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1. AutoPrognosis 2.0: Democratizing diagnostic and prognostic modeling in healthcare with automated machine learning

   https://doi.org/10.1371/journal.pdig.0000276  

   Imrie, Fergus; Cebere, Bogdan; McKinney, Eoin F.; van der Schaar, Mihaela (June 2023, PLOS Digital Health)

   Guillot, Gilles (Ed.)

   Diagnostic and prognostic models are increasingly important in medicine and inform many clinical decisions. Recently, machine learning approaches have shown improvement over conventional modeling techniques by better capturing complex interactions between patient covariates in a data-driven manner. However, the use of machine learning introduces technical and practical challenges that have thus far restricted widespread adoption of such techniques in clinical settings. To address these challenges and empower healthcare professionals, we present an open-source machine learning framework, AutoPrognosis 2.0, to facilitate the development of diagnostic and prognostic models. AutoPrognosis leverages state-of-the-art advances in automated machine learning to develop optimized machine learning pipelines, incorporates model explainability tools, and enables deployment of clinical demonstrators,withoutrequiring significant technical expertise. To demonstrate AutoPrognosis 2.0, we provide an illustrative application where we construct a prognostic risk score for diabetes using the UK Biobank, a prospective study of 502,467 individuals. The models produced by our automated framework achieve greater discrimination for diabetes than expert clinical risk scores. We have implemented our risk score as a web-based decision support tool, which can be publicly accessed by patients and clinicians. By open-sourcing our framework as a tool for the community, we aim to provide clinicians and other medical practitioners with an accessible resource to develop new risk scores, personalized diagnostics, and prognostics using machine learning techniques. Software:https://github.com/vanderschaarlab/AutoPrognosis 

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2. ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data

   https://doi.org/10.1038/s41467-023-35945-y  

   Du, Yuxuan; Fuhrman, Jed A.; Sun, Fengzhu (January 2023, Nature Communications)

   Abstract The introduction of high-throughput chromosome conformation capture (Hi-C) into metagenomics enables reconstructing high-quality metagenome-assembled genomes (MAGs) from microbial communities. Despite recent advances in recovering eukaryotic, bacterial, and archaeal genomes using Hi-C contact maps, few of Hi-C-based methods are designed to retrieve viral genomes. Here we introduce ViralCC, a publicly available tool to recover complete viral genomes and detect virus-host pairs using Hi-C data. Compared to other Hi-C-based methods, ViralCC leverages the virus-host proximity structure as a complementary information source for the Hi-C interactions. Using mock and real metagenomic Hi-C datasets from several different microbial ecosystems, including the human gut, cow fecal, and wastewater, we demonstrate that ViralCC outperforms existing Hi-C-based binning methods as well as state-of-the-art tools specifically dedicated to metagenomic viral binning. ViralCC can also reveal the taxonomic structure of viruses and virus-host pairs in microbial communities. When applied to a real wastewater metagenomic Hi-C dataset, ViralCC constructs a phage-host network, which is further validated using CRISPR spacer analyses. ViralCC is an open-source pipeline available athttps://github.com/dyxstat/ViralCC. 

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3. Coupling dynamics and evolutionary information with structure to identify protein regulatory and functional binding sites

   https://doi.org/10.1002/prot.25749  

   Mishra, Sambit K.; Kandoi, Gaurav; Jernigan, Robert L. (June 2019, Proteins: Structure, Function, and Bioinformatics)

