Integrating Document Clustering and Topic Modeling

Document clustering and topic modeling are two closely related tasks which can mutually benefit each other. Topic modeling can project documents into a topic space which facilitates effective document clustering. Cluster labels discovered by document clustering can be incorporated into topic models to extract local topics specific to each cluster and global topics shared by all clusters. In this paper, we propose a multi-grain clustering topic model (MGCTM) which integrates document clustering and topic modeling into a unified framework and jointly performs the two tasks to achieve the overall best performance. Our model tightly couples two components: a mixture component used for discovering latent groups in document collection and a topic model component used for mining multi-grain topics including local topics specific to each cluster and global topics shared across clusters.We employ variational inference to approximate the posterior of hidden variables and learn model parameters. Experiments on two datasets demonstrate the effectiveness of our model.Comment: Appears in Proceedings of the Twenty-Ninth Conference on Uncertainty in Artificial Intelligence (UAI2013

A Font Search Engine for Large Font Databases

A search engine for font recognition is presented and evaluated. The intended usage is the search in very large font databases. The input to the search engine is an image of a text line, and the output is the name of the font used when rendering the text. After pre-processing and segmentation of the input image, a local approach is used, where features are calculated for individual characters. The method is based on eigenimages calculated from edge filtered character images, which enables compact feature vectors that can be computed rapidly. In this study the database contains 2763 different fonts for the English alphabet. To resemble a real life situation, the proposed method is evaluated with printed and scanned text lines and character images. Our evaluation shows that for 99.1% of the queries, the correct font name can be found within the five best matches

Radical Recognition in Off-Line Handwritten Chinese Characters Using Non-Negative Matrix Factorization

In the past decade, handwritten Chinese character recognition has received renewed interest with the emergence of touch screen devices. Other popular applications include on-line Chinese character dictionary look-up and visual translation in mobile phone applications. Due to the complex structure of Chinese characters, this classification task is not exactly an easy one, as it involves knowledge from mathematics, computer science, and linguistics. Given a large image database of handwritten character data, the goal of my senior project is to use Non-Negative Matrix Factorization (NMF), a recent method for finding a suitable representation (parts-based representation) of image data, to detect specific sub-components in Chinese characters. NMF has only been applied to typed (printed) Chinese characters in different fonts. This project focuses specifically on how well NMF works on handwritten characters. In addition, research in Chinese character classification has mainly been done using holistic approaches - treating each character as an inseparable unit. By using NMF, this project takes a different approach by focusing on a more specific problem in Chinese character classification: radical (sub-component) detection. Finally, a possible application of radical detection will be proposed. This interactive application can potentially help Chinese language learners better recognize characters by radicals

*K-means and Cluster Models for Cancer Signatures

We present *K-means clustering algorithm and source code by expanding statistical clustering methods applied in https://ssrn.com/abstract=2802753 to quantitative finance. *K-means is statistically deterministic without specifying initial centers, etc. We apply *K-means to extracting cancer signatures from genome data without using nonnegative matrix factorization (NMF). *K-means' computational cost is a fraction of NMF's. Using 1,389 published samples for 14 cancer types, we find that 3 cancers (liver cancer, lung cancer and renal cell carcinoma) stand out and do not have cluster-like structures. Two clusters have especially high within-cluster correlations with 11 other cancers indicating common underlying structures. Our approach opens a novel avenue for studying such structures. *K-means is universal and can be applied in other fields. We discuss some potential applications in quantitative finance.Comment: 124 pages, 69 figures; a trivial typo corrected; to appear in Biomolecular Detection and Quantificatio

Discovering a Domain Knowledge Representation for Image Grouping: Multimodal Data Modeling, Fusion, and Interactive Learning

In visually-oriented specialized medical domains such as dermatology and radiology, physicians explore interesting image cases from medical image repositories for comparative case studies to aid clinical diagnoses, educate medical trainees, and support medical research. However, general image classification and retrieval approaches fail in grouping medical images from the physicians\u27 viewpoint. This is because fully-automated learning techniques cannot yet bridge the gap between image features and domain-specific content for the absence of expert knowledge. Understanding how experts get information from medical images is therefore an important research topic. As a prior study, we conducted data elicitation experiments, where physicians were instructed to inspect each medical image towards a diagnosis while describing image content to a student seated nearby. Experts\u27 eye movements and their verbal descriptions of the image content were recorded to capture various aspects of expert image understanding. This dissertation aims at an intuitive approach to extracting expert knowledge, which is to find patterns in expert data elicited from image-based diagnoses. These patterns are useful to understand both the characteristics of the medical images and the experts\u27 cognitive reasoning processes. The transformation from the viewed raw image features to interpretation as domain-specific concepts requires experts\u27 domain knowledge and cognitive reasoning. This dissertation also approximates this transformation using a matrix factorization-based framework, which helps project multiple expert-derived data modalities to high-level abstractions. To combine additional expert interventions with computational processing capabilities, an interactive machine learning paradigm is developed to treat experts as an integral part of the learning process. Specifically, experts refine medical image groups presented by the learned model locally, to incrementally re-learn the model globally. This paradigm avoids the onerous expert annotations for model training, while aligning the learned model with experts\u27 sense-making

Bayesian sparsity and class sparsity priors for dictionary learning and coding

Dictionary learning methods continue to gain popularity for the solution of challenging inverse problems. In the dictionary learning approach, the computational forward model is replaced by a large dictionary of possible outcomes, and the problem is to identify the dictionary entries that best match the data, akin to traditional query matching in search engines. Sparse coding techniques are used to guarantee that the dictionary matching identifies only few of the dictionary entries, and dictionary compression methods are used to reduce the complexity of the matching problem. In this article, we propose a work flow to facilitate the dictionary matching process. First, the full dictionary is divided into subdictionaries that are separately compressed. The error introduced by the dictionary compression is handled in the Bayesian framework as a modeling error. Furthermore, we propose a new Bayesian data-driven group sparsity coding method to help identify subdictionaries that are not relevant for the dictionary matching. After discarding irrelevant subdictionaries, the dictionary matching is addressed as a deflated problem using sparse coding. The compression and deflation steps can lead to substantial decreases of the computational complexity. The effectiveness of compensating for the dictionary compression error and using the novel group sparsity promotion to deflate the original dictionary are illustrated by applying the methodology to real world problems, the glitch detection in the LIGO experiment and hyperspectral remote sensing

Applications of Multi-view Learning Approaches for Software Comprehension

Program comprehension concerns the ability of an individual to make an understanding of an existing software system to extend or transform it. Software systems comprise of data that are noisy and missing, which makes program understanding even more difficult. A software system consists of various views including the module dependency graph, execution logs, evolutionary information and the vocabulary used in the source code, that collectively defines the software system. Each of these views contain unique and complementary information; together which can more accurately describe the data. In this paper, we investigate various techniques for combining different sources of information to improve the performance of a program comprehension task. We employ state-of-the-art techniques from learning to 1) find a suitable similarity function for each view, and 2) compare different multi-view learning techniques to decompose a software system into high-level units and give component-level recommendations for refactoring of the system, as well as cross-view source code search. The experiments conducted on 10 relatively large Java software systems show that by fusing knowledge from different views, we can guarantee a lower bound on the quality of the modularization and even improve upon it. We proceed by integrating different sources of information to give a set of high-level recommendations as to how to refactor the software system. Furthermore, we demonstrate how learning a joint subspace allows for performing cross-modal retrieval across views, yielding results that are more aligned with what the user intends by the query. The multi-view approaches outlined in this paper can be employed for addressing problems in software engineering that can be encoded in terms of a learning problem, such as software bug prediction and feature location