Dataset Information

Semi-supervised neighborhoods and localized patient outcome prediction.

ABSTRACT: Robust statistical methods that can provide patients and their healthcare providers with individual predictions are needed to help guide informed medical decisions. Ideally an individual prediction would display the full range of possible outcomes (full predictive distribution), would be obtained with a user-specified level of precision, and would be minimally reliant on statistical model assumptions. We propose a novel method that satisfies each of these criteria via the semi-supervised creation of an axis-parallel covariate neighborhood constructed around a given point defining the patient of interest. We then provide non-parametric estimates of the outcome distribution for the subset of subjects in this neighborhood, which we refer to as a localized prediction. We implement local prediction methods using dynamic graphical methods which allow the user to vary key options such as the choice of the variables defining the neighborhood, and the size of the neighborhood.

SUBMITTER: Kosel AE

PROVIDER: S-EPMC6821385 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Publications

Semi-supervised neighborhoods and localized patient outcome prediction.

Kosel Alison E AE Heagerty Patrick J PJ

Biostatistics (Oxford, England) 20190701 3

Robust statistical methods that can provide patients and their healthcare providers with individual predictions are needed to help guide informed medical decisions. Ideally an individual prediction would display the full range of possible outcomes (full predictive distribution), would be obtained with a user-specified level of precision, and would be minimally reliant on statistical model assumptions. We propose a novel method that satisfies each of these criteria via the semi-supervised creatio ...[more]

PMID: 29912289

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Project description:Src homology 2 (SH2) domains are the largest family of the peptide-recognition modules (PRMs) that bind to phosphotyrosine containing peptides. Knowledge about binding partners of SH2-domains is key for a deeper understanding of different cellular processes. Given the high binding specificity of SH2, in-silico ligand peptide prediction is of great interest. Currently however, only a few approaches have been published for the prediction of SH2-peptide interactions. Their main shortcomings range from limited coverage, to restrictive modeling assumptions (they are mainly based on position specific scoring matrices and do not take into consideration complex amino acids inter-dependencies) and high computational complexity. We propose a simple yet effective machine learning approach for a large set of known human SH2 domains. We used comprehensive data from micro-array and peptide-array experiments on 51 human SH2 domains. In order to deal with the high data imbalance problem and the high signal-to-noise ration, we casted the problem in a semi-supervised setting. We report competitive predictive performance w.r.t. state-of-the-art. Specifically we obtain 0.83 AUC ROC and 0.93 AUC PR in comparison to 0.71 AUC ROC and 0.87 AUC PR previously achieved by the position specific scoring matrices (PSSMs) based SMALI approach. Our work provides three main contributions. First, we showed that better models can be obtained when the information on the non-interacting peptides (negative examples) is also used. Second, we improve performance when considering high order correlations between the ligand positions employing regularization techniques to effectively avoid overfitting issues. Third, we developed an approach to tackle the data imbalance problem using a semi-supervised strategy. Finally, we performed a genome-wide prediction of human SH2-peptide binding, uncovering several findings of biological relevance. We make our models and genome-wide predictions, for all the 51 SH2-domains, freely available to the scientific community under the following URLs: http://www.bioinf.uni-freiburg.de/Software/SH2PepInt/SH2PepInt.tar.gz and http://www.bioinf.uni-freiburg.de/Software/SH2PepInt/Genome-wide-predictions.tar.gz, respectively.

Project description:BackgroundA new learning-based patient similarity measurement was proposed to measure patients' similarity for heterogeneous electronic medical records (EMRs) data.MethodsWe first calculated feature-level similarities according to the features' attributes. A domain expert provided patient similarity scores of 30 randomly selected patients. These similarity scores and feature-level similarities for 30 patients comprised the labeled sample set, which was used for the semi-supervised learning algorithm to learn the patient-level similarities for all patients. Then we used the k-nearest neighbor (kNN) classifier to predict four liver conditions. The predictive performances were compared in four different situations. We also compared the performances between personalized kNN models and other machine learning models. We assessed the predictive performances by the area under the receiver operating characteristic curve (AUC), F1-score, and cross-entropy (CE) loss.ResultsAs the size of the random training samples increased, the kNN models using the learned patient similarity to select near neighbors consistently outperformed those using the Euclidean distance to select near neighbors (all P values < 0.001). The kNN models using the learned patient similarity to identify the top k nearest neighbors from the random training samples also had a higher best-performance (AUC: 0.95 vs. 0.89, F1-score: 0.84 vs. 0.67, and CE loss: 1.22 vs. 1.82) than those using the Euclidean distance. As the size of the similar training samples increased, which composed the most similar samples determined by the learned patient similarity, the performance of kNN models using the simple Euclidean distance to select the near neighbors degraded gradually. When exchanging the role of the Euclidean distance, and the learned patient similarity in selecting the near neighbors and similar training samples, the performance of the kNN models gradually increased. These two kinds of kNN models had the same best-performance of AUC 0.95, F1-score 0.84, and CE loss 1.22. Among the four reference models, the highest AUC and F1-score were 0.94 and 0.80, separately, which were both lower than those for the simple and similarity-based kNN models.ConclusionsThis learning-based method opened an opportunity for similarity measurement based on heterogeneous EMR data and supported the secondary use of EMR data.

Dataset Information

Semi-supervised neighborhoods and localized patient outcome prediction.

Publications

Semi-supervised neighborhoods and localized patient outcome prediction.

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