Public genomic repositories are notoriously lacking in racially and ethnically diverse samples. This limits the reaches of exploration and has in fact been one of the driving factors for the initiation of the All of Us project. Our particular focus here is to provide a model-based framework for accurately predicting DNA methylation from genetic data using racially sparse public repository data. Epigenetic alterations are of great interest in cancer research but public repository data is limited in the information it provides. However, genetic data is more plentiful. Our phenotype of interest is cervical cancer in The Cancer Genome Atlas (TCGA) repository. Being able to generate such predictions would nicely complement other work that has generated gene-level predictions of gene expression for normal samples. We develop a new prediction approach which uses shared random effects from a nested error mixed effects regression model. The sharing of random effects allows borrowing of strength across racial groups greatly improving predictive accuracy. Additionally, we show how to further borrow strength by combining data from different cancers in TCGA even though the focus of our predictions is DNA methylation in cervical cancer. We compare our methodology against other popular approaches including the elastic net shrinkagemore »
Can x2vec save lives? Integrating graph and language embeddings for automatic mental health classification
Graph and language embedding models are becoming commonplace in large scale analyses given their ability to represent complex sparse data densely in low-dimensional space. Integrating these models’ complementary relational and communicative data may be especially helpful if predicting rare events or classifying members of hidden populations—tasks requiring huge and sparse datasets for generalizable analyses. For example, due to social stigma and comorbidities, mental health support groups often form in amorphous online groups. Predicting suicidality among individuals in these settings using standard network analyses is prohibitive due to resource limits (e.g., memory), and adding auxiliary data like text to such models exacerbates complexity- and sparsity-related issues. Here, I show how merging graph and language embedding models (
- Publication Date:
- NSF-PAR ID:
- 10303681
- Journal Name:
- Journal of Physics: Complexity
- Volume:
- 1
- Issue:
- 3
- Page Range or eLocation-ID:
- Article No. 035005
- ISSN:
- 2632-072X
- Publisher:
- IOP Publishing
- Sponsoring Org:
- National Science Foundation
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Availability and implementation Data and source codes are available at https://github.com/Shen-Lab/CPAC.
Supplementary information Supplementary data aremore »
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Abstract Monitoring wildlife abundance across space and time is an essential task to study their population dynamics and inform effective management. Acoustic recording units are a promising technology for efficiently monitoring bird populations and communities. While current acoustic data models provide information on the presence/absence of individual species, new approaches are needed to monitor population abundance, ideally across large spatio‐temporal regions.
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Abstract Background Natural language processing (NLP) tasks in the health domain often deal with limited amount of labeled data due to high annotation costs and naturally rare observations. To compensate for the lack of training data, health NLP researchers often have to leverage knowledge and resources external to a task at hand. Recently, pretrained large-scale language models such as the Bidirectional Encoder Representations from Transformers (BERT) have been proven to be a powerful way of learning rich linguistic knowledge from massive unlabeled text and transferring that knowledge to downstream tasks. However, previous downstream tasks often used training data at such a large scale that is unlikely to obtain in the health domain. In this work, we aim to study whether BERT can still benefit downstream tasks when training data are relatively small in the context of health NLP.
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