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Protein Function Prediction

2 papers with code ยท Medical

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Combining graph and sequence information to learn protein representations

ICLR 2020

Using these representations, we train machine learning models that outperform existing methods on the task of tissue-specific protein function prediction on 10 out of 13 tissues.

PROTEIN FUNCTION PREDICTION REPRESENTATION LEARNING

Strategies for Pre-training Graph Neural Networks

ICLR 2020

Many applications of machine learning require a model to make accurate pre-dictions on test examples that are distributionally different from training ones, while task-specific labels are scarce during training.

GRAPH CLASSIFICATION MOLECULAR PROPERTY PREDICTION PROTEIN FUNCTION PREDICTION

Using Ontologies To Improve Performance In Massively Multi-label Prediction Models

28 May 2019

Massively multi-label prediction/classification problems arise in environments like health-care or biology where very precise predictions are useful.

DISEASE PREDICTION PROTEIN FUNCTION PREDICTION

Using Ontologies To Improve Performance In Massively Multi-label Prediction

ICLR 2019

Massively multi-label prediction/classification problems arise in environments like health-care or biology where it is useful to make very precise predictions.

DISEASE PREDICTION PROTEIN FUNCTION PREDICTION

Deep Robust Framework for Protein Function Prediction using Variable-Length Protein Sequences

4 Nov 2018

The order of amino acids in a sequence enables a protein to acquire a particular stable conformation that is responsible for the functions of the protein.

PROTEIN FUNCTION PREDICTION

Hierarchical Multi-Label Classification Networks

ICML 2018

One of the most challenging machine learning problems is a particular case of data classification in which classes are hierarchically structured and objects can be assigned to multiple paths of the class hierarchy at the same time.

MULTI-LABEL CLASSIFICATION PROTEIN FUNCTION PREDICTION TEXT CLASSIFICATION

Positive and Unlabeled Learning through Negative Selection and Imbalance-aware Classification

18 May 2018

Motivated by applications in protein function prediction, we consider a challenging supervised classification setting in which positive labels are scarce and there are no explicit negative labels.

ACTIVE LEARNING PROTEIN FUNCTION PREDICTION

ProLanGO: Protein Function Prediction Using Neural~Machine Translation Based on a Recurrent Neural Network

19 Oct 2017

With the development of next generation sequencing techniques, it is fast and cheap to determine protein sequences but relatively slow and expensive to extract useful information from protein sequences because of limitations of traditional biological experimental techniques.

MACHINE TRANSLATION PROTEIN FUNCTION PREDICTION

Auto-clustering Output Layer: Automatic Learning of Latent Annotations in Neural Networks

28 Feb 2017

As the proposed output layer modification duplicates the softmax nodes at the output layer for each class, GAR allows for competitive learning between these duplicates on a traditional error-correction learning framework to ultimately enable a neural network to learn the latent annotations in this partially supervised setup.

IMAGE CLASSIFICATION PROTEIN FUNCTION PREDICTION TEXT CATEGORIZATION

Deep Recurrent Neural Network for Protein Function Prediction from Sequence

28 Jan 2017

Some RNN predictions for the ferritin-like iron sequestering function were experimentally validated, even though their sequences differ significantly from known, characterized proteins and from each other and cannot be easily predicted using popular bioinformatics methods.

FEATURE ENGINEERING PROTEIN FUNCTION PREDICTION