   Abstract Binding sites in proteins can be either specifically functional binding sites (active sites) that bind specific substrates with high affinity or regulatory binding sites (allosteric sites), that modulate the activity of functional binding sites through effector molecules. Owing to their significance in determining protein function, the identification of protein functional and regulatory binding sites is widely acknowledged as an important biological problem. In this work, we present a novel binding site prediction method, Active and Regulatory site Prediction (AR‐Pred), which supplements protein geometry, evolutionary, and physicochemical features with information about protein dynamics to predict putative active and allosteric site residues. As the intrinsic dynamics of globular proteins plays an essential role in controlling binding events, we find it to be an important feature for the identification of protein binding sites. We train and validate our predictive models on multiple balanced training and validation sets with random forest machine learning and obtain an ensemble of discrete models for each prediction type. Our models for active site prediction yield a median area under the curve (AUC) of 91% and Matthews correlation coefficient (MCC) of 0.68, whereas the less well‐defined allosteric sites are predicted at a lower level with a median AUC of 80% and MCC of 0.48. When tested on an independent set of proteins, our models for active site prediction show comparable performance to two existing methods and gains compared to two others, while the allosteric site models show gains when tested against three existing prediction methods. AR‐Pred is available as a free downloadable package athttps://github.com/sambitmishra0628/AR-PRED_source. 

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4. Harnessing the Power of Vocal Signals in COVID-19 Detection Utilizing Machine Learning

   https://doi.org/10.1109/BigData62323.2024.10825050  

   Mann, Aleesa; Jadhav, Ajinkya P; Matovu, Richard; Gupta, Vibhuti (January 2025, IEEE)

   The global COVID-19 pandemic has strained healthcare systems and highlighted the need for accessible and efficient diagnostic methods. Traditional diagnostic tools, such as nasal swabs and biosensors, while accurate, pose significant logistical challenges and high costs, limiting their scalability. This paper explores an alternative, non-invasive approach to COVID-19 detection using machine learning algorithms to analyze vocal patterns, particularly cough and breathing sounds. Leveraging a publicly available dataset, we developed machine learning models capable of classifying audio samples as COVID-19 positive or negative. Our models achieve an AUC of up to 85% and an F1- score of 81%, demonstrating the potential of machine learning in enabling rapid, cost-effective COVID-19 diagnosis. These findings suggest that audio-based diagnostics could be a practical and scalable solution, particularly in resource-limited settings where traditional methods are less feasible. 

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5. Machine Learning Highlights Downtrending of COVID-19 Patients with a Distinct Laboratory Profile

   https://doi.org/10.34133/2021/7574903  

   Yang, He S.; Hou, Yu; Zhang, Hao; Chadburn, Amy; Westblade, Lars F.; Fedeli, Richard; Steel, Peter A.; Racine-Brzostek, Sabrina E.; Velu, Priya; Sepulveda, Jorge L.; et al (June 2021, Health Data Science)

   null (Ed.)

   Background . New York City (NYC) experienced an initial surge and gradual decline in the number of SARS-CoV-2-confirmed cases in 2020. A change in the pattern of laboratory test results in COVID-19 patients over this time has not been reported or correlated with patient outcome. Methods . We performed a retrospective study of routine laboratory and SARS-CoV-2 RT-PCR test results from 5,785 patients evaluated in a NYC hospital emergency department from March to June employing machine learning analysis. Results . A COVID-19 high-risk laboratory test result profile (COVID19-HRP), consisting of 21 routine blood tests, was identified to characterize the SARS-CoV-2 patients. Approximately half of the SARS-CoV-2 positive patients had the distinct COVID19-HRP that separated them from SARS-CoV-2 negative patients. SARS-CoV-2 patients with the COVID19-HRP had higher SARS-CoV-2 viral loads, determined by cycle threshold values from the RT-PCR, and poorer clinical outcome compared to other positive patients without the COVID12-HRP. Furthermore, the percentage of SARS-CoV-2 patients with the COVID19-HRP has significantly decreased from March/April to May/June. Notably, viral load in the SARS-CoV-2 patients declined, and their laboratory profile became less distinguishable from SARS-CoV-2 negative patients in the later phase. Conclusions . Our longitudinal analysis illustrates the temporal change of laboratory test result profile in SARS-CoV-2 patients and the COVID-19 evolvement in a US epicenter. This analysis could become an important tool in COVID-19 population disease severity tracking and prediction. In addition, this analysis may play an important role in prioritizing high-risk patients, assisting in patient triaging and optimizing the usage of resources. 

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