A scenario analysis under epistemic uncertainty in Natech accidents: imprecise probability reasoning in Bayesian Network

The increasing frequency and severity of Natech accidents warn us to investigate the occurrence mechanism of these events. Cascading disasters chain magnifies the impact of natural hazards due to its propagation through critical infrastructures and socio-economic networks. In order to manipulate imprecise probabilities of cascading events in Natech scenarios, this work proposes an improved Bayesian network （BN） combining with evidence theory to better deal with epistemic uncertainty in Natech accidents than traditional BNs. Effective inference algorithms have been developed to propagate system faulty in a socio-economic system. The conditional probability table (CPT) of BN in the traditional probability approach is modified by utilizing an OR/AND gate to obtain the belief mass propagation in the framework of evidence theory. Our improved Bayesian network methodology makes it possible to assess the impact and damage of Natech accidents under the environment of complex interdependence among accidents with insufficient data. Finally, a case study of Guangdong province, an area prone to natural disasters, is given. The modified Bayesian network is carried out to analyze this area’s Natech scenario. After diagnostic analysis and sensitivity analysis of human factors and the natural factor, we are able to locate the key nodes in the cascading disaster chain. Findings can provide useful theoretical support for urban managers of industrial cities to enhance disaster prevention and mitigation ability.

Gene regulation network inference using k-nearest neighbor-based mutual information estimation- Revisiting an old DREAM

Background: A cell exhibits a variety of responses to internal and external cues. These responses are possible, in part, due to the presence of an elaborate gene regulatory network (GRN) in every single cell. In the past twenty years, many groups worked on reconstructing the topological structure of GRNs from large-scale gene expression data using a variety of inference algorithms. Insights gained about participating players in GRNs may ultimately lead to therapeutic benefits. Mutual information (MI) is a widely used metric within this inference/reconstruction pipeline as it can detect any correlation (linear and non-linear) between any number of variables (n-dimensions). However, the use of MI with continuous data (for example, normalized fluorescence intensity measurement of gene expression levels) is sensitive to data size, correlation strength and underlying distributions, and often requires laborious and, at times, ad hoc optimization. Results: In this work, we first show that estimating MI of a bi- and tri-variate Gaussian distribution using k-nearest neighbor (kNN) MI estimation results in significant error reduction as compared to commonly used methods based on fixed binning. Second, we demonstrate that implementing the MI-based kNN Kraskov-Stoogbauer-Grassberger (KSG) algorithm leads to a significant improvement in GRN reconstruction for popular inference algorithms, such as Context Likelihood of Relatedness (CLR). Finally, through extensive in-silico benchmarking we show that a new inference algorithm CMIA (Conditional Mutual Information Augmentation), inspired by CLR, in combination with the KSG-MI estimator, outperforms commonly used methods. Conclusions: Using three canonical datasets containing 15 synthetic networks, the newly developed method for GRN reconstruction - which combines CMIA, and the KSG-MI estimator - achieves an improvement of 20-35% in precision-recall measures over the current gold standard in the field. This new method will enable researchers to discover new gene interactions or choose gene candidates for experimental validations.

mPrivacy: A Privacy Policy Engine and Safeguard Mechanism in Mobile Devices

Within the scope of mobile privacy, there are many attack methods that can leak users’ private information. The communication between applications can be used to violate permissions and access private information without asking for the user’s authorization. Hence, many researchers made protection mechanisms against privilege escalation. However, attackers can further utilize inference algorithms to derive new information out of available data or improve the information quality without violating privilege limits. In this work. we describe the notion of Information Escalation Attack and propose a detection and protection mechanism using Inference Graph and Policy Engine for the user to control their policy on the App’s privilege in information escalation. Our implementation results show that the proposed privacy protection service is feasible and provides good useability.

A Performance Evaluation Model of Single-Cell Pseudotime Trajectory Inference Algorithms

The study on single-cell pseudotime trajectory is of great significance to the exploration of the environmental factors of life and diseases. The large scale and complexity of single-cell data make the single-cell pseudotime trajectory algorithms face great challenges. A performance evaluation model is proposed to measure the performance of existing pseudotime trajectory inference algorithms and mine the problems existing in the inference algorithms in order to promote the improvement of the inference algorithms. Under the condition of given original single-cell data, the model uses the Spearman correlation coefficient to evaluate the performance of the inference algorithms from noise resistance and robustness. Experiments on the algorithms Monocle2 and Scout were conducted to analyze the application effect of the model.

Applicability of several rooted phylogenetic network algorithms for representing the evolutionary history of SARS-CoV-2

Background Rooted phylogenetic networks are used to display complex evolutionary history involving so-called reticulation events, such as genetic recombination. Various methods have been developed to construct such networks, using for example a multiple sequence alignment or multiple phylogenetic trees as input data. Coronaviruses are known to recombine frequently, but rooted phylogenetic networks have not yet been used extensively to describe their evolutionary history. Here, we created a workflow to compare the evolutionary history of SARS-CoV-2 with other SARS-like viruses using several rooted phylogenetic network inference algorithms. This workflow includes filtering noise from sets of phylogenetic trees by contracting edges based on branch length and bootstrap support, followed by resolution of multifurcations. We explored the running times of the network inference algorithms, the impact of filtering on the properties of the produced networks, and attempted to derive biological insights regarding the evolution of SARS-CoV-2 from them. Results The network inference algorithms are capable of constructing rooted phylogenetic networks for coronavirus data, although running-time limitations require restricting such datasets to a relatively small number of taxa. Filtering generally reduces the number of reticulations in the produced networks and increases their temporal consistency. Taxon bat-SL-CoVZC45 emerges as a major and structural source of discordance in the dataset. The tested algorithms often indicate that SARS-CoV-2/RaTG13 is a tree-like clade, with possibly some reticulate activity further back in their history. A smaller number of constructed networks posit SARS-CoV-2 as a possible recombinant, although this might be a methodological artefact arising from the interaction of bat-SL-CoVZC45 discordance and the optimization criteria used. Conclusion Our results demonstrate that as part of a wider workflow and with careful attention paid to running time, rooted phylogenetic network algorithms are capable of producing plausible networks from coronavirus data. These networks partly corroborate existing theories about SARS-CoV-2, and partly produce new avenues for exploration regarding the location and significance of reticulate activity within the wider group of SARS-like viruses. Our workflow may serve as a model for pipelines in which phylogenetic network algorithms can be used to analyse different datasets and test different hypotheses.

Object-Based Scene Classification Modeled by Hidden Markov Models Architecture

Multiclass classification problems such as document classification, medical diagnosis or scene classification are very challenging to address due to similarities between mutual classes. The use of reliable tools is necessary to get good classification results. This paper addresses the scene classification problem using objects as attributes. The process of classification is modeled by a famous mathematical tool: The Hidden Markov Models. We introduce suitable relations that scale the parameters of the Hidden Markov Model into variables of scene classification. The construction of Hidden Markov Chains is supported with weight measures and sorting functions. Lastly, inference algorithms extract most suitable scene categories from the Discrete Markov Chain. A parallelism approach constructs several Discrete Markov Chains in order to improve the accuracy of the classification process. We provide numerous tests on different datasets and compare classification accuracies with some state of the art methods. The proposed approach distinguishes itself by outperforming the other.

Application of first-order logic to identify organizers and perpetrators of illegal actions in teams of a limited circle of people

There are three main families of inference algorithms in first-order logic: direct inference and its application to deductive databases and production systems; backward inference procedures and logic programming systems; theorem proving systems based on the resolution method. When solving specific problems, the most effective algorithms are those that allow you to cover all the facts and axioms and must be taken into account in the process of inference. An example is considered in which it is necessary to prove the guilt of a person in murder. On the basis of statements, a knowledge base is formed from expressions, with the help of which an expression of first-order logic is compiled and proved using direct logical inference. The proof of the reasoning obtained in direct inference using the proof tree is given. However, direct inference provides for the implementation of all admissible stages of logical inference based on all known facts. The article also considers a method based on the resolution when implementing the reverse inference, taking into account the expression obtained in the direct inference. This expression is converted into a conjunctive normal formula using the laws of Boolean algebra and is proved by the elimination of events using the conjunction operation.

Interpretable deep generative models for genomics

Deep neural networks implementing generative models for dimensionality reduction have been extensively used for the visualization and analysis of genomic data. One of their key limitations is lack of interpretability: it is challenging to quantitatively identify which input features are used to construct the embedding dimensions, thus preventing insight into why cells are organized in a particular data visualization, for example. Here we present a scalable, interpretable variational autoencoder (siVAE) that is interpretable by design: it learns feature embeddings that guide the interpretation of the cell embeddings in a manner analogous to factor loadings of factor analysis. siVAE is as powerful and nearly as fast to train as the standard VAE but achieves full interpretability of the embedding dimensions. We exploit a number of connections between dimensionality reduction and gene network inference to identify gene neighborhoods and gene hubs, without the explicit need for gene network inference. Finally, we observe a systematic difference in the gene neighborhoods identified by dimensionality reduction methods and gene network inference algorithms in general, suggesting they provide complementary information about the underlying structure of the gene co-expression network.

ei.Datasets: Real Data Sets for Assessing Ecological Inference Algorithms

Ecological inference models aim to infer individual-level relationships using aggregate data. They are routinely used to estimate voter transitions between elections, disclose split-ticket voting behaviors, or infer racial voting patterns in U.S. elections. A large number of procedures have been proposed in the literature to solve these problems; therefore, an assessment and comparison of them are overdue. The secret ballot however makes this a difficult endeavor since real individual data are usually not accessible. The most recent work on ecological inference has assessed methods using a very small number of data sets with ground truth, combined with artificial, simulated data. This article dramatically increases the number of real instances by presenting a unique database (available in the R package ei.Datasets) composed of data from more than 550 elections where the true inner-cell values of the global cross-classification tables are known. The article describes how the data sets are organized, details the data curation and data wrangling processes performed, and analyses the main features characterizing the different data sets.

Probing 3′UTRs as modular regulators of gene expression

Genes are commonly abstracted into a coding sequence and cis-regulatory elements (CREs), such as promoter and terminator regions, and short sequence motifs within these regions. Modern cloning techniques allow easy assembly of synthetic genetic constructs from discrete cis-regulatory modules. However, it is unclear how much the contributions of CREs to gene expression depend on other CREs in the host gene. Using budding yeast, we probe the extent of composability, or independent effects, of distinct CREs. We confirm that the quantitative effect of a terminator on gene expression depends on both promoter and coding sequence. We then explore whether individual cis-regulatory motifs within terminator regions display similar context dependence, focusing on putative regulatory motifs inferred using transcriptome-wide datasets of mRNA decay. We construct a library of diverse reporter genes, consisting of different combinations of motifs within various terminator contexts, paired with different promoters, to test the extent of composability. Our results show that the effect of a motif on RNA abundance depends both on its host terminator, and also on the associated promoter sequence. Consequently, this emphasises the need for improved motif inference algorithms that include both local and global context effects, which in turn could aid researchers in the accurate use of diverse CREs for the engineering of synthetic genetic constructs.