SymptomID: A Framework for Rapid Symptom Identification in Pandemics Using News Reports

SymptomGraph: Identifying Symptom Clusters from Narrative Clinical Notes using Graph Clustering

Patients with cancer or other chronic diseases often experience different symptoms before or after treatments. The symptoms could be physical, gastrointestinal, psychological, or cognitive (memory loss), or other types. Previous research focuses on understanding the individual symptoms or symptom correlations by collecting data through symptom surveys and using traditional statistical methods to analyze the symptoms, such as principal component analysis or factor analysis. This research proposes a computational system, SymptomGraph, to identify the symptom clusters in the narrative text of written clinical notes in electronic health records (EHR). SymptomGraph is developed to use a set of natural language processing (NLP) and artificial intelligence (AI) methods to first extract the clinician-documented symptoms from clinical notes. Then, a semantic symptom expression clustering method is used to discover a set of typical symptoms. A symptom graph is built based on the co-occurrences of the symptoms. Finally, a graph clustering algorithm is developed to discover the symptom clusters. Although SymptomGraph is applied to the narrative clinical notes, it can be adapted to analyze symptom survey data. We applied Symptom-Graph on a colorectal cancer patient with and without diabetes (Type 2) data set to detect the patient symptom clusters one year after the chemotherapy. Our results show that SymptomGraph can identify the typical symptom clusters of colorectal cancer patients' post-chemotherapy. The results also show that colorectal cancer patients with diabetes often show more symptoms of peripheral neuropathy, younger patients have mental dysfunctions of alcohol or tobacco abuse, and patients at later cancer stages show more memory loss symptoms. Our system can be generalized to extract and analyze symptom clusters of other chronic diseases or acute diseases like COVID-19.

A Human-in-the-loop Segmented Mixed-effects Modeling Method For Analyzing Wearables Data

Wearables are an important source of big data as they provide real-time high-resolution data logs of health indicators of individuals. Higher-order associations between pairs of variables is common in wearables data. Representing higher-order association curves as piece-wise linear segments in a regression model makes them more interpretable. However, existing methods for identifying the change points for segmented modeling either overfit or have low external validity for wearables data containing repeated measures. Therefore, we propose a human-in-the-loop method for segmented modeling of higher-order pairwise associations between variables in wearables data. Our method uses the smooth function estimated by a generalized additive mixed model to allow the analyst to annotate change point estimates for a segmented mixed-effects model, and thereafter employs the Brent's constrained optimization procedure to fine-tuning the manually provided estimates. We validate our method using three real-world wearables datasets. Our method not only outperforms state-of-the-art modeling methods in terms of prediction performance but also provides more interpretable results. Our study contributes to health data science in terms of developing a new method for interpretable modeling of wearables data. Our analysis uncovers interesting insights on higher order associations for health researchers.

Learning the Morphological and Syntactic Grammars for Named Entity Recognition

In some languages, Named Entity Recognition (NER) is severely hindered by complex linguistic structures, such as inflection, that will confuse the data-driven models when perceiving the word’s actual meaning. This work tries to alleviate these problems by introducing a novel neural network based on morphological and syntactic grammars. The experiments were performed in four Nordic languages, which have many grammar rules. The model was named the NorG network (Nor: Nordic Languages, G: Grammar). In addition to learning from the text content, the NorG network also learns from the word writing form, the POS tag, and dependency. The proposed neural network consists of a bidirectional Long Short-Term Memory (Bi-LSTM) layer to capture word-level grammars, while a bidirectional Graph Attention (Bi-GAT) layer is used to capture sentence-level grammars. Experimental results from four languages show that the grammar-assisted network significantly improves the results against baselines. We also investigate how the NorG network works on each grammar component by some exploratory experiments.