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Schizophrenia (SZ) is a prevalent mental disorder characterized by cognitive, emotional, and behavioral changes. Symptoms of SZ include hallucinations, illusions, delusions, lack of motivation, and difficulties in concentration. While the exact causes of SZ remain unproven, factors such as brain injuries, stress, and psychotropic drugs have been implicated in its development. SZ can be classified into different types, including paranoid, disorganized, catatonic, undifferentiated, and residual. Diagnosing SZ involves employing various tools, including clinical interviews, physical examinations, psychological evaluations, the Diagnostic and Statistical Manual of Mental Disorders (DSM), and neuroimaging techniques. Electroencephalography (EEG) recording is a significant functional neuroimaging modality that provides valuable insights into brain function during SZ. However, EEG signal analysis poses challenges for neurologists and scientists due to the presence of artifacts, long-term recordings, and the utilization of multiple channels. To address these challenges, researchers have introduced artificial intelligence (AI) techniques, encompassing conventional machine learning (ML) and deep learning (DL) methods, to aid in SZ diagnosis. This study reviews papers focused on SZ diagnosis utilizing EEG signals and AI methods. The introduction section provides a comprehensive explanation of SZ diagnosis methods and intervention techniques. Subsequently, review papers in this field are discussed, followed by an introduction to the AI methods employed for SZ diagnosis and a summary of relevant papers presented in tabular form. Additionally, this study reports on the most significant challenges encountered in SZ diagnosis, as identified through a review of papers in this field. Future directions to overcome these challenges are also addressed. The discussion section examines the specific details of each paper, culminating in the presentation of conclusions and findings. [ABSTRACT FROM AUTHOR]

Post Translational Modification (PTM) plays an essential role in the biological and molecular mechanisms. They are also considered as a vital element in cell signaling and networking pathways. Among different PTMs, Methylation is regarded as one of the most important types. Methylation plays a crucial role in maintaining the dynamic balance, stability, and remodeling of chromatins. Methylation also leads to different abnormalities in cells and is responsible for many serious diseases. Methylation can be detected by experimental approaches such as methylation-specific antibodies, mass spectrometry, or characterizing methylation sites using the radioactive labeling method. However, these approaches are time-consuming and costly. Therefore, there is a demand for fast and accurate computational techniques to solve these issues. This study proposes a novel machine learning approach called MethEvo to predict methylation sites in proteins. To build this model, we use an evolutionary-based bi-gram profile approach to extract features. We also use SVM as our classification technique to build MethEvo. Our results demonstrate that MethEvo achieves 98.7%, 98.8%, 98.4%, and 0.974 in terms of accuracy, specificity, sensitivity, and Matthews Correlation Coefficient (MCC). MethEvo and its source code are publicly available at: https://github.com/islamsadia88/MethEvo. [ABSTRACT FROM AUTHOR]

Skin cancer, primarily resulting from the abnormal growth of skin cells, is among the most common cancer types. In recent decades, the incidence of skin cancer cases worldwide has risen significantly (one in every three newly diagnosed cancer cases is a skin cancer). Such an increase can be attributed to changes in our social and lifestyle habits coupled with devastating man-made alterations to the global ecosystem. Despite such a notable increase, diagnosis of skin cancer is still challenging, which becomes critical as its early detection is crucial for increasing the overall survival rate. This calls for advancements of innovative computer-aided systems to assist medical experts with their decision making. In this context, there has been a recent surge of interest in machine learning (ML), in particular, deep neural networks (DNNs), to provide complementary assistance to expert physicians. While DNNs have a high processing capacity far beyond that of human experts, their outputs are deterministic, i.e., providing estimates without prediction confidence. Therefore, it is of paramount importance to develop DNNs with uncertainty-awareness to provide confidence in their predictions. Monte Carlo dropout (MCD) is vastly used for uncertainty quantification; however, MCD suffers from overconfidence and being miss calibrated. In this paper, we use MCD algorithm to develop an uncertainty-aware DNN that assigns high predictive entropy to erroneous predictions and enable the model to optimize the hyper-parameters during training, which leads to more accurate uncertainty quantification. We use two synthetic (two moons and blobs) and a real dataset (skin cancer) to validate our algorithm. Our experiments on these datasets prove effectiveness of our approach in quantifying reliable uncertainty. Our method achieved 85.65 ± 0.18 prediction accuracy, 83.03 ± 0.25 uncertainty accuracy, and 1.93 ± 0.3 expected calibration error outperforming vanilla MCD and MCD with loss enhanced based on predicted entropy. [ABSTRACT FROM AUTHOR]

