Dataset Information

Computational Methods for Identifying Similar Diseases.

ABSTRACT: Although our knowledge of human diseases has increased dramatically, the molecular basis, phenotypic traits, and therapeutic targets of most diseases still remain unclear. An increasing number of studies have observed that similar diseases often are caused by similar molecules, can be diagnosed by similar markers or phenotypes, or can be cured by similar drugs. Thus, the identification of diseases similar to known ones has attracted considerable attention worldwide. To this end, the associations between diseases at the molecular, phenotypic, and taxonomic levels were used to measure the pairwise similarity in diseases. The corresponding performance assessment strategies for these methods involving the terms "category-based," "simulated-patient-based," and "benchmark-data-based" were thus further emphasized. Then, frequently used methods were evaluated using a benchmark-data-based strategy. To facilitate the assessment of disease similarity scores, researchers have designed dozens of tools that implement these methods for calculating disease similarity. Currently, disease similarity has been advantageous in predicting noncoding RNA (ncRNA) function and therapeutic drugs for diseases. In this article, we review disease similarity methods, evaluation strategies, tools, and their applications in the biomedical community. We further evaluate the performance of these methods and discuss the current limitations and future trends for calculating disease similarity.

SUBMITTER: Cheng L

PROVIDER: S-EPMC6838934 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Computational Methods for Identifying Similar Diseases.

Cheng Liang L Zhao Hengqiang H Wang Pingping P Zhou Wenyang W Luo Meng M Li Tianxin T Han Junwei J Liu Shulin S Jiang Qinghua Q

Molecular therapy. Nucleic acids 20190928

Although our knowledge of human diseases has increased dramatically, the molecular basis, phenotypic traits, and therapeutic targets of most diseases still remain unclear. An increasing number of studies have observed that similar diseases often are caused by similar molecules, can be diagnosed by similar markers or phenotypes, or can be cured by similar drugs. Thus, the identification of diseases similar to known ones has attracted considerable attention worldwide. To this end, the associations ...[more]

PMID: 31678735

Similar Datasets

Project description:Finding electrophysiological features that are similar across patients with epilepsy may facilitate identifying treatment options for one patient that worked in patients with similar brain activity patterns. Three non-linear iEEG (intracranial electroencephalogram) embedding methods of finding similar cross-patient iEEG records in a large iEEG dataset were developed and compared. About 1 million iEEG records from 256 patients with drug-resistant focal onset seizures who were treated in prospective trials of the RNS System were used for analyses. Data from 200, 25, and 31 patients were randomly selected to be in the train, validation, and test datasets. In method 1, ResNet50 convolutional neural network (CNN) model pre-trained on the ImageNet dataset was used for extracting feature maps from spectrogram images (ImageNet-ResNet) of iEEG records. In method 2, ResNet50 custom trained on an iEEG classification task using ~138,000 manually labeled iEEG records was used as the feature extractor (ESC-ResNet). Feature maps were passed through dimensionality reduction and k nearest neighbors were found in the reduced feature space. In method 3, a 256 dimensional iEEG embedding space was learned via contrastive learning by training a ResNet50 model with triplet training sets generated using within-patient iEEG clustering (CL-ResNet). All three methods had comparable performance when identifying iEEG records from the search dataset similar to test iEEG records of baseline (non-seizure) and interictal spiking activity. Epileptic interictal spikes are represented by vertical (broadband) edges in spectrogram images, and hence even generic features extracted using models trained on everyday images appear to be sufficient to represent iEEG records with similar levels of interictal spiking activity in close proximity. In the case of electrographic seizures, however, the ESC-ResNet model, identified cross-patient iEEG records with electrographic seizure morphology features that were most similar to the test iEEG records. For nuanced electrographic seizure iEEG representation learning, domain specific model training with manually generated labels had the advantage. Finally, representative iEEG records were selected from every patient using an unsupervised clustering method which effectively reduced the number of iEEG records in the search dataset from ~750,000 to 2,148, thus substantially reducing the time required for finding similar cross-patient iEEG records.

Dataset Information

Computational Methods for Identifying Similar Diseases.

Publications

Computational Methods for Identifying Similar Diseases.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets