Effect of APOE ε4 on multimodal brain connectomic traits: a persistent homology study

Unified topological inference for brain networks in temporal lobe epilepsy using the Wasserstein distance

Persistent homology offers a powerful tool for extracting hidden topological signals from brain networks. It captures the evolution of topological structures across multiple scales, known as filtrations, thereby revealing topological features that persist over these scales. These features are summarized in persistence diagrams, and their dissimilarity is quantified using the Wasserstein distance. However, the Wasserstein distance does not follow a known distribution, posing challenges for the application of existing parametric statistical models. To tackle this issue, we introduce a unified topological inference framework centered on the Wasserstein distance. Our approach has no explicit model and distributional assumptions. The inference is performed in a completely data driven fashion. We apply this method to resting-state functional magnetic resonance images (rs-fMRI) of temporal lobe epilepsy patients collected from two different sites: the University of Wisconsin-Madison and the Medical College of Wisconsin. Importantly, our topological method is robust to variations due to sex and image acquisition, obviating the need to account for these variables as nuisance covariates. We successfully localize the brain regions that contribute the most to topological differences. A MATLAB package used for all analyses in this study is available at https://github.com/laplcebeltrami/PH-STAT.

Unified Topological Inference for Brain Networks in Temporal Lobe Epilepsy Using the Wasserstein Distance

Persistent homology offers a powerful tool for extracting hidden topological signals from brain networks. It captures the evolution of topological structures across multiple scales, known as filtrations, thereby revealing topological features that persist over these scales. These features are summarized in persistence diagrams, and their dissimilarity is quantified using the Wasserstein distance. However, the Wasserstein distance does not follow a known distribution, posing challenges for the application of existing parametric statistical models. To tackle this issue, we introduce a unified topological inference framework centered on the Wasserstein distance. Our approach has no explicit model and distributional assumptions. The inference is performed in a completely data driven fashion. We apply this method to resting-state functional magnetic resonance images (rs-fMRI) of temporal lobe epilepsy patients collected from two different sites: the University of Wisconsin-Madison and the Medical College of Wisconsin. Importantly, our topological method is robust to variations due to sex and image acquisition, obviating the need to account for these variables as nuisance covariates. We successfully localize the brain regions that contribute the most to topological differences. A MATLAB package used for all analyses in this study is available at https://github.com/laplcebeltrami/PH-STAT.

Characterizing Topological Properties of Brain Functional Networks Using Multi-Threshold Derivative for End-Stage Renal Disease with Mild Cognitive Impairment

Patients with end-stage renal disease (ESRD) experience changes in both the structure and function of their brain networks. In the past, cognitive impairment was often classified based on connectivity features, which only reflected the characteristics of the binary brain network or weighted brain network. It exhibited limited interpretability and stability. This study aims to quantitatively characterize the topological properties of brain functional networks (BFNs) using multi-threshold derivative (MTD), and to establish a new classification framework for end-stage renal disease with mild cognitive impairment (ESRDaMCI). The dynamic BFNs (DBFNs) were constructed and binarized with multiple thresholds, and then their topological properties were extracted from each binary brain network. These properties were then quantified by calculating their derivative curves and expressing them as multi-threshold derivative (MTD) features. The classification results of MTD features were compared with several commonly used DBFN features, and the effectiveness of MTD features in the classification of ESRDaMCI was evaluated based on the classification performance test. The results indicated that the linear fusion of MTD features improved classification performance and outperformed individual MTD features. Its accuracy, sensitivity, and specificity were 85.98 ± 2.92%, 86.10 ± 4.11%, and 81.54 ± 4.27%, respectively. Finally, the feature weights of MTD were analyzed, and MTD-cc had the highest weight percentage of 28.32% in the fused features. The MTD features effectively supplemented traditional feature quantification by addressing the issue of indistinct classification differentiation. It improved the quantification of topological properties and provided more detailed features for diagnosing cognitive disorders.

Graph Theory-Based Approach in Brain Connectivity Modeling and Alzheimer's Disease Detection

There is strong evidence that the pathological findings of Alzheimer's disease (AD), consisting of accumulated amyloid plaques and neurofibrillary tangles, could spread around the brain through synapses and neural connections of neighboring brain sections. Graph theory is a helpful tool in depicting the complex human brain divided into various regions of interest (ROIs) and the connections among them. Thus, applying graph theory-based models in the study of brain connectivity comes natural in the study of AD propagation mechanisms. Moreover, graph theory-based computational approaches have been lately applied in order to boost data-driven analysis, extract model measures and robustness-effectiveness indexes, and provide insights on casual interactions between regions of interest (ROI), as imposed by the models' architecture.

