Artificial intelligence is an advanced method to identify novel anticancer targets and discover novel drugs from biology networks because the networks can effectively preserve and quantify the interaction between components of cell systems underlying human diseases such as cancer. Here, we review and discuss how to employ artificial intelligence approaches to identify novel anticancer targets and discover drugs. First, we describe the scope of artificial intelligence biology analysis for novel anticancer target investigations. Second, we review and discuss the basic principles and theory of commonly used network-based and machine learning-based artificial intelligence algorithms. Finally, we showcase the applications of artificial intelligence approaches in cancer target identification and drug discovery. Taken together, the artificial intelligence models have provided us with a quantitative framework to study the relationship between network characteristics and cancer, thereby leading to the identification of potential anticancer targets and the discovery of novel drug candidates.

Proteins participate in various essential processes in vivo via interactions with other molecules. Identifying the residues participating in these interactions not only provides biological insights for protein function studies but also has great significance for drug discoveries. Therefore, predicting protein-ligand binding sites has long been under intense research in the fields of bioinformatics and computer aided drug discovery. In this review, we first introduce the research background of predicting protein-ligand binding sites and then classify the methods into four categories, namely, 3D structure-based, template similarity-based, traditional machine learning-based and deep learning-based methods. We describe representative algorithms in each category and elaborate on machine learning and deep learning-based prediction methods in more detail. Finally, we discuss the trends and challenges of the current research such as molecular dynamics simulation based cryptic binding sites prediction, and highlight prospective directions for the near future.

Motivation: Recently, copy number variation (CNV) has gained considerable interest as a type of genomic variation that plays an important role in complex phenotypes and disease susceptibility. Since a number of CNV detection methods have recently been developed, it is necessary to help investigators choose suitable methods for CNV detection depending on their objectives. For this reason, this study compared ten commonly used CNV detection applications, including CNVnator, ReadDepth, RDXplorer, LUMPY and Control-FREEC, benchmarking the applications by sensitivity, specificity and computational demands. Taking the DGV gold standard variants as a standard dataset, we evaluated the ten applications with real sequencing data at sequencing depths from 5X to 50X. Among the ten methods benchmarked, LUMPY performs the best for both high sensitivity and specificity at each sequencing depth. For the purpose of high specificity, Canvas is also a good choice. If high sensitivity is preferred, CNVnator and RDXplorer are better choices. Additionally, CNVnator and GROM-RD perform well for low-depth sequencing data. Our results provide a comprehensive performance evaluation for these selected CNV detection methods and facilitate future development and improvement in CNV prediction methods. As an important type of genomic structural variation, CNVs are associated with complex phenotypes because they change the number of copies of genes in cells, affecting coding sequences and playing an important role in the susceptibility or resistance to human diseases. To identify CNVs, several experimental methods have been developed, but their resolution is very low, and the detection of short CNVs presents a bottleneck. In recent years, the advancement of high-throughput sequencing techniques has made it possible to precisely detect CNVs, especially short ones. Many CNV detection applications were developed based on the availability of high-throughput sequencing data. Due to different CNV detection algorithms, the CNVs identified by different applications vary greatly. Therefore, it is necessary to help investigators choose suitable applications for CNV detection depending upon their objectives. For this reason, we not only compared ten commonly used CNV detection applications but also benchmarked the applications by sensitivity, specificity and computational demands. Our results show that the sequencing depth can strongly affect CNV detection. Among the ten applications benchmarked, LUMPY performs best for both high sensitivity and specificity for each sequencing depth. We also give recommended applications for specific purposes, for example, CNVnator and RDXplorer for high sensitivity and CNVnator and GROM-RD for low-depth sequencing data.

Physical exercise is an important method for both the physical and mental health of the senior population. However, excessive exertion can lead to increased risks of falls, severe injuries, and diminished quality of life. Therefore, simple and effective methods for fatigue monitoring during exercise are highly desirable, particularly in community settings. The purpose of this study was to explore the possibility of real-time detection of exercise-induced fatigue using surface Electromyogram (sEMG) features, including the kurtosis and skewness of the Probability Density Function (PDF) in the community settings to solve the issues of low sensitivity and high computational complexity of commonly used sEMG features. sEMG signals from six forearm muscles were recorded during hand grip tasks at 20% maximal voluntary contraction (MVC) task-to-failure contractions from 30 healthy community-dwelling elders at their respective community centers. PDF shape features of the sEMG, namely kurtosis and skewness, were computed from 25 s of non-fatigue stable phase and 25 s of fatigue data for comparison. Statistical tests were conducted to compare and test for the significance of these features. We further proposed a novel fatigue indicator, Temporal-Mean-Kurtosis (TMK) of channel-averaged kurtosis, to detect fatigue with relatively low computational complexity and adequate sensitivity in community settings. ANOVA and post-hoc analyses were performed to examine the performance of TMK. Statistically significant differences were found between the non-fatigue period and the fatigue period for both kurtosis and skewness, with increasing values when approaching fatigue. TMK was shown to be sensitive in detecting fatigue with respect to time with lower computational complexity than the Sample Entropy. This study investigated PDF shape features of sEMG signals during a handgrip exercise to identify muscle fatigue in older adults in community experiments. Results revealed significant changes in kurtosis upon fatigue, indicating that PDF shape features were suitable convenient detectors of muscle fatigue in community experiments. The proposed indicator, TMK, showed potential sensitivity in tracking muscle fatigue over time in community-based settings with limited computational complexity, highlighting the promise of sEMG’s PDF features in detecting muscle fatigue among the elderly.