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1. Data-driven mobility models for COVID-19 simulation

   https://doi.org/10.1145/3423455.3430305  

   Pesavento, John ; Chen, Andy ; Yu, Rayan ; Kim, Joon-Seok ; Kavak, Hamdi ; Anderson, Taylor ; Züfle, Andreas ( November 2020 , Proceedings of the 3rd ACM SIGSPATIAL International Workshop on Advances in Resilient and Intelligent Cities (ARIC '20))

   null (Ed.)

   Agent-based models (ABM) play a prominent role in guiding critical decision-making and supporting the development of effective policies for better urban resilience and response to the COVID-19 pandemic. However, many ABMs lack realistic representations of human mobility, a key process that leads to physical interaction and subsequent spread of disease. Therefore, we propose the application of Latent Dirichlet Allocation (LDA), a topic modeling technique, to foot-traffic data to develop a realistic model of human mobility in an ABM that simulates the spread of COVID-19. In our novel approach, LDA treats POIs as "words" and agent home census block groups (CBGs) as "documents" to extract "topics" of POIs that frequently appear together in CBG visits. These topics allow us to simulate agent mobility based on the LDA topic distribution of their home CBG. We compare the LDA based mobility model with competitor approaches including a naive mobility model that assumes visits to POIs are random. We find that the naive mobility model is unable to facilitate the spread of COVID-19 at all. Using the LDA informed mobility model, we simulate the spread of COVID-19 and test the effect of changes to the number of topics, various parameters, and public health interventions. By examining the simulated number of cases over time, we find that the number of topics does indeed impact disease spread dynamics, but only in terms of the outbreak's timing. Further analysis of simulation results is needed to better understand the impact of topics on simulated COVID-19 spread. This study contributes to strengthening human mobility representations in ABMs of disease spread. 

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2. Using Topic Modeling for Code Discovery in Large Scale Text Data

   https://doi.org/https://doi.org/10.1007/978-3-030-67788-6_2  

   Cai, Zhiqiang ; Siebert-Evenstone, Amanda ; Eagan, Brendan R. ; Shaffer, David W. ( January 2021 , Advances in Quantitative Ethnography: Second International Conference, ICQE 2020, Malibu, CA, USA, February 1-3, 2021, Proceedings)

   Ruis, Andrew ; Lee, Seung B. (Ed.)

   When text datasets are very large, manually coding line by line becomes impractical. As a result, researchers sometimes try to use machine learning algorithms to automatically code text data. One of the most popular algorithms is topic modeling. For a given text dataset, a topic model provides probability distributions of words for a set of “topics” in the data, which researchers then use to interpret meaning of the topics. A topic model also gives each document in the dataset a score for each topic, which can be used as a non-binary coding for what proportion of a topic is in the document. Unfortunately, it is often difficult to interpret what the topics mean in a defensible way, or to validate document topic proportion scores as meaningful codes. In this study, we examine how keywords from codes developed by human experts were distributed in topics generated from topic modeling. The results show that (1) top keywords of a single topic often contain words from multiple human-generated codes; and conversely, (2) words from human-generated codes appear as high-probability keywords in multiple topic. These results explain why directly using topics from topic models as codes is problematic. However, they also imply that topic modeling makes it possible for researchers to discover codes from short word lists. 

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3. Text Mining of CHO Cell Bibliome: Topic Modeling and Document Classification

   Wang, Qinghua ; Olshin, Jonathan ; Vijay-Shanker, K. ; Wu, Cathy ( August 2022 , bioRxiv)

