Dataset Information

Cross-cancer Prediction: A Novel Machine Learning Approach to Discover Molecular Targets for Development of Treatments for Multiple Cancers.

ABSTRACT: Conventional cancer drug development has long been limited to organ- or tissue-specific cancer types. However, it has become increasingly known that specific genetic abnormalities are responsible for the carcinogenesis of multiple cancers. The recent US Food and Drug Administration (FDA) approval of the first multi-cancer drug, Keytruda, has demonstrated the feasibility of developing new drugs that target multiple cancers. Despite a promising future, methodological development for identifying multi-cancer molecular targets remains encumbered. This study developed a novel machine learning approach to identify such genes responsible for multiple cancers by synthesizing salient genomic information from cancer-specific classification models. This approach centered on the cross-cancer prediction method for identifying groups of cancers with high cross-cancer predictability. Furthermore, a robust hybrid classifier, comprising Prediction Analysis for Microarrays and Random Forest, was developed to integrate predictive models for gene inference. This approach has successfully identified key genes shared by endometrial cancer, mammary gland ductal carcinoma, and small cell lung cancer. The results are supported by published experimental evidence. This framework holds potential to transform the current methods of discovering multi-cancer molecular targets for clinical oncology.

SUBMITTER: Gao K

PROVIDER: S-EPMC6198390 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Cross-cancer Prediction: A Novel Machine Learning Approach to Discover Molecular Targets for Development of Treatments for Multiple Cancers.

Gao Katie K Wang Dayong D Huang Yi Y

Cancer informatics 20181022

Conventional cancer drug development has long been limited to organ- or tissue-specific cancer types. However, it has become increasingly known that specific genetic abnormalities are responsible for the carcinogenesis of multiple cancers. The recent US Food and Drug Administration (FDA) approval of the first multi-cancer drug, Keytruda, has demonstrated the feasibility of developing new drugs that target multiple cancers. Despite a promising future, methodological development for identifying mu ...[more]

PMID: 30364884

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Project description:ObjectiveTo build a supervised machine learning-based classifier, which can accurately predict whether Tai Chi practitioners may experience knee pain after years of exercise.DesignA prospective approach was used. Data were collected using face-to-face through a self-designed questionnaire.SettingSingle centre in Shanghai, China.ParticipantsA total of 1750 Tai Chi practitioners with a course of Tai Chi exercise over 5 years were randomly selected.MeasuresAll participants were measured by a questionnaire survey including personal information, Tai Chi exercise pattern and Irrgang Knee Outcome Survey Activities of Daily Living Scale. The validity of the questionnaire was analysed by logical analysis and test, and the reliability of this questionnaire was mainly tested by a re-test method. Dataset 1 was established by whether the participant had knee pain, and dataset 2 by whether the participant's knee pain affected daily living function. Then both datasets were randomly assigned to a training and validating dataset and a test dataset in a ratio of 7:3. Six machine learning algorithms were selected and trained by our dataset. The area under the receiver operating characteristic curve was used to evaluate the performance of the trained models, which determined the best prediction model.ResultsA total of 1703 practitioners completed the questionnaire and 47 were eliminated for lack of information. The total reliability of the scale is 0.94 and the KMO (Kaiser-Meyer-Olkin measure of sampling adequacy) value of the scale validity was 0.949 (>0.7). The CatBoost algorithm-based machine-learning model achieved the best predictive performance in distinguishing practitioners with different degrees of knee pain after Tai Chi practice. 'Having knee pain before Tai Chi practice', 'knee joint warm-up' and 'duration of each exercise' are the top three factors associated with pain after Tai Chi exercise in the model. 'Having knee pain before Tai Chi practice', 'Having Instructor' and 'Duration of each exercise' were most relevant to whether pain interfered with daily life in the model.ConclusionCatBoost-based machine learning classifier accurately predicts knee pain symptoms after practicing Tai Chi. This study provides an essential reference for practicing Tai Chi scientifically to avoid knee pain.

