topology. The combination of features learned through multiple networks can enhance the expression ability. RF is an effective method of supervised learning. Therefore, the Line-RF combination method is a widely applicable method.


2020 ◽  
Author(s):  
Mikołaj Morzy ◽  
Bartłomiej Balcerzak ◽  
Adam Wierzbicki ◽  
Adam Wierzbicki

BACKGROUND With the rapidly accelerating spread of dissemination of false medical information on the Web, the task of establishing the credibility of online sources of medical information becomes a pressing necessity. The sheer number of websites offering questionable medical information presented as reliable and actionable suggestions with possibly harmful effects poses an additional requirement for potential solutions, as they have to scale to the size of the problem. Machine learning is one such solution which, when properly deployed, can be an effective tool in fighting medical disinformation on the Web. OBJECTIVE We present a comprehensive framework for designing and curating of machine learning training datasets for online medical information credibility assessment. We show how the annotation process should be constructed and what pitfalls should be avoided. Our main objective is to provide researchers from medical and computer science communities with guidelines on how to construct datasets for machine learning models for various areas of medical information wars. METHODS The key component of our approach is the active annotation process. We begin by outlining the annotation protocol for the curation of high-quality training dataset, which then can be augmented and rapidly extended by employing the human-in-the-loop paradigm to machine learning training. To circumvent the cold start problem of insufficient gold standard annotations, we propose a pre-processing pipeline consisting of representation learning, clustering, and re-ranking of sentences for the acceleration of the training process and the optimization of human resources involved in the annotation. RESULTS We collect over 10 000 annotations of sentences related to selected subjects (psychiatry, cholesterol, autism, antibiotics, vaccines, steroids, birth methods, food allergy testing) for less than $7 000 employing 9 highly qualified annotators (certified medical professionals) and we release this dataset to the general public. We develop an active annotation framework for more efficient annotation of non-credible medical statements. The results of the qualitative analysis support our claims of the efficacy of the presented method. CONCLUSIONS A set of very diverse incentives is driving the widespread dissemination of medical disinformation on the Web. An effective strategy of countering this spread is to use machine learning for automatically establishing the credibility of online medical information. This, however, requires a thoughtful design of the training pipeline. In this paper we present a comprehensive framework of active annotation. In addition, we publish a large curated dataset of medical statements labelled as credible, non-credible, or neutral.


2019 ◽  
Vol 57 (7) ◽  
pp. 4360-4374 ◽  
Author(s):  
Xiaohui Wei ◽  
Wen Zhu ◽  
Bo Liao ◽  
Lijun Cai

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