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Abstract Free-text analysis using machine learning (ML)-based natural language processing (NLP) shows promise for diagnosing psychiatric conditions. Chat Generative Pre-trained Transformer (ChatGPT) has demonstrated preliminary initial feasibility for this purpose; however, whether it can accurately assess mental illness remains to be determined. This study evaluates the effectiveness of ChatGPT and the text-embedding-ada-002 (ADA) model in detecting post-traumatic stress disorder following childbirth (CB-PTSD), a maternal postpartum mental illness affecting millions of women annually, with no standard screening protocol. Using a sample of 1295 women who gave birth in the last six months and were 18+ years old, recruited through hospital announcements, social media, and professional organizations, we explore ChatGPT’s and ADA’s potential to screen for CB-PTSD by analyzing maternal childbirth narratives. The PTSD Checklist for DSM-5 (PCL-5; cutoff 31) was used to assess CB-PTSD. By developing an ML model that utilizes numerical vector representation of the ADA model, we identify CB-PTSD via narrative classification. Our model outperformed (F1 score: 0.81) ChatGPT and six previously published large text-embedding models trained on mental health or clinical domains data, suggesting that the ADA model can be harnessed to identify CB-PTSD. Our modeling approach could be generalized to assess other mental health disorders.

Abstract Collective attention and memory involving significant events can be quantitatively studied via social media data. Previous studies analyzed user attention to discrete events that do not change post-event, and assume universal public attention patterns. However, dynamic events with ongoing updates are common, yielding varied individual attention patterns. We explore memory of U.S. companies filing Chapter 11 bankruptcy and being mentioned on X (formerly Twitter). Unlike discrete events, Chapter 11 entails ongoing financial changes as the company typically remains operational, influencing post-event attention dynamics. We collected 248,936 X mentions for 74 companies before and after each bankruptcy. Attention surged after bankruptcy, with distinct Low and High persistence levels compared with pre-bankruptcy attention. The two tweeting patterns were modeled using biexponential models, successfully predicting (F1-score: 0.81) post-bankruptcy attention persistence. Studying bankruptcy events on social media reveals diverse attention patterns, demonstrates how pre-bankruptcy attention affects post-bankruptcy recollection, and provides insights into memory of dynamic events.

The aim of this narrative review is to consolidate knowledge on the role of the hypothalamic-pituitary-adrenal (HPA) axis in depression pathophysiology at different reproductive stages across the female lifespan. Despite growing evidence about the impact of gonadal hormones on mood disorders, no previous review has examined the interaction between such hormonal changes and the HPA axis within the context of depressive disorders in women. We will focus on HPA axis function in depressive disorders at different reproductive stages including the menstrual cycle (e.g., premenstrual dysphoric disorder [PMDD]), perinatally (e.g., postpartum depression), and in perimenopausal depression. Each of these reproductive stages is characterized by vast physiological changes and presents major neuroendocrine reorganization. The HPA axis is one of the main targets of such functional alterations, and with its key role in stress response, it is an etiological factor in vulnerable windows for depression across the female lifespan. We begin with an overview of the HPA axis and a brief summary of techniques for measuring HPA axis parameters. We then describe the hormonal milieu of each of these key reproductive stages, and integrate information about HPA axis function in depression across these reproductive stages, describing similarities and differences. The role of a history of stress and trauma exposure as a contributor to female depression in the context of HPA axis involvement across the reproductive stages is also presented. This review advances the pursuit of understanding common biological mechanisms across depressive disorders among women. Our overarching goal is to identify unmet needs in characterizing stress-related markers of depression in women in the context of hormonal changes across the lifespan, and to support future research in women’s mental health as it pertains to pathophysiology, early diagnosis, and treatment targets.

Abstract Background PubMed contains millions of abstracts that co-mention terms that describe drugs with other biomedical terms such as genes or diseases. Unique opportunities exist for leveraging these co-mentions by integrating them with other drug-drug similarity resources such as the Library of Integrated Network-based Cellular Signatures (LINCS) L1000 signatures to develop novel hypotheses. Results DrugShot is a web-based server application and an Appyter that enables users to enter any biomedical search term into a simple input form to receive ranked lists of drugs and other small molecules based on their relevance to the search term. To produce ranked lists of small molecules, DrugShot cross-references returned PubMed identifiers (PMIDs) with DrugRIF or AutoRIF, which are curated resources of drug-PMID associations, to produce an associated small molecule list where each small molecule is ranked according to total co-mentions with the search term from shared PubMed IDs. Additionally, using two types of drug-drug similarity matrices, lists of small molecules are predicted to be associated with the search term. Such predictions are based on literature co-mentions and signature similarity from LINCS L1000 drug-induced gene expression profiles. Conclusions DrugShot prioritizes drugs and small molecules associated with biomedical search terms. In addition to listing known associations, DrugShot predicts additional drugs and small molecules related to any search term. Hence, DrugShot can be used to prioritize drugs and preclinical compounds for drug repurposing and suggest indications and adverse events for preclinical compounds. DrugShot is freely and openly available at: https://maayanlab.cloud/drugshot and https://appyters.maayanlab.cloud/#/DrugShot .