It is now well-known that genetic mutations contribute to development of tumors, in which at least 15% of cancer patients experience a causative genetic abnormality including De Novo somatic point mutations. This highlights the importance of identifying responsible mutations and the associated biomarkers (e.g., genes) for early detection in high-risk cancer patients. The next-generation sequencing technologies have provided an excellent opportunity for researchers to study associations between De Novo somatic mutations and cancer progression by identifying cancer subtypes and subtype-specific biomarkers. Simple linear classification models have been used for somatic point mutation-based cancer classification (SMCC); however, because of cancer genetic heterogeneity (ranging from 50 to 80%), high data sparsity, and the small number of cancer samples, the simple linear classifiers resulted in poor cancer subtypes classification. In this study, we have evaluated three advanced deep neural network-based classifiers to find and optimized the best model for cancer subtyping. To address the above-mentioned complexity, we have used pre-processing clustered gene filtering (CGF) and indexed sparsity reduction (ISR), regularization methods, a Global-Max-Pooling layer, and an embedding layer. We have evaluated and optimized the three deep learning models CNN, LSTM, and a hybrid model of CNN + LSTM on publicly available TCGA-DeepGene dataset, a re-formulated subset of The Cancer Genome Atlas (TCGA) dataset and tested the performance measurement of these models is 10-cross-validation accuracy. Evaluating all the three models using a same criterion on the test dataset revealed that the CNN, LSTM, and CNN + LSTM have 66.45% accuracy, 40.89% accuracy, and 41.20% accuracy in somatic point mutation-based cancer classification. Based on our results, we propose the CNN model for further experiments on cancer subtyping based on DNA mutations. [ABSTRACT FROM AUTHOR]

Non-coding RNAs (ncRNAs) form a large portion of the mammalian genome. However, their biological functions are poorly characterized in cancers. In this study, using a newly developed tool, SomaGene, we analyze de novo somatic point mutations from the International Cancer Genome Consortium (ICGC) whole-genome sequencing data of 1,855 breast cancer samples. We identify 1030 candidates of ncRNAs that are significantly and explicitly mutated in breast cancer samples. By integrating data from the ENCODE regulatory features and FANTOM5 expression atlas, we show that the candidate ncRNAs significantly enrich active chromatin histone marks (1.9 times), CTCF binding sites (2.45 times), DNase accessibility (1.76 times), HMM predicted enhancers (2.26 times) and eQTL polymorphisms (1.77 times). Importantly, we show that the 1030 ncRNAs contain a much higher level (3.64 times) of breast cancer-associated genome-wide association (GWAS) single nucleotide polymorphisms (SNPs) than genome-wide expectation. Such enrichment has not been seen with GWAS SNPs from other cancers. Using breast cell line related Hi-C data, we then show that 82% of our candidate ncRNAs (1.9 times) significantly interact with the promoter of protein-coding genes, including previously known cancer-associated genes, suggesting the critical role of candidate ncRNA genes in the activation of essential regulators of development and differentiation in breast cancer. We provide an extensive web-based resource (https://www.ihealthe.unsw.edu.au/research) to communicate our results with the research community. Our list of breast cancer-specific ncRNA genes has the potential to provide a better understanding of the underlying genetic causes of breast cancer. Lastly, the tool developed in this study can be used to analyze somatic mutations in all cancers. The SomaGene tool is developed to identify non-coding RNAs (ncRNAs) mutated in breast cancer but can be used for other cancers. Candidate ncRNAs are shown to be enriched for regulatory features and to contain specific trait loci polymorphisms. [ABSTRACT FROM AUTHOR]

