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The Insiders' Guide to Generative and Discriminative Machine Learning Models - KDnuggets


In this article, we will look at the difference between generative and discriminative models, how they contrast, and one another. Discriminative machine learning is to recognize the rig output among possible output choices. Given something about the data, and done by learning parameters. Classification is additionally mentioned as discriminative modeling. This is often on the grounds; the model must separate instances of input variables across classes.

Bayesian Meta-Learning Is All You Need


Update: This post is part of a blog series on Meta-Learning that I'm working on. Check out part 1 and part 2. In my previous post, "Meta-Learning Is All You Need," I discussed the motivation for the meta-learning paradigm, explained the mathematical underpinning, and reviewed the three approaches to design a meta-learning algorithm (namely, black-box, optimization-based, and non-parametric). I also mentioned in the post that there are two views of the meta-learning problem: a deterministic view and a probabilistic view, according to Chelsea Finn. Note: The content of this post is primarily based on CS330's lecture 5 on Bayesian meta-learning. It is accessible to the public.

Transcriptomic signatures across human tissues identify functional rare genetic variation


Every human genome contains tens of thousands of rare genetic variants—which include single nucleotide changes, insertions or deletions, and larger structural variants—and some may have a functional effect. Ferraro et al. examined data from individuals in the Genotype-Tissue Expression (GTEx) project for outliers across tissues caused by gene expression, splicing, and allele-specific expression. Single rare variants were observed that affected the expression and allele-specific expression of multiple genes and, in the case of a gene fusion event, splicing. Experimental and computational validation suggest that many individuals carry more than 50 rare variants that affect transcription in some way. Although most variants were predicted to not affect an individual's phenotype, a small percentage showed likely disease-related associations, emphasizing the importance of studying the impact of rare genetic variation on the transcriptome. Science , this issue p. [eaaz5900][1] ### INTRODUCTION The human genome contains tens of thousands of rare (minor allele frequency <1%) variants, some of which contribute to disease risk. Using 838 samples with whole-genome and multitissue transcriptome sequencing data in the Genotype-Tissue Expression (GTEx) project version 8, we assessed how rare genetic variants contribute to extreme patterns in gene expression (eOutliers), allelic expression (aseOutliers), and alternative splicing (sOutliers). We integrated these three signals across 49 tissues with genomic annotations to prioritize high-impact rare variants (RVs) that associate with human traits. ### RATIONALE Outlier gene expression aids in identifying functional RVs. Transcriptome sequencing provides diverse measurements beyond gene expression, including allele-specific expression and alternative splicing, which can provide additional insight into RV functional effects. ### RESULTS After identifying multitissue eOutliers, aseOutliers, and sOutliers, we found that outlier individuals of each type were significantly more likely to carry an RV near the corresponding gene. Among eOutliers, we observed strong enrichment of rare structural variants. sOutliers were particularly enriched for RVs that disrupted or created a splicing consensus sequence. aseOutliers provided the strongest enrichment signal when evaluated from just a single tissue. We developed Watershed, a probabilistic model for personal genome interpretation that improves over standard genomic annotation–based methods for scoring RVs by integrating these three transcriptomic signals from the same individual and replicates in an independent cohort. To assess whether outlier RVs identified in GTEx associate with traits, we evaluated these variants for association with diverse traits in the UK Biobank, the Million Veterans Program, and the Jackson Heart Study. We found that transcriptome-assisted prioritization identified RVs with larger trait effect sizes and were better predictors of effect size than genomic annotation alone. ### CONCLUSION With >800 genomes matched with transcriptomes across 49 tissues, we were able to study RVs that underlie extreme changes in the transcriptome. To capture the diversity of these extreme changes, we developed and integrated approaches to identify expression, allele-specific expression, and alternative splicing outliers, and characterized the RV landscape underlying each outlier signal. We demonstrate that personal genome interpretation and RV discovery is enhanced by using these signals. This approach provides a new means to integrate a richer set of functional RVs into models of genetic burden, improve disease gene identification, and enable the delivery of precision genomics. ![Figure][2] Transcriptomic signatures identify functional rare genetic variation. We identified genes in individuals that show outlier expression, allele-specific expression, or alternative splicing and assessed enrichment of nearby rare variation. We integrated these three outlier signals with genomic annotation data to prioritize functional RVs and to intersect those variants with disease loci to identify potential RV trait associations. Rare genetic variants are abundant across the human genome, and identifying their function and phenotypic impact is a major challenge. Measuring aberrant gene expression has aided in identifying functional, large-effect rare variants (RVs). Here, we expanded detection of genetically driven transcriptome abnormalities by analyzing gene expression, allele-specific expression, and alternative splicing from multitissue RNA-sequencing data, and demonstrate that each signal informs unique classes of RVs. We developed Watershed, a probabilistic model that integrates multiple genomic and transcriptomic signals to predict variant function, validated these predictions in additional cohorts and through experimental assays, and used them to assess RVs in the UK Biobank, the Million Veterans Program, and the Jackson Heart Study. Our results link thousands of RVs to diverse molecular effects and provide evidence to associate RVs affecting the transcriptome with human traits. [1]: /lookup/doi/10.1126/science.aaz5900 [2]: pending:yes

What is the Bayesian theorem?


