Finding Clusters of Similar-minded People on Twitter Regarding the Covid-19 Pandemic

Two clustering methods to determine users with similar opinions on the Covid-19 pandemic and the related public debate in Germany will be presented in this paper. We believe, they can helpgaining an overview over similar-minded groups and could support the prevention of fake-news distribution. The first method uses a new approach to create a network based on retweetrelationships between users and the most retweeted users, the so-called influencers. The second method extracts hashtags from users posts to create a “user feature vector” which is then clustered, using a consensus matrix based on previous work, to identify groups using the same language. With both approaches it was possible to identify clusters that seem to fit groups of different public opinions in Germany. However, we also found that clusters from one approach cannot be associated with clusters from the other due to filtering steps in the two methods.

A Decision Support System and Visualisation Tools for AHP-GDM

The Precise Consistency Consensus Matrix (PCCM) is a decisional tool for AHP-Group Decision Making (AHP-GDM). Based on the initial pairwise comparison matrices of the individuals, the PCCM constructs a consensus matrix for the group using the concept of consistency. This paper presents a decision support system (PRIOR-PCCM) that facilitates the construction of the PCCM in the context of AHP-GDM, and the calculus of four indicators that allows comparison of the behaviour of group consensus matrices. PRIOR-PCCM incorporates the possibility of considering different weights for the decision makers and includes a module that permits the extension of the initial PCCM which can achieve the minimum number of non-null entries required for deriving priorities or establishing a complete PCCM matrix. It also includes two cardinal indicators for measuring consistency and compatibility and two ordinal indicators for evaluating the number of violations of consistency and priority. The paper introduces some new visualisation tools that improve comprehension of the process followed for obtaining the PCCM matrix and allow the cognitive exploitation of the results. These original contributions are illustrated with a case study.

Sc-GPE: A Graph Partitioning-Based Cluster Ensemble Method for Single-Cell

Clustering is an efficient way to analyze single-cell RNA sequencing data. It is commonly used to identify cell types, which can help in understanding cell differentiation processes. However, different clustering results can be obtained from different single-cell clustering methods, sometimes including conflicting conclusions, and biologists will often fail to get the right clustering results and interpret the biological significance. The cluster ensemble strategy can be an effective solution for the problem. As the graph partitioning-based clustering methods are good at clustering single-cell, we developed Sc-GPE, a novel cluster ensemble method combining five single-cell graph partitioning-based clustering methods. The five methods are SNN-cliq, PhenoGraph, SC3, SSNN-Louvain, and MPGS-Louvain. In Sc-GPE, a consensus matrix is constructed based on the five clustering solutions by calculating the probability that the cell pairs are divided into the same cluster. It solved the problem in the hypergraph-based ensemble approach, including the different cluster labels that were assigned in the individual clustering method, and it was difficult to find the corresponding cluster labels across all methods. Then, to distinguish the different importance of each method in a clustering ensemble, a weighted consensus matrix was constructed by designing an importance score strategy. Finally, hierarchical clustering was performed on the weighted consensus matrix to cluster cells. To evaluate the performance, we compared Sc-GPE with the individual clustering methods and the state-of-the-art SAME-clustering on 12 single-cell RNA-seq datasets. The results show that Sc-GPE obtained the best average performance, and achieved the highest NMI and ARI value in five datasets.

Splicing Enhancers at Intron–Exon Borders Participate in Acceptor Splice Sites Recognition

Acceptor splice site recognition (3′ splice site: 3′ss) is a fundamental step in precursor messenger RNA (pre-mRNA) splicing. Generally, the U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) heterodimer recognizes the 3′ss, of which U2AF35 has a dual function: (i) It binds to the intron–exon border of some 3′ss and (ii) mediates enhancer-binding splicing activators’ interactions with the spliceosome. Alternative mechanisms for 3′ss recognition have been suggested, yet they are still not thoroughly understood. Here, we analyzed 3′ss recognition where the intron–exon border is bound by a ubiquitous splicing regulator SRSF1. Using the minigene analysis of two model exons and their mutants, BRCA2 exon 12 and VARS2 exon 17, we showed that the exon inclusion correlated much better with the predicted SRSF1 affinity than 3′ss quality, which were assessed using the Catalog of Inferred Sequence Binding Preferences of RNA binding proteins (CISBP-RNA) database and maximum entropy algorithm (MaxEnt) predictor and the U2AF35 consensus matrix, respectively. RNA affinity purification proved SRSF1 binding to the model 3′ss. On the other hand, knockdown experiments revealed that U2AF35 also plays a role in these exons’ inclusion. Most probably, both factors stochastically bind the 3′ss, supporting exon recognition, more apparently in VARS2 exon 17. Identifying splicing activators as 3′ss recognition factors is crucial for both a basic understanding of splicing regulation and human genetic diagnostics when assessing variants’ effects on splicing.