Emotion recognition is defined as identifying human emotion and is directly related to different fields such as human–computer interfaces, human emotional processing, irrational analysis, medical diagnostics, data-driven animation, human–robot communication, and many more. This paper proposes a new facial emotional recognition model using a convolutional neural network. Our proposed model, "ConvNet", detects seven specific emotions from image data including anger, disgust, fear, happiness, neutrality, sadness, and surprise. The features extracted by the Local Binary Pattern (LBP), region based Oriented FAST and rotated BRIEF (ORB) and Convolutional Neural network (CNN) from facial expressions images were fused to develop the classification model through training by our proposed CNN model (ConvNet). Our method can converge quickly and achieves good performance which the authors can develop a real-time schema that can easily fit the model and sense emotions. Furthermore, this study focuses on the mental or emotional stuff of a man or woman using the behavioral aspects. To complete the training of the CNN network model, we use the FER2013 databases at first, and then apply the generalization techniques to the JAFFE and CK+ datasets respectively in the testing stage to evaluate the performance of the model. In the generalization approach on the JAFFE dataset, we get a 92.05% accuracy, while on the CK+ dataset, we acquire a 98.13% accuracy which achieve the best performance among existing methods. We also test the system's success by identifying facial expressions in real-time. ConvNet consists of four layers of convolution together with two fully connected layers. The experimental results show that the ConvNet is able to achieve 96% training accuracy which is much better than current existing models. However, when compared to other validation methods, the suggested technique was more accurate. ConvNet also achieved validation accuracy of 91.01% for the FER2013 dataset. We also made all the materials publicly accessible for the research community at: https://github.com/Tanoy004/Emotion-recognition-through-CNN. [ABSTRACT FROM AUTHOR]

The zinc finger antiviral protein (ZAP) is known to restrict viral replication by binding to the CpG rich regions of viral RNA, and subsequently inducing viral RNA degradation. This enzyme has recently been shown to be capable of restricting SARS-CoV-2. These data have led to the hypothesis that the low abundance of CpG in the SARS-CoV-2 genome is due to an evolutionary pressure exerted by the host ZAP. To investigate this hypothesis, we performed a detailed analysis of many coronavirus sequences and ZAP RNA binding preference data. Our analyses showed neither evidence for an evolutionary pressure acting specifically on CpG dinucleotides, nor a link between the activity of ZAP and the low CpG abundance of the SARS-CoV-2 genome. [ABSTRACT FROM AUTHOR]

In order to improve the performance of a clustering on a data set, a number of primary partitions are generated and stored in an ensemble and their aggregated consensus partition is used as their clustering. It is widely accepted that the consensus partition outperforms the primary partitions. In this paper, an ensemble clustering method called multi-level consensus clustering (MLCC) is proposed. To construct the MLCC, a cluster–cluster similarity matrix which is achieved by an innovative similarity metric is first generated. The mentioned cluster–cluster similarity matrix is based on a multi-level similarity metric. In fact, it can be computed in a new defined multi-level space. Then, a point–point similarity matrix which is boosted using the mentioned cluster–cluster similarity matrix is generated. The new consensus function applies an average linkage hierarchical clusterer algorithm on the mentioned point–point similarity matrix to make consensus partition. MLCC is better than traditional clustering ensembles and simple versions of clustering ensembles on traditional cluster–cluster similarity matrix. Its computational cost is not very bad too. Accuracy and robustness of the proposed method are compared with those of the modern clustering algorithms through the experimental tests. Also, time analysis is presented in the experimental results. [ABSTRACT FROM AUTHOR]

The ensemble clustering tries to aggregate a number of basic clusterings with the aim of producing a more consistent, robust and well-performing consensus clustering result. The current paper wants to introduce an ensemble clustering method. The proposed method, called consensus function based on two level clustering (CFTLC), introduces a new consensus clustering where it makes a cluster clustering task through applying an average hierarchical clustering on a cluster–cluster similarity matrix obtained by an innovative similarity metric. By applying the average hierarchical clustering algorithm, a set of meta clusters has been attained. Considering each meta cluster as a consensus cluster in the consensus clustering output, it then assigns each data point to a meta cluster through defining an object-cluster similarity. Before doing anything, CFTLC converts the primary partitions into a binary cluster representation where the primary ensemble has been broken into a number of basic binary clusters (BC). CFTLC first combines the basic BCs with the maximum cluster–cluster similarity. This step is iterated as long as a predefined number of meta clusters are ready. At the subsequent step, it assigns each data point to exactly one meta cluster. The proposed method has been experimentally compared with the state of the art clustering algorithms in terms of accuracy and robustness. [ABSTRACT FROM AUTHOR]

