Sparse Image Representation with Epitomes

Sparse coding, which is the decomposition of a vector using only a few basis elements, is widely used in machine learning and image processing. The basis set, also called dictionary, is learned to adapt to specific data. This approach has proven to be very effective in many image processing tasks. Traditionally, the dictionary is an unstructured "flat" set of atoms. In this paper, we study structured dictionaries which are obtained from an epitome, or a set of epitomes. The epitome is itself a small image, and the atoms are all the patches of a chosen size inside this image. This considerably reduces the number of parameters to learn and provides sparse image decompositions with shiftinvariance properties. We propose a new formulation and an algorithm for learning the structured dictionaries associated with epitomes, and illustrate their use in image denoising tasks.Comment: Computer Vision and Pattern Recognition, Colorado Springs : United States (2011

Video modeling via implicit motion representations

Video modeling refers to the development of analytical representations for explaining the intensity distribution in video signals. Based on the analytical representation, we can develop algorithms for accomplishing particular video-related tasks. Therefore video modeling provides us a foundation to bridge video data and related-tasks. Although there are many video models proposed in the past decades, the rise of new applications calls for more efficient and accurate video modeling approaches.;Most existing video modeling approaches are based on explicit motion representations, where motion information is explicitly expressed by correspondence-based representations (i.e., motion velocity or displacement). Although it is conceptually simple, the limitations of those representations and the suboptimum of motion estimation techniques can degrade such video modeling approaches, especially for handling complex motion or non-ideal observation video data. In this thesis, we propose to investigate video modeling without explicit motion representation. Motion information is implicitly embedded into the spatio-temporal dependency among pixels or patches instead of being explicitly described by motion vectors.;Firstly, we propose a parametric model based on a spatio-temporal adaptive localized learning (STALL). We formulate video modeling as a linear regression problem, in which motion information is embedded within the regression coefficients. The coefficients are adaptively learned within a local space-time window based on LMMSE criterion. Incorporating a spatio-temporal resampling and a Bayesian fusion scheme, we can enhance the modeling capability of STALL on more general videos. Under the framework of STALL, we can develop video processing algorithms for a variety of applications by adjusting model parameters (i.e., the size and topology of model support and training window). We apply STALL on three video processing problems. The simulation results show that motion information can be efficiently exploited by our implicit motion representation and the resampling and fusion do help to enhance the modeling capability of STALL.;Secondly, we propose a nonparametric video modeling approach, which is not dependent on explicit motion estimation. Assuming the video sequence is composed of many overlapping space-time patches, we propose to embed motion-related information into the relationships among video patches and develop a generic sparsity-based prior for typical video sequences. First, we extend block matching to more general kNN-based patch clustering, which provides an implicit and distributed representation for motion information. We propose to enforce the sparsity constraint on a higher-dimensional data array signal, which is generated by packing the patches in the similar patch set. Then we solve the inference problem by updating the kNN array and the wanted signal iteratively. Finally, we present a Bayesian fusion approach to fuse multiple-hypothesis inferences. Simulation results in video error concealment, denoising, and deartifacting are reported to demonstrate its modeling capability.;Finally, we summarize the proposed two video modeling approaches. We also point out the perspectives of implicit motion representations in applications ranging from low to high level problems

Template Matching with Noisy Patches: A Contrast-Invariant GLR Test

International audienceMatching patches from a noisy image to atoms in a dictionary of patches is a key ingredient to many techniques in image processing and computer vision. By representing with a single atom all patches that are identical up to a radiometric transformation, dictionary size can be kept small, thereby retaining good computational efficiency. Identification of the atom in best match with a given noisy patch then requires a contrast-invariant criterion. In the light of detection theory, we propose a new criterion that ensures contrast invariance and robustness to noise. We discuss its theoretical grounding and assess its performance under Gaussian, gamma and Poisson noises

Computational Methods on Study of Differentially Expressed Proteins in Maize Proteomes Associated with Resistance to Aflatoxin Accumulation

Plant breeders have focused on improving maize resistance to Aspergillus flavus infection and aflatoxin accumulation by breeding with genotypes having the desirable traits. Various maize inbred lines have been developed for the breeding of resistance. Identification of differentially expressed proteins among such maize inbred lines will facilitate the development of gene markers and expedite the breeding process. Computational biology and proteomics approaches on the investigation of differentially expressed proteins were explored in this research. The major research objectives included 1) application of computational methods in homology and comparative modeling to study 3D protein structures and identify single nucleotide polymorphisms (SNPs) involved in changes of protein structures and functions, which can in turn increase the efficiency of the development of DNA markers; 2) investigation of methods on total protein profiling including purification, separation, visualization, and computational analysis at the proteome level. Special research goals were set on the development of open source computational methods using Matlab image processing tools to quantify and compare protein expression levels visualized by 2D protein electrophoresis gel techniques

BEMDEC: An Adaptive and Robust Methodology for Digital Image Feature Extraction

The intriguing study of feature extraction, and edge detection in particular, has, as a result of the increased use of imagery, drawn even more attention not just from the field of computer science but also from a variety of scientific fields. However, various challenges surrounding the formulation of feature extraction operator, particularly of edges, which is capable of satisfying the necessary properties of low probability of error (i.e., failure of marking true edges), accuracy, and consistent response to a single edge, continue to persist. Moreover, it should be pointed out that most of the work in the area of feature extraction has been focused on improving many of the existing approaches rather than devising or adopting new ones. In the image processing subfield, where the needs constantly change, we must equally change the way we think. In this digital world where the use of images, for variety of purposes, continues to increase, researchers, if they are serious about addressing the aforementioned limitations, must be able to think outside the box and step away from the usual in order to overcome these challenges. In this dissertation, we propose an adaptive and robust, yet simple