AHP-Group Decision Making Based on Consistency

The Precise consistency consensus matrix (PCCM) is a consensus matrix for AHP-group decision making in which the value of each entry belongs, simultaneously, to all the individual consistency stability intervals. This new consensus matrix has shown significantly better behaviour with regards to consistency than other group consensus matrices, but it is slightly worse in terms of compatibility, understood as the discrepancy between the individual positions and the collective position that synthesises them. This paper includes an iterative algorithm for improving the compatibility of the PCCM. The sequence followed to modify the judgments of the PCCM is given by the entries that most contribute to the overall compatibility of the group. The procedure is illustrated by means of its application to a real-life situation (a local context) with three decision makers and four alternatives. The paper also offers, for the first time in the scientific literature, a detailed explanation of the process followed to solve the optimisation problem proposed for the consideration of different weights for the decision makers in the calculation of the PCCM.

A Decision Support System and Visualisation Tools for AHP-GDM

The Precise Consistency Consensus Matrix (PCCM) is a decisional tool for AHP-Group Decision Making (AHP-GDM). Based on the initial pairwise comparison matrices of the individuals, the PCCM constructs a consensus matrix for the group using the concept of consistency. This paper presents a decision support system (PRIOR-PCCM) that facilitates the construction of the PCCM in the context of AHP-GDM, and the calculus of four indicators that allows comparison of the behaviour of group consensus matrices. PRIOR-PCCM incorporates the possibility of considering different weights for the decision makers and includes a module that permits the extension of the initial PCCM which can achieve the minimum number of non-null entries required for deriving priorities or establishing a complete PCCM matrix. It also includes two cardinal indicators for measuring consistency and compatibility and two ordinal indicators for evaluating the number of violations of consistency and priority. The paper introduces some new visualisation tools that improve comprehension of the process followed for obtaining the PCCM matrix and allow the cognitive exploitation of the results. These original contributions are illustrated with a case study.

TraRECo: A Greedy Approach based de novo Transcriptome Assembler with Read Error Correction using Consensus Matrix

BackgroundChallenges in developing a good de novo transcriptome assembler include how to deal with read errors and sequence repeats. Almost all de novo assemblers utilize de Bruijn graph, which has a complexity linearly growing with data size while suffers from errors and repeat. Although one can correct errors by inspecting topological structure of the graph, it is an uneasy task when there are too many branches. There are two research directions: improving either graph reliability or path search precision. We focused on improving the reliability.ResultsWe present TraRECo, a greedy approach to de novo assembly employing error-aware graph construction. The idea is similar to overlap-layout-consensus approach used for genome assembly, but is different in that consensus is made through the entire graph construction step. Basically, we built contigs by direct read alignment within a distance margin and performed junction search to construct splicing graphs. While doing so, however, a contig of length l was represented by 4×1 matrix (called consensus matrix), of which each element was the base count of aligned reads so far. A representative sequence is obtained, by taking majority in each column of the consensus matrix, to be used for further read alignment. Once splicing graphs were obtained, we used IsoLasso to find paths with noticeable read depth. The experiments using real and simulated reads showed that the method provides considerable improvements in sensitivity and reasonably better performances when comparing both sensitivity and precision. This could be achieved by making more erroneous reads to be participated in graph construction, which, in turn, improved the depth information quality used for the subsequent path search step. The results for simulated reads showed also challenges are still remaining since non-negligible percentage of transcripts with high abundance were not recovered by the assemblers we considered.Conclusionde novo assembly is mainly to explore not-yet-discovered isoforms and must be able to represent as much reads as possible in an efficient way. In this sense, TraRECo provides us a potential alternative to improve graph reliability, even though the computational burden can be much higher than single k-mer de Bruijn graph approach.

Consensus clustering approach to group brain connectivity matrices

A novel approach rooted on the notion of consensus clustering, a strategy developed for community detection in complex networks, is proposed to cope with the heterogeneity that characterizes connectivity matrices in health and disease. The method can be summarized as follows: (a) define, for each node, a distance matrix for the set of subjects by comparing the connectivity pattern of that node in all pairs of subjects; (b) cluster the distance matrix for each node; (c) build the consensus network from the corresponding partitions; and (d) extract groups of subjects by finding the communities of the consensus network thus obtained. Different from the previous implementations of consensus clustering, we thus propose to use the consensus strategy to combine the information arising from the connectivity patterns of each node. The proposed approach may be seen either as an exploratory technique or as an unsupervised pretraining step to help the subsequent construction of a supervised classifier. Applications on a toy model and two real datasets show the effectiveness of the proposed methodology, which represents heterogeneity of a set of subjects in terms of a weighted network, the consensus matrix.