Robustness evaluations of pathway activity inference methods on gene expression data.

BACKGROUND: With the exponential growth of high-throughput technologies, multiple pathway analysis methods have been proposed to estimate pathway activities from gene expression profiles. These pathway activity inference methods can be divided into two main categories: non-Topology-Based (non-TB) and Pathway Topology-Based (PTB) methods. Although some review and survey articles discussed the topic from different aspects, there is a lack of systematic assessment and comparisons on the robustness of these approaches. RESULTS: Thus, this study presents comprehensive robustness evaluations of seven widely used pathway activity inference methods using six cancer datasets based on two assessments. The first assessment seeks to investigate the robustness of pathway activity in pathway activity inference methods, while the second assessment aims to assess the robustness of risk-active pathways and genes predicted by these methods. The mean reproducibility power and total number of identified informative pathways and genes were evaluated. Based on the first assessment, the mean reproducibility power of pathway activity inference methods generally decreased as the number of pathway selections increased. Entropy-based Directed Random Walk (e-DRW) distinctly outperformed other methods in exhibiting the greatest reproducibility power across all cancer datasets. On the other hand, the second assessment shows that no methods provide satisfactory results across datasets. CONCLUSION: However, PTB methods generally appear to perform better in producing greater reproducibility power and identifying potential cancer markers compared to non-TB methods.

Metaheuristic Algorithms Based on Compromise Programming for the Multi-Objective Urban Shipment Problem.

The Vehicle Routing Problem (VRP) and its variants are found in many fields, especially logistics. In this study, we introduced an adaptive method to a complex VRP. It combines multi-objective optimization and several forms of VRPs with practical requirements for an urban shipment system. The optimizer needs to consider terrain and traffic conditions. The proposed model also considers customers' expectations and shipper considerations as goals, and a common goal such as transportation cost. We offered compromise programming to approach the multi-objective problem by decomposing the original multi-objective problem into a minimized distance-based problem. We designed a hybrid version of the genetic algorithm with the local search algorithm to solve the proposed problem. We evaluated the effectiveness of the proposed algorithm with the Tabu Search algorithm and the original genetic algorithm on the tested dataset. The results show that our method is an effective decision-making tool for the multi-objective VRP and an effective solver for the new variation of VRP.

Recent Applications of Artificial Intelligence in the Detection of Gastrointestinal, Hepatic and Pancreatic Diseases.

There has been substantial progress in artificial intelligence (AI) algorithms and their medical sciences applications in the last two decades. AI-assisted programs have already been established for remote health monitoring using sensors and smartphones. A variety of AI-based prediction models are available for gastrointestinal, inflammatory, non-malignant diseases, and bowel bleeding using wireless capsule endoscopy, hepatitis-associated fibrosis using electronic medical records, and pancreatic carcinoma utilizing endoscopic ultrasounds. AI-based models may be of immense help for healthcare professionals in the identification, analysis, and decision support using endoscopic images to establish prognosis and risk assessment of patients' treatment employing multiple factors. Enough randomized clinical trials are warranted to establish the efficacy of AI-algorithms assisted and non-AI-based treatments before approval of such techniques from medical regulatory authorities. In this article, available AI approaches and AI-based prediction models for detecting gastrointestinal, hepatic, and pancreatic diseases are reviewed. The limitations of AI techniques in such diseases' prognosis, risk assessment, and decision support are discussed.

A deep neural network-based approach for prediction of mutagenicity of compounds.

We are exposed to various chemical compounds present in the environment, cosmetics, and drugs almost every day. Mutagenicity is a valuable property that plays a significant role in establishing a chemical compound's safety. Exposure and handling of mutagenic chemicals in the environment pose a high health risk; therefore, identification and screening of these chemicals are essential. Considering the time constraints and the pressure to avoid laboratory animals' use, the shift to alternative methodologies that can establish a rapid and cost-effective detection without undue over-conservation seems critical. In this regard, computational detection and identification of the mutagens in environmental samples like drugs, pesticides, dyes, reagents, wastewater, cosmetics, and other substances is vital. From the last two decades, there have been numerous efforts to develop the prediction models for mutagenicity, and by far, machine learning methods have demonstrated some noteworthy performance and reliability. However, the accuracy of such prediction models has always been one of the major concerns for the researchers working in this area. The mutagenicity prediction models were developed using deep neural network (DNN), support vector machine, k-nearest neighbor, and random forest. The developed classifiers were based on 3039 compounds and validated on 1014 compounds; each of them encoded with 1597 molecular feature vectors. DNN-based prediction model yielded highest prediction accuracy of 92.95% and 83.81% with the training and test data, respectively. The area under the receiver's operating curve and precision-recall curve values were found to be 0.894 and 0.838, respectively. The DNN-based classifier not only fits the data with better performance as compared to traditional machine learning algorithms, viz., support vector machine, k-nearest neighbor, and random forest (with and without feature reduction) but also yields better performance metrics. In current work, we propose a DNN-based model to predict mutagenicity of compounds.

Incremental Interval Type-2 Fuzzy Clustering of Data Streams using Single Pass Method.

Data Streams create new challenges for fuzzy clustering algorithms, specifically Interval Type-2 Fuzzy C-Means (IT2FCM). One problem associated with IT2FCM is that it tends to be sensitive to initialization conditions and therefore, fails to return global optima. This problem has been addressed by optimizing IT2FCM using Ant Colony Optimization approach. However, IT2FCM-ACO obtain clusters for the whole dataset which is not suitable for clustering large streaming datasets that may be coming continuously and evolves with time. Thus, the clusters generated will also evolve with time. Additionally, the incoming data may not be available in memory all at once because of its size. Therefore, to encounter the challenges of a large data stream environment we propose improvising IT2FCM-ACO to generate clusters incrementally. The proposed algorithm produces clusters by determining appropriate cluster centers on a certain percentage of available datasets and then the obtained cluster centroids are combined with new incoming data points to generate another set of cluster centers. The process continues until all the data are scanned. The previous data points are released from memory which reduces time and space complexity. Thus, the proposed incremental method produces data partitions comparable to IT2FCM-ACO. The performance of the proposed method is evaluated on large real-life datasets. The results obtained from several fuzzy cluster validity index measures show the enhanced performance of the proposed method over other clustering algorithms. The proposed algorithm also improves upon the run time and produces excellent speed-ups for all datasets.