Graph analytical approaches permit identifying novel genes involved in complex diseases, but are limited by (i) inferring structural network similarity of connected gene nodes, ignoring potentially relevant unconnected nodes; (ii) using homogeneous graphs, missing gene-disease associations’ complexity; (iii) relying on disease/gene-phenotype associations’ similarities, involving highly incomplete data; (iv) using binary classification, with gene-disease edges as positive training samples, and non-associated gene and disease nodes as negative samples that may include currently unknown disease genes; or (v) reporting predicted novel associations without systematically evaluating their accuracy. Addressing these limitations, we develop the Heterogeneous Integrated Graph for Predicting Disease Genes (HetIG-PreDiG) model that includes gene-gene, gene-disease, and gene-tissue associations. We predict novel disease genes using low-dimensional representation of nodes accounting for network structure, and extending beyond network structure using the developed Gene-Disease Prioritization Score (GDPS) reflecting the degree of gene-disease association via gene co-expression data. For negative training samples, we select non-associated gene and disease nodes with lower GDPS that are less likely to be affiliated. We evaluate the developed model’s success in predicting novel disease genes by analyzing the prediction probabilities of gene-disease associations. HetIG-PreDiG successfully predicts (Micro-F1 = 0.95) gene-disease associations, outperforming baseline models, and is validated using published literature, thus advancing our understanding of complex genetic diseases.

This editorial is intended to provide a brief history of the application of Information Theory to the fields of Computational Biology and Bioinformatics; to succinctly summarize the current state of associated research, and open challenges; and to describe the scope of the invited content for this Special Issue of the journal Entropy with the theme of “Information Theory in Computational Biology” [...]

Summary: In a short period, many research publications that report sets of experimentally validated drugs as potential COVID-19 therapies have emerged. To organize this accumulating knowledge, we developed the COVID-19 Drug and Gene Set Library (https://amp.pharm.mssm.edu/covid19/), a collection of drug and gene sets related to COVID-19 research from multiple sources. The platform enables users to view, download, analyze, visualize, and contribute drug and gene sets related to COVID-19 research. To evaluate the content of the library, we compared the results from six in vitro drug screens for COVID-19 repurposing candidates. Surprisingly, we observe low overlap across screens while highlighting overlapping candidates that should receive more attention as potential therapeutics for COVID-19. Overall, the COVID-19 Drug and Gene Set Library can be used to identify community consensus, make researchers and clinicians aware of new potential therapies, enable machine-learning applications, and facilitate the research community to work together toward a cure. The Bigger Picture: The COVID-19 pandemic requires rapid response by the research community to develop vaccines and therapeutics. While the development of vaccines may take years, drug repurposing can offer pandemic mitigation much quicker. In vitro drug screening is the first step toward identifying and prioritizing potential safe therapeutics for COVID-19. However, these screens are done by different laboratories across the world using different methods. As a result, these screens produce different lists of hits. Here, we attempted to consolidate the results from these drug screens to find out whether consensus emerges. In addition, we utilized machine-learning methods to further predict and prioritize the validity of the hits from these drug screens. Such analysis identified molecular mechanisms that may explain how some of these drugs interfere with viral replication inside human cells. As more SARS-CoV-2 drug screens are published, a clearer picture of the most promising drug candidates is expected to emerge.

Publicly available RNA-seq data is provided mostly in raw form, resulting in a barrier for integrative analyses. Here, Lachmann et al. develop a high-throughput processing infrastructure and search database (ARCHS4) that provides processed RNA-seq data for 187,946 publicly available mouse and human samples to support exploration and reuse.

Understanding the complex process of information spread in online social networks (OSNs) enables the efficient maximization/minimization of the spread of useful/harmful information. Users assume various roles based on their behaviors while engaging with information in these OSNs. Recent reviews on information spread in OSNs have focused on algorithms and challenges for modeling the local node-to-node cascading paths of viral information. However, they neglected to analyze non-viral information with low reach size that can also spread globally beyond OSN edges (links) via non-neighbors through, for example, pushed information via content recommendation algorithms. Previous reviews have also not fully considered user roles in the spread of information. To address these gaps, we: (i) provide a comprehensive survey of the latest studies on role-aware information spread in OSNs, also addressing the different temporal spreading patterns of viral and non-viral information; (ii) survey modeling approaches that consider structural, non-structural, and hybrid features, and provide a taxonomy of these approaches; (iii) review software platforms for the analysis and visualization of role-aware information spread in OSNs; and (iv) describe how information spread models enable useful applications in OSNs such as detecting influential users. We conclude by highlighting future research directions for studying information spread in OSNs, accounting for dynamic user roles.

A wealth of gene expression data is publicly available, yet is little use without additional human curation. Ma’ayan and colleagues report a crowdsourcing project involving over 70 participants to annotate and analyse thousands of human disease-related gene expression datasets.