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1. 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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2. 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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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. The Evolution of Topic Modeling

   https://doi.org/10.1145/3507900  

   Churchill, Rob ; Singh, Lisa ( January 2022 , ACM Computing Surveys)

   Topic models have been applied to everything from books to newspapers to social media posts in an effort to identify the most prevalent themes of a text corpus. We provide an in-depth analysis of unsupervised topic models from their inception to today. We trace the origins of different types of contemporary topic models, beginning in the 1990s, and we compare their proposed algorithms, as well as their different evaluation approaches. Throughout, we also describe settings in which topic models have worked well and areas where new research is needed, setting the stage for the next generation of topic models. 

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5. GraphBTM: Graph Enhanced Autoencoded Variational Inference for Biterm Topic Model

   Zhu, Qile ; Feng, Zheng ; Li, Xiaolin ( January 2018 , Conference on Empirical Methods in Natural Language Processing (EMNLP 2018))

   Discovering the latent topics within texts has been a fundamental task for many applica- tions. However, conventional topic models suffer different problems in different settings. The Latent Dirichlet Allocation (LDA) may not work well for short texts due to the data sparsity (i.e., the sparse word co-occurrence patterns in short documents). The Biterm Topic Model (BTM) learns topics by mod- eling the word-pairs named biterms in the whole corpus. This assumption is very strong when documents are long with rich topic in- formation and do not exhibit the transitivity of biterms. In this paper, we propose a novel way called GraphBTM to represent biterms as graphs and design Graph Convolutional Net- works (GCNs) with residual connections to extract transitive features from biterms. To overcome the data sparsity of LDA and the strong assumption of BTM, we sample a fixed number of documents to form a mini-corpus as a training instance. We also propose a dataset called All News extracted from (Thompson, 2017), in which documents are much longer than 20 Newsgroups. We present an amortized variational inference method for GraphBTM. Our method generates more coherent topics compared with previous approaches. Exper- iments show that the sampling strategy im- proves performance by a large margin. 

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