Artificial intelligence to deep learning: machine intelligence approach for drug discovery

Drug designing and development is an important area of research for pharmaceutical companies and chemical scientists. However, low efficacy, off-target delivery, time consumption, and high cost impose a hurdle and challenges that impact drug design and discovery. Further, complex and big data from genomics, proteomics, microarray data, and clinical trials also impose an obstacle in the drug discovery pipeline. Artificial intelligence and machine learning technology play a crucial role in drug discovery and development. In other words, artificial neural networks and deep learning algorithms have modernized the area. Machine learning and deep learning algorithms have been implemented in several drug discovery processes such as peptide synthesis, structure-based virtual screening, ligand-based virtual screening, toxicity prediction, drug monitoring and release, pharmacophore modeling, quantitative structure-activity relationship, drug repositioning, polypharmacology, and physiochemical activity. Evidence from the past strengthens the implementation of artificial intelligence and deep learning in this field. Moreover, novel data mining, curation, and management techniques provided critical support to recently developed modeling algorithms. In summary, artificial intelligence and deep learning advancements provide an excellent opportunity for rational drug design and discovery process, which will eventually impact mankind. The primary concern associated with drug design and development is time consumption and production cost. Further, inefficiency, inaccurate target delivery, and inappropriate dosage are other hurdles that inhibit the process of drug delivery and development. With advancements in technology, computer-aided drug design integrating artificial intelligence algorithms can eliminate the challenges and hurdles of traditional drug design and development. Artificial intelligence is referred to as superset comprising machine learning, whereas machine learning comprises supervised learning, unsupervised learning, and reinforcement learning. Further, deep learning, a subset of machine learning, has been extensively implemented in drug design and development. The artificial neural network, deep neural network, support vector machines, classification and regression, generative adversarial networks, symbolic learning, and meta-learning are examples of the algorithms applied to the drug design and discovery process. Artificial intelligence has been applied to different areas of drug design and development process, such as from peptide synthesis to molecule design, virtual screening to molecular docking, quantitative structure-activity relationship to drug repositioning, protein misfolding to protein-protein interactions, and molecular pathway identification to polypharmacology. Artificial intelligence principles have been applied to the classification of active and inactive, monitoring drug release, pre-clinical and clinical development, primary and secondary drug screening, biomarker development, pharmaceutical manufacturing, bioactivity identification and physiochemical properties, prediction of toxicity, and identification of mode of action.

An In Silico Method for Predicting Drug Synergy Based on Multitask Learning

To make better use of all kinds of knowledge to predict drug synergy, it is crucial to successfully establish a drug synergy prediction model and leverage the reconstruction of sparse known drug targets. Therefore, we present an in silico method that predicts the synergy scores of drug pairs based on multitask learning (DSML) that could fuse drug targets, protein-protein interactions, anatomical therapeutic chemical codes, a priori knowledge of drug combinations. To simultaneously reconstruct drug-target protein interactions and synergistic drug combinations, DSML benefits indirectly from the associations with relation through proteins. In cross-validation experiments, DSML improved the ability to predict drug synergy. Moreover, the reconstruction of drug-target interactions and the incorporation of multisource knowledge significantly improved drug combination predictions by a large margin. The potential drug combinations predicted by DSML demonstrate its ability to predict drug synergy.

Accelerating bioinformatics research with International Conference on Intelligent Biology and Medicine 2020

The International Association for Intelligent Biology and Medicine (IAIBM) is a nonprofit organization that promotes intelligent biology and medical science. It hosts an annual International Conference on Intelligent Biology and Medicine (ICIBM), which was initially established in 2012. Due to the coronavirus (COVID-19) pandemic, the ICIBM 2020 was held for the first time as a virtual online conference on August 9 to 10. The virtual conference had ~ 300 registered participants and featured 41 online real-time presentations. ICIBM 2020 received a total of 75 manuscript submissions, and 12 were selected to be published in this special issue of BMC Bioinformatics. These 12 manuscripts cover a wide range of bioinformatics topics including network analysis, imaging analysis, machine learning, gene expression analysis, and sequence analysis.