Beast code in Giters

drhchen's starred repositories

Klebsiella_pneumoniae_drug_mutations_discovery

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gff3toembl

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

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ProNA2020

ProNA2020: System predicting protein-DNA, protein-RNA and protein-protein binding sites from sequence

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pydca

Direct coupling analysis software for protein and RNA sequences

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Predicting-ICU-Patient-Clinical-Deterioration---Report

For this project, I used publicly available Electronic Health Records (EHRs) datasets. The MIT Media Lab for Computational Physiology has developed MIMIC-IIIv1.4 dataset based on 46,520 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center of Boston between 2001 and 2012. MIMIC-IIIv1.4 dataset is freely available to researchers across the world. A formal request should be made directly to www.mimic.physionet.org, to gain access to the data. There is a required course on human research ‘Data or Specimens Only Research’ prior to data access request. I have secured one here -www.citiprogram.org/verify/?kb6607b78-5821-4de5-8cad-daf929f7fbbf-33486907. We built flexible and better performing model using the same 17 variables used in the SAPS II severity prediction model. The question ‘Can we improve the prediction performance of widely used severity scores using a more flexible model?’ is the central question of our project. I used the exact 17 variables used to develop the SAPS II severity prediction algorithm. These are 13 physiological variables, three underlying (chronic) disease variables and one admission variable. The physiological variables includes demographic (age), vital (Glasgow Comma Scale, systolic blood pressure, Oxygenation, Renal, White blood cells count, serum bicarbonate level, blood sodium level, blood potassium level, and blood bilirubin level). The three underlying disease variables includes Acquired Immunodeficiency Syndrome (AIDS), metastatic cancer, and hematologic malignancy. Finally, whether admission was scheduled surgical or unscheduled surgical was included in the model. The dataset has 26 relational tables including patient’s hospital admission, callout information when patient was ready for discharge, caregiver information, electronic charted events including vital signs and any additional information relevant to patient care, patient demographic data, list of services the patient was admitted or transferred under, ICU stay types, diagnoses types, laboratory measurments, microbiology tests and sensitivity, prescription data and billing information. Although I have full access to the MIMIC-IIIv1.4 datasets, I can not share any part of the data publicly. If you are interested to learn more about the data, there is a MIMIC III Demo dataset based on 100 patients https://mimic.physionet.org/gettingstarted/demo/. If you are interested to requesting access to the data - https://mimic.physionet.org/gettingstarted/access/. Linked repositories: Exploratory-Data-Analysis-Clinical-Deterioration, Data-Wrangling-MIMICIII-Database, Clinical-Deterioration-Prediction-Model--Inferential-Statistics, Clinical-Deterioration-Prediction-Model--Ensemble-Algorithms-, Clinical-Deterioration-Prediction-Model--Logistic-Regression, Clinical-Deterioration-Prediction-Model---KNN © 2020 GitHub, Inc.

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breast-cancer-gene-expression

This project aims to predict people who will survive breast cancer using machine learning models with the help of clinical data and gene expression profiles of the patients.

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