Clustering ensembles combine multiple partitions of data into a single clustering solution of better quality. Inspired by the success of supervised bagging and boosting algorithms, we propose non-adaptive and adaptive resampling schemes for the integration of multiple independent and dependent clusterings. We investigate the effectiveness of bagging techniques, comparing the efficacy of sampling with and without replacement, in conjunction with several consensus algorithms. In our adaptive approach, individual partitions in the ensemble are sequentially generated by clustering specially selected subsamples of the given dataset. The sampling probability for each data point dynamically depends on the consistency of its previous assignments in the ensemble. New subsamples are then drawn to increasingly focus on the problematic regions of the input feature space. A measure of data point clustering consistency is therefore defined to guide this adaptation. Experimental results show improved stability and accuracy for clustering structures obtained via bootstrapping, subsampling, and adaptive techniques. A meaningful consensus partition for an entire set of data points emerges from multiple clusterings of bootstraps and subsamples. Subsamples of small size can reduce computational cost and measurement complexity for many unsupervised data mining tasks with distributed sources of data. This empirical study also compares the performance of adaptive and non-adaptive clustering ensembles using different consensus functions on a number of datasets. By focusing attention on the data points with the least consistent clustering assignments, whether one can better approximate the inter-cluster boundaries or can at least create diversity in boundaries and this results in improving clustering accuracy and convergence speed as a function of the number of partitions in the ensemble. The comparison of adaptive and non-adaptive approaches is a new avenue for research, and this study helps to pave the way for the useful application of distributed data mining methods. [ABSTRACT FROM AUTHOR]

Recent advances in high-throughput technologies have provided an unprecedented opportunity to identify molecular markers of disease processes. This plethora of complex-omics data has simultaneously complicated the problem of extracting meaningful molecular signatures and opened up new opportunities for more sophisticated integrative and holistic approaches. In this era, effective integration of data-driven and knowledge-based approaches for biomarker identification has been recognised as key to improving the identification of high-performance biomarkers, and necessary for translational applications. Here, we have evaluated the role of circulating microRNA as a means of predicting the prognosis of patients with colorectal cancer, which is the second leading cause of cancer-related death worldwide. We have developed a multi-objective optimisation method that effectively integrates a data-driven approach with the knowledge obtained from the microRNA-mediated regulatory network to identify robust plasma microRNA signatures which are reliable in terms of predictive power as well as functional relevance. The proposed multi-objective framework has the capacity to adjust for conflicting biomarker objectives and to incorporate heterogeneous information facilitating systems approaches to biomarker discovery. We have found a prognostic signature of colorectal cancer comprising 11 circulating microRNAs. The identified signature predicts the patients' survival outcome and targets pathways underlying colorectal cancer progression. The altered expression of the identified microRNAs was confirmed in an independent public data set of plasma samples of patients in early stage vs advanced colorectal cancer. Furthermore, the generality of the proposed method was demonstrated across three publicly available miRNA data sets associated with biomarker studies in other diseases. MiRNA biomarker discovery: a network-based, knowledge-driven approach The identification of robust and reproducible molecular markers is one of the biggest challenges in personalised cancer medicine. The increasing use of systems biology approaches has prompted researchers to integrate heterogeneous data into existing knowledge bases whose incorporation into the biomarker discovery workflow may adjust for data heterogeneity and limitation, and offer more precise, robust and consistent biomarkers. In this study, we have sought to determine network-based miRNA biomarker signatures from the plasma of colorectal cancer patients that hold prognostic utility. We performed miRNA profiling and then constructed an miRNA-mediated gene regulatory network and developed a multi-objective optimisation-based computational framework to identify miRNA biomarkers using both the miRNA expression profile and knowledge from this miRNA-mediated regulatory network. We have demonstrated the ability of the proposed approach in identifying robust, accurate and reproducible biomarkers. [ABSTRACT FROM AUTHOR]