Asymptotic Analysis of Generative Semi-Supervised Learning

Semisupervised learning has emerged as a popular framework for improving modeling accuracy while controlling labeling cost. Based on an extension of stochastic composite likelihood we quantify the asymptotic accuracy of generative semi-supervised learning. In doing so, we complement distribution-free analysis by providing an alternative framework to measure the value associated with different labeling policies and resolve the fundamental question of how much data to label and in what manner. We demonstrate our approach with both simulation studies and real world experiments using naive Bayes for text classification and MRFs and CRFs for structured prediction in NLP.Comment: 12 pages, 9 figure

Abstraction, aggregation and recursion for generating accurate and simple classifiers

An important goal of inductive learning is to generate accurate and compact classifiers from data. In a typical inductive learning scenario, instances in a data set are simply represented as ordered tuples of attribute values. In our research, we explore three methodologies to improve the accuracy and compactness of the classifiers: abstraction, aggregation, and recursion;Firstly, abstraction is aimed at the design and analysis of algorithms that generate and deal with taxonomies for the construction of compact and robust classifiers. In many applications of the data-driven knowledge discovery process, taxonomies have been shown to be useful in constructing compact, robust, and comprehensible classifiers. However, in many application domains, human-designed taxonomies are unavailable. We introduce algorithms for automated construction of taxonomies inductively from both structured (such as UCI Repository) and unstructured (such as text and biological sequences) data. We introduce AVT-Learner, an algorithm for automated construction of attribute value taxonomies (AVT) from data, and Word Taxonomy Learner (WTL), an algorithm for automated construction of word taxonomy from text and sequence data. We describe experiments on the UCI data sets and compare the performance of AVT-NBL (an AVT-guided Naive Bayes Learner) with that of the standard Naive Bayes Learner (NBL). Our results show that the AVTs generated by AVT-Learner are compeitive with human-generated AVTs (in cases where such AVTs are available). AVT-NBL using AVTs generated by AVT-Learner achieves classification accuracies that are comparable to or higher than those obtained by NBL; and the resulting classifiers are significantly more compact than those generated by NBL. Similarly, our experimental results of WTL and WTNBL on protein localization sequences and Reuters newswire text categorization data sets show that the proposed algorithms can generate Naive Bayes classifiers that are more compact and often more accurate than those produced by standard Naive Bayes learner for the Multinomial Model;Secondly, we apply aggregation to construct features as a multiset of values for the intrusion detection task. For this task, we propose a bag of system calls representation for system call traces and describe misuse and anomaly detection results on the University of New Mexico (UNM) and MIT Lincoln Lab (MIT LL) system call sequences with the proposed representation. With the feature representation as input, we compare the performance of several machine learning techniques for misuse detection and show experimental results on anomaly detection. The results show that standard machine learning and clustering techniques using the simple bag of system calls representation based on the system call traces generated by the operating system\u27s kernel is effective and often performs better than approaches that use foreign contiguous sequences in detecting intrusive behaviors of compromised processes;Finally, we construct a set of classifiers by recursive application of the Naive Bayes learning algorithms. Naive Bayes (NB) classifier relies on the assumption that the instances in each class can be described by a single generative model. This assumption can be restrictive in many real world classification tasks. We describe recursive Naive Bayes learner (RNBL), which relaxes this assumption by constructing a tree of Naive Bayes classifiers for sequence classification, where each individual NB classifier in the tree is based on an event model (one model for each class at each node in the tree). In our experiments on protein sequences, Reuters newswire documents and UC-Irvine benchmark data sets, we observe that RNBL substantially outperforms NB classifier. Furthermore, our experiments on the protein sequences and the text documents show that RNBL outperforms C4.5 decision tree learner (using tests on sequence composition statistics as the splitting criterion) and yields accuracies that are comparable to those of support vector machines (SVM) using similar information

Modern considerations for the use of naive Bayes in the supervised classification of genetic sequence data

2021 Spring.Includes bibliographical references.Genetic sequence classification is the task of assigning a known genetic label to an unknown genetic sequence. Often, this is the first step in genetic sequence analysis and is critical to understanding data produced by molecular techniques like high throughput sequencing. Here, we explore an algorithm called naive Bayes that was historically successful in classifying 16S ribosomal gene sequences for microbiome analysis. We extend the naive Bayes classifier to perform the task of general sequence classification by leveraging advancements in computational parallelism and the statistical distributions that underlie naive Bayes. In Chapter 2, we show that our implementation of naive Bayes, called WarpNL, performs within a margin of error of modern classifiers like Kraken2 and local alignment. We discuss five crucial aspects of genetic sequence classification and show how these areas affect classifier performance: the query data, the reference sequence database, the feature encoding method, the classification algorithm, and access to computational resources. In Chapter 3, we cover the critical computational advancements introduced in WarpNL that make it efficient in a modern computing framework. This includes efficient feature encoding, introduction of a log-odds ratio for comparison of naive Bayes posterior estimates, description of schema for parallel and distributed naive Bayes architectures, and use of machine learning classifiers to perform outgroup sequence classification. Finally in Chapter 4, we explore a variant of the Dirichlet multinomial distribution that underlies the naive Bayes likelihood, called the beta-Liouville multinomial. We show that the beta-Liouville multinomial can be used to enhance classifier performance, and we provide mathematical proofs regarding its convergence during maximum likelihood estimation. Overall, this work explores the naive Bayes algorithm in a modern context and shows that it is competitive for genetic sequence classification

