Math Search for the Masses: Multimodal Search Interfaces and Appearance-Based Retrieval

We summarize math search engines and search interfaces produced by the Document and Pattern Recognition Lab in recent years, and in particular the min math search interface and the Tangent search engine. Source code for both systems are publicly available. "The Masses" refers to our emphasis on creating systems for mathematical non-experts, who may be looking to define unfamiliar notation, or browse documents based on the visual appearance of formulae rather than their mathematical semantics.Comment: Paper for Invited Talk at 2015 Conference on Intelligent Computer Mathematics (July, Washington DC

MARS: Microarray analysis, retrieval, and storage system

BACKGROUND: Microarray analysis has become a widely used technique for the study of gene-expression patterns on a genomic scale. As more and more laboratories are adopting microarray technology, there is a need for powerful and easy to use microarray databases facilitating array fabrication, labeling, hybridization, and data analysis. The wealth of data generated by this high throughput approach renders adequate database and analysis tools crucial for the pursuit of insights into the transcriptomic behavior of cells. RESULTS: MARS (Microarray Analysis and Retrieval System) provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a laboratory information management system (LIMS), a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways. The incorporation of ontologies and the use of MAGE-ML enables an export of studies stored in MARS to public repositories and other databases accepting these documents. CONCLUSION: We have developed an integrated system tailored to serve the specific needs of microarray based research projects using a unique fusion of Web based and standalone applications connected to the latest J2EE application server technology. The presented system is freely available for academic and non-profit institutions. More information can be found at

Implementation of an information retrieval system within a central knowledge management system

Páginas numeradas: I-XIII, 14-126Estágio realizado na Wipro Portugal SA e orientado pelo Eng.º Hugo NetoTese de mestrado integrado. Engenharia Informática e Computação. Faculdade de Engenharia. Universidade do Porto. 201

Pattern Recognition

Pattern recognition is a very wide research field. It involves factors as diverse as sensors, feature extraction, pattern classification, decision fusion, applications and others. The signals processed are commonly one, two or three dimensional, the processing is done in real- time or takes hours and days, some systems look for one narrow object class, others search huge databases for entries with at least a small amount of similarity. No single person can claim expertise across the whole field, which develops rapidly, updates its paradigms and comprehends several philosophical approaches. This book reflects this diversity by presenting a selection of recent developments within the area of pattern recognition and related fields. It covers theoretical advances in classification and feature extraction as well as application-oriented works. Authors of these 25 works present and advocate recent achievements of their research related to the field of pattern recognition