Project description:OBJECTIVES:Unplanned readmissions to the intensive care unit (ICU) are highly undesirable, increasing variance in care, making resource planning difficult and potentially increasing length of stay and mortality in some settings. Identifying patients who are likely to suffer unplanned ICU readmission could reduce the frequency of this adverse event. SETTING:A single academic, tertiary care hospital in the UK. PARTICIPANTS:A set of 3326 ICU episodes collected between October 2014 and August 2016. All records were of patients who visited an ICU at some point during their stay. We excluded patients who were ?16 years of age; visited ICUs other than the general and neurosciences ICU; were missing crucial electronic patient record measurements; or had indeterminate ICU discharge outcomes or very early or extremely late discharge times. After exclusion, 2018 outcome-labelled episodes remained. PRIMARY AND SECONDARY OUTCOME MEASURES:Area under the receiver operating characteristic curve (AUROC) for prediction of unplanned ICU readmission or in-hospital death within 48?hours of first ICU discharge. RESULTS:In 10-fold cross-validation, an ensemble predictor was trained on data from both the target hospital and the Medical Information Mart for Intensive Care (MIMIC-III) database and tested on the target hospital's data. This predictor discriminated between patients with the unplanned ICU readmission or death outcome and those without this outcome, attaining mean AUROC of 0.7095 (SE 0.0260), superior to the purpose-built Stability and Workload Index for Transfer (SWIFT) score (AUROC=0.6082, SE 0.0249; p=0.014, pairwise t-test). CONCLUSIONS:Despite the inherent difficulties, we demonstrate that a novel machine learning algorithm based on transfer learning could achieve good discrimination, over and above that of the treating clinicians or the value added by the SWIFT score. Accurate prediction of unplanned readmission could be used to target resources more efficiently.

Project description:Different types of chemicals and products may exhibit various health risks when administered into the human body. For toxicity reasons, the number of new drugs entering the market through the conventional drug development process has been reduced over the years. However, with the advent of big data and artificial intelligence, machine learning techniques have emerged as a potential solution for predicting toxicity and ensuring efficient drug development and chemical safety. An ML model for toxicity prediction can reduce experimental costs and time while addressing ethical concerns by drastically reducing the need for animals and clinical trials. Herein, MolToxPred, an ML-based tool, has been developed using a stacked model approach to predict the potential toxicity of small molecules and metabolites. The stacked model consists of random forest, multi-layer perceptron, and LightGBM as base classifiers and Logistic Regression as the meta classifier. For training and validation purposes, a comprehensive set of toxic and non-toxic molecules is curated. Different structural and physicochemical-based features in the form of molecular descriptors and fingerprints were employed. MolToxPred utilizes a comprehensive feature selection process and optimizes its hyperparameters through Bayesian optimization with stratified 5-fold cross-validation. In the evaluation phase, MolToxPred achieved an AUROC of 87.76% on the test set and 88.84% on an external validation set. The McNemar test was used as the post-hoc test to determine if the stacked models' performance was significantly different compared to the base learners. The developed stacked model outperformed its base classifiers and an existing tool in the literature, reaffirming its better performance. The hypothesis is that the incorporation of a diverse set of data, the subsequent feature selection, and a stacked ensemble approach give MolToxPred the edge over other methods. In addition to this, an attempt has been made to identify structural alerts responsible for endpoints of the Tox21 data to determine the association of a molecule with a plausible downstream pathway of action. MolToxPred may be helpful for drug discovery and regulatory pipelines in pharmaceutical and other industries for in silico toxicity prediction of small molecule candidates.

Dataset Information

Cross-cancer Prediction: A Novel Machine Learning Approach to Discover Molecular Targets for Development of Treatments for Multiple Cancers.

Publications

Cross-cancer Prediction: A Novel Machine Learning Approach to Discover Molecular Targets for Development of Treatments for Multiple Cancers.

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