The EM Algorithm and the Rise of Computational Biology

In the past decade computational biology has grown from a cottage industry with a handful of researchers to an attractive interdisciplinary field, catching the attention and imagination of many quantitatively-minded scientists. Of interest to us is the key role played by the EM algorithm during this transformation. We survey the use of the EM algorithm in a few important computational biology problems surrounding the "central dogma"; of molecular biology: from DNA to RNA and then to proteins. Topics of this article include sequence motif discovery, protein sequence alignment, population genetics, evolutionary models and mRNA expression microarray data analysis.Comment: Published in at http://dx.doi.org/10.1214/09-STS312 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

Bayesian nonparametric discovery of isoforms and individual specific quantification

Most human protein-coding genes can be transcribed into multiple distinct mRNA isoforms. These alternative splicing patterns encourage molecular diversity, and dysregulation of isoform expression plays an important role in disease etiology. However, isoforms are difficult to characterize from short-read RNA-seq data because they share identical subsequences and occur in different frequencies across tissues and samples. Here, we develop BIISQ, a Bayesian nonparametric model for isoform discovery and individual specific quantification from short-read RNA-seq data. BIISQ does not require isoform reference sequences but instead estimates an isoform catalog shared across samples. We use stochastic variational inference for efficient posterior estimates and demonstrate superior precision and recall for simulations compared to state-of-the-art isoform reconstruction methods. BIISQ shows the most gains for low abundance isoforms, with 36% more isoforms correctly inferred at low coverage versus a multi-sample method and 170% more versus single-sample methods. We estimate isoforms in the GEUVADIS RNA-seq data and validate inferred isoforms by associating genetic variants with isoform ratios

Anomaly Detection and Exploratory Causal Analysis for SAP HANA

Nowadays, the good functioning of the equipment, networks and systems will be the key for the business of a company to continue operating because it is never avoidable for the companies to use information technology to support their business in the era of big data. However, the technology is never infallible, faults that give rise to sometimes critical situations may appear at any time. To detect and prevent failures, it is very essential to have a good monitoring system which is responsible for controlling the technology used by a company (hardware, networks and communications, operating systems or applications, among others) in order to analyze their operation and performance, and to detect and alert about possible errors. The aim of this thesis is thus to further advance the field of anomaly detection and exploratory causal inference which are two major research areas in a monitoring system, to provide efficient algorithms with regards to the usability, maintainability and scalability. The analyzed results can be viewed as a starting point for the root cause analysis of the system performance issues and to avoid falls in the system or minimize the time of resolution of the issues in the future. The algorithms were performed on the historical data of SAP HANA database at last and the results gained in this thesis indicate that the tools have succeeded in providing some useful information for diagnosing the performance issues of the system

Time2Graph: Revisiting Time Series Modeling with Dynamic Shapelets

Time series modeling has attracted extensive research efforts; however, achieving both reliable efficiency and interpretability from a unified model still remains a challenging problem. Among the literature, shapelets offer interpretable and explanatory insights in the classification tasks, while most existing works ignore the differing representative power at different time slices, as well as (more importantly) the evolution pattern of shapelets. In this paper, we propose to extract time-aware shapelets by designing a two-level timing factor. Moreover, we define and construct the shapelet evolution graph, which captures how shapelets evolve over time and can be incorporated into the time series embeddings by graph embedding algorithms. To validate whether the representations obtained in this way can be applied effectively in various scenarios, we conduct experiments based on three public time series datasets, and two real-world datasets from different domains. Experimental results clearly show the improvements achieved by our approach compared with 17 state-of-the-art baselines.Comment: An extended version with 11 pages including appendix; Accepted by AAAI'202

Optimization with Sparsity-Inducing Penalties

Sparse estimation methods are aimed at using or obtaining parsimonious representations of data or models. They were first dedicated to linear variable selection but numerous extensions have now emerged such as structured sparsity or kernel selection. It turns out that many of the related estimation problems can be cast as convex optimization problems by regularizing the empirical risk with appropriate non-smooth norms. The goal of this paper is to present from a general perspective optimization tools and techniques dedicated to such sparsity-inducing penalties. We cover proximal methods, block-coordinate descent, reweighted $\ell_2$-penalized techniques, working-set and homotopy methods, as well as non-convex formulations and extensions, and provide an extensive set of experiments to compare various algorithms from a computational point of view

Scalable Design with Posterior-Based Operating Characteristics

To design trustworthy Bayesian studies, criteria for posterior-based operating characteristics - such as power and the type I error rate - are often defined in clinical, industrial, and corporate settings. These posterior-based operating characteristics are typically assessed by exploring sampling distributions of posterior probabilities via simulation. In this paper, we propose a scalable method to determine optimal sample sizes and decision criteria that maps posterior probabilities to low-dimensional conduits for the data. Our method leverages this mapping and large-sample theory to explore sampling distributions of posterior probabilities in a targeted manner. This targeted exploration approach prompts consistent sample size recommendations with fewer simulation repetitions than standard methods. We repurpose the posterior probabilities computed in that approach to efficiently investigate various sample sizes and decision criteria using contour plots.Comment: arXiv admin note: text overlap with arXiv:2310.1242

PSI-BLAST pseudocounts and the minimum description length principle

Position specific score matrices (PSSMs) are derived from multiple sequence alignments to aid in the recognition of distant protein sequence relationships. The PSI-BLAST protein database search program derives the column scores of its PSSMs with the aid of pseudocounts, added to the observed amino acid counts in a multiple alignment column. In the absence of theory, the number of pseudocounts used has been a completely empirical parameter. This article argues that the minimum description length principle can motivate the choice of this parameter. Specifically, for realistic alignments, the principle supports the practice of using a number of pseudocounts essentially independent of alignment size. However, it also implies that more highly conserved columns should use fewer pseudocounts, increasing the inter-column contrast of the implied PSSMs. A new method for calculating pseudocounts that significantly improves PSI-BLAST's; retrieval accuracy is now employed by default