Segmentation, Diarization and Speech Transcription: Surprise Data Unraveled

In this thesis, research on large vocabulary continuous speech recognition for unknown audio conditions is presented. For automatic speech recognition systems based on statistical methods, it is important that the conditions of the audio used for training the statistical models match the conditions of the audio to be processed. Any mismatch will decrease the accuracy of the recognition. If it is unpredictable what kind of data can be expected, or in other words if the conditions of the audio to be processed are unknown, it is impossible to tune the models. If the material consists of `surprise data' the output of the system is likely to be poor. In this thesis methods are presented for which no external training data is required for training models. These novel methods have been implemented in a large vocabulary continuous speech recognition system called SHoUT. This system consists of three subsystems: speech/non-speech classification, speaker diarization and automatic speech recognition. The speech/non-speech classification subsystem separates speech from silence and unknown audible non-speech events. The type of non-speech present in audio recordings can vary from paper shuffling in recordings of meetings to sound effects in television shows. Because it is unknown what type of non-speech needs to be detected, it is not possible to train high quality statistical models for each type of non-speech sound. The speech/non-speech classification subsystem, also called the speech activity detection subsystem, does not attempt to classify all audible non-speech in a single run. Instead, first a bootstrap speech/silence classification is obtained using a standard speech activity component. Next, the models for speech, silence and audible non-speech are trained on the target audio using the bootstrap classification. This approach makes it possible to classify speech and non-speech with high accuracy, without the need to know what kinds of sound are present in the audio recording. Once all non-speech is filtered out of the audio, it is the task of the speaker diarization subsystem to determine how many speakers occur in the recording and exactly when they are speaking. The speaker diarization subsystem applies agglomerative clustering to create clusters of speech fragments for each speaker in the recording. First, statistical speaker models are created on random chunks of the recording and by iteratively realigning the data, retraining the models and merging models that represent the same speaker, accurate speaker models are obtained for speaker clustering. This method does not require any statistical models developed on a training set, which makes the diarization subsystem insensitive for variation in audio conditions. Unfortunately, because the algorithm is of complexity $O(n^3)$, this clustering method is slow for long recordings. Two variations of the subsystem are presented that reduce the needed computational effort, so that the subsystem is applicable for long audio recordings as well. The automatic speech recognition subsystem developed for this research, is based on Viterbi decoding on a fixed pronunciation prefix tree. Using the fixed tree, a flexible modular decoder could be developed, but it was not straightforward to apply full language model look-ahead efficiently. In this thesis a novel method is discussed that makes it possible to apply language model look-ahead effectively on the fixed tree. Also, to obtain higher speech recognition accuracy on audio with unknown acoustical conditions, a selection from the numerous known methods that exist for robust automatic speech recognition is applied and evaluated in this thesis. The three individual subsystems as well as the entire system have been successfully evaluated on three international benchmarks. The diarization subsystem has been evaluated at the NIST RT06s benchmark and the speech activity detection subsystem has been tested at RT07s. The entire system was evaluated at N-Best, the first automatic speech recognition benchmark for Dutch

Arbitrary Keyword Spotting in Handwritten Documents

Despite the existence of electronic media in today’s world, a considerable amount of written communications is in paper form such as books, bank cheques, contracts, etc. There is an increasing demand for the automation of information extraction, classification, search, and retrieval of documents. The goal of this research is to develop a complete methodology for the spotting of arbitrary keywords in handwritten document images. We propose a top-down approach to the spotting of keywords in document images. Our approach is composed of two major steps: segmentation and decision. In the former, we generate the word hypotheses. In the latter, we decide whether a generated word hypothesis is a specific keyword or not. We carry out the decision step through a two-level classification where first, we assign an input image to a keyword or non-keyword class; and then transcribe the image if it is passed as a keyword. By reducing the problem from the image domain to the text domain, we do not only address the search problem in handwritten documents, but also the classification and retrieval, without the need for the transcription of the whole document image. The main contribution of this thesis is the development of a generalized minimum edit distance for handwritten words, and to prove that this distance is equivalent to an Ergodic Hidden Markov Model (EHMM). To the best of our knowledge, this work is the first to present an exact 2D model for the temporal information in handwriting while satisfying practical constraints. Some other contributions of this research include: 1) removal of page margins based on corner detection in projection profiles; 2) removal of noise patterns in handwritten images using expectation maximization and fuzzy inference systems; 3) extraction of text lines based on fast Fourier-based steerable filtering; 4) segmentation of characters based on skeletal graphs; and 5) merging of broken characters based on graph partitioning. Our experiments with a benchmark database of handwritten English documents and a real-world collection of handwritten French documents indicate that, even without any word/document-level training, our results are comparable with two state-of-the-art word spotting systems for English and French documents

Advances in Image Processing, Analysis and Recognition Technology

For many decades, researchers have been trying to make computers’ analysis of images as effective as the system of human vision is. For this purpose, many algorithms and systems have previously been created. The whole process covers various stages, including image processing, representation and recognition. The results of this work can be applied to many computer-assisted areas of everyday life. They improve particular activities and provide handy tools, which are sometimes only for entertainment, but quite often, they significantly increase our safety. In fact, the practical implementation of image processing algorithms is particularly wide. Moreover, the rapid growth of computational complexity and computer efficiency has allowed for the development of more sophisticated and effective algorithms and tools. Although significant progress has been made so far, many issues still remain, resulting in the need for the development of novel approaches