   Chinese hamster ovary (CHO) cells are widely used for mass production of therapeutic proteins in the pharmaceutical industry. With the growing need in optimizing the performance of producer CHO cell lines, research on CHO cell line development and bioprocess continues to increase in recent decades. Bibliographic mapping and classification of relevant research studies will be essential for identifying research gaps and trends in literature. To qualitatively and quantitatively understand the CHO literature, we have conducted topic modeling using a CHO bioprocess bibliome manually compiled in 2016, and compared the topics uncovered by the Latent Dirichlet Allocation (LDA) models with the human labels of the CHO bibliome. The results show a significant overlap between the manually selected categories and computationally generated topics, and reveal the machine-generated topic-specific characteristics. To identify relevant CHO bioprocessing papers from new scientific literature, we have developed a supervised learning model, Logistic Regression, to identify specific article topics and evaluated the results using three CHO bibliome datasets, Bioprocessing set, Glycosylation set, and Phenotype set. The use of top terms as features supports the explainability of document classification results to yield insights on new CHO bioprocessing papers. 

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4. Clustered Latent Dirichlet Allocation for Scientific Discovery

   https://doi.org/10.1109/BigData47090.2019.9005964  

   Gropp, Christopher ; Herzog, Alexander ; Safro, Ilya ; Wilson, Paul W. ; Apon, Amy W. ( December 2019 , 2019 IEEE International Conference on Big Data (Big Data))

   null (Ed.)

   Topic modeling, a method for extracting the underlying themes from a collection of documents, is an increasingly important component of the design of intelligent systems enabling the sense-making of highly dynamic and diverse streams of text data related but not limited to scientific discovery. Traditional methods such as Dynamic Topic Modeling (DTM) do not lend themselves well to direct parallelization because of dependencies from one time step to another. In this paper, we introduce and empirically analyze Clustered Latent Dirichlet Allocation (CLDA), a method for extracting dynamic latent topics from a collection of documents. Our approach is based on data decomposition in which the data is partitioned into segments, followed by topic modeling on the individual segments. The resulting local models are then combined into a global solution using clustering. The decomposition and resulting parallelization leads to very fast runtime even on very large datasets. Our approach furthermore provides insight into how the composition of topics changes over time and can also be applied using other data partitioning strategies over any discrete features of the data, such as geographic features or classes of users. In this paper CLDA is applied successfully to seventeen years of NIPS conference papers (2,484 documents and 3,280,697 words), seventeen years of computer science journal abstracts (533,588 documents and 46,446,184 words), and to forty years of the PubMed corpus (4,025,976 documents and 386,847,695 words). On the PubMed corpus, we demonstrate the versatility of CLDA by segmenting the data by both time and by journal. Our runtime on this corpus demonstrates an ability to function on very large scale datasets. 

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5. Hard for humans, hard for machines: predicting readmission after psychiatric hospitalization using narrative notes

   https://doi.org/10.1038/s41398-020-01104-w  

   Boag, William ; Kovaleva, Olga ; McCoy, Jr, Thomas H. ; Rumshisky, Anna ; Szolovits, Peter ; Perlis, Roy H. ( January 2021 , Translational Psychiatry)

   Machine learning has been suggested as a means of identifying individuals at greatest risk for hospital readmission, including psychiatric readmission. We sought to compare the performance of predictive models that use interpretable representations derived via topic modeling to the performance of human experts and nonexperts. We examined all 5076 admissions to a general psychiatry inpatient unit between 2009 and 2016 using electronic health records. We developed multiple models to predict 180-day readmission for these admissions based on features derived from narrative discharge summaries, augmented by baseline sociodemographic and clinical features. We developed models using a training set comprising 70% of the cohort and evaluated on the remaining 30%. Baseline models using demographic features for prediction achieved an area under the curve (AUC) of 0.675 [95% CI 0.674–0.676] on an independent testing set, while language-based models also incorporating bag-of-words features, discharge summaries topics identified by Latent Dirichlet allocation (LDA), and prior psychiatric admissions achieved AUC of 0.726 [95% CI 0.725–0.727]. To characterize the difficulty of the task, we also compared the performance of these classifiers to both expert and nonexpert human raters, with and without feedback, on a subset of 75 test cases. These models outperformed humans on average, including predictions by experienced psychiatrists. Typical note tokens or topics associated with readmission risk were related to pregnancy/postpartum state, family relationships, and psychosis.

    

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