Bayesian is interactive representations of probabilistic interactions between a number of variables. They were designed to ease the presumption of independence in the Naïve Bayes and thus allow for the dependency of variables. The first example, assume I need to see whether God exists. Initially, I have to concur with some techniques to quantify it. Something like'in the event that God existed, at that point harmony, ought to be multiple times more probable than war'.

Top 8 Open Source Tools For Bayesian Networks


Bayesian Network, also known as Bayes network is a probabilistic directed acyclic graphical model, which can be used for time series prediction, anomaly detection, diagnostics and more. In machine learning, the Bayesian inference is known for its robust set of tools for modelling any random variable, including the business performance indicators, the value of a regression parameter, among others. This method is also known as one of the best approaches to modelling uncertainty. In this article, we list down the top eight open-source tools for Bayesian Networks. Bayesian inference Using Gibbs Sampling or BUGS is a software package for the Bayesian analysis of statistical models by utilising the Markov chain Monte Carlo techniques.

Why you should try the Bayesian approach of A/B testing


"Critical thinking is an active and ongoing process. It requires that we all think like Bayesians, updating our knowledge as new information comes in." ― Daniel J. Levitin, A Field Guide to Lies: Critical Thinking in the Information Age Before we delve into the intuition behind using the Bayesian approach of estimation, we need to understand a few concepts. Inferential statistics is when you infer something about a whole population based on a sample of that population, as opposed to descriptive statistics which describes something about the whole population. When it comes to inferential statistics, there are two main philosophies: frequentist inference and Bayesian inference. The frequentist approach is known to be the more traditional approach to statistical inference, and thus studied more in most statistics courses (especially introductory courses). However, many would argue that the Bayesian approach is much closer to the way humans naturally perceive probability.

Artificial Intelligence Review


On the evaluation and combination of state-of-the-art features in Twitter sentiment analysis Authors Content type: OriginalPaper Published: 27 August 2020 Nature inspired optimization algorithms or simply variations of metaheuristics? Nature inspired optimization algorithms or simply variations of metaheuristics? Nature inspired optimization algorithms or simply variations of metaheuristics? Electric Charged Particles Optimization and its application to the optimal design of a circular antenna array Authors H. R. E. H. Bouchekara Content type: OriginalPaper Published: 20 August 2020 CHIRPS: Explaining random forest classification Authors Mohamed Medhat Gaber R. Muhammad Atif Azad Content type: OriginalPaper Published: 04 June 2020 Image classifiers and image deep learning classifiers evolved in detection of Oryza sativa diseases: survey Authors N. V. Raja Reddy Goluguri Content type: EditorialNotes Published: 28 May 2020 Novel classes of coverings based multigranulation fuzzy rough sets and corresponding applications to multiple attribute group decision-making Authors (first, second and last of 4) José Carlos R. Alcantud Content type: OriginalPaper Published: 19 May 2020

13 Algorithms and 4 Learning Methods of Machine Learning


According to the similarity of the function and form of the algorithm, we can classify the algorithm, such as tree-based algorithm, neural network-based algorithm, and so on. Of course, the scope of machine learning is very large, and it is difficult for some algorithms to be clearly classified into a certain category. Regression algorithm is a type of algorithm that tries to explore the relationship between variables by using a measure of error. Regression algorithm is a powerful tool for statistical machine learning. In the field of machine learning, when people talk about regression, sometimes they refer to a type of problem and sometimes a type of algorithm.

Would Bayesian approaches improve COVID-19 forecasts?


Modelling for the pandemic has shown that this debate should still be front and center. The frequentists are mostly in the spotlight advising world leaders. If you listen close you will hear a common refrain'we just need more data.' This is, of course, the age-old problem of statistical significance. However, today, we aren't in a harmless lab study, these data are only realized through death.

Bayesian Neural Networks with TensorFlow Probability


Machine learning models are usually developed from data as deterministic machines that map input to output using a point estimate of parameter weights calculated by maximum-likelihood methods. However, there is a lot of statistical fluke going on in the background. For instance, a dataset itself is a finite random set of points of arbitrary size from a unknown distribution superimposed by additive noise, and for such a particular collection of points, different models (i.e. Hence, there is some uncertainty about the parameters and predictions being made. Bayesian statistics provides a framework to deal with the so-called aleoteric and epistemic uncertainty, and with the release of TensorFlow Probability, probabilistic modeling has been made a lot easier, as I shall demonstrate with this post.