AIMC Topic: Neural Networks, Computer

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MINDG: a drug-target interaction prediction method based on an integrated learning algorithm.

Bioinformatics (Oxford, England)
MOTIVATION: Drug-target interaction (DTI) prediction refers to the prediction of whether a given drug molecule will bind to a specific target and thus exert a targeted therapeutic effect. Although intelligent computational approaches for drug target ...

A Bayesian convolutional neural network-based generalized linear model.

Biometrics
Convolutional neural networks (CNNs) provide flexible function approximations for a wide variety of applications when the input variables are in the form of images or spatial data. Although CNNs often outperform traditional statistical models in pred...

SGCLDGA: unveiling drug-gene associations through simple graph contrastive learning.

Briefings in bioinformatics
Drug repurposing offers a viable strategy for discovering new drugs and therapeutic targets through the analysis of drug-gene interactions. However, traditional experimental methods are plagued by their costliness and inefficiency. Despite graph conv...

Optimal fusion of genotype and drug embeddings in predicting cancer drug response.

Briefings in bioinformatics
Predicting cancer drug response using both genomics and drug features has shown some success compared to using genomics features alone. However, there has been limited research done on how best to combine or fuse the two types of features. Using a vi...

TransPTM: a transformer-based model for non-histone acetylation site prediction.

Briefings in bioinformatics
Protein acetylation is one of the extensively studied post-translational modifications (PTMs) due to its significant roles across a myriad of biological processes. Although many computational tools for acetylation site identification have been develo...

Deep learning in structural bioinformatics: current applications and future perspectives.

Briefings in bioinformatics
In this review article, we explore the transformative impact of deep learning (DL) on structural bioinformatics, emphasizing its pivotal role in a scientific revolution driven by extensive data, accessible toolkits and robust computing resources. As ...

BERT-TFBS: a novel BERT-based model for predicting transcription factor binding sites by transfer learning.

Briefings in bioinformatics
Transcription factors (TFs) are proteins essential for regulating genetic transcriptions by binding to transcription factor binding sites (TFBSs) in DNA sequences. Accurate predictions of TFBSs can contribute to the design and construction of metabol...

DeepSS2GO: protein function prediction from secondary structure.

Briefings in bioinformatics
Predicting protein function is crucial for understanding biological life processes, preventing diseases and developing new drug targets. In recent years, methods based on sequence, structure and biological networks for protein function annotation hav...

Prior knowledge-guided multilevel graph neural network for tumor risk prediction and interpretation via multi-omics data integration.

Briefings in bioinformatics
The interrelation and complementary nature of multi-omics data can provide valuable insights into the intricate molecular mechanisms underlying diseases. However, challenges such as limited sample size, high data dimensionality and differences in omi...

Improving drug response prediction via integrating gene relationships with deep learning.

Briefings in bioinformatics
Predicting the drug response of cancer cell lines is crucial for advancing personalized cancer treatment, yet remains challenging due to tumor heterogeneity and individual diversity. In this study, we present a deep learning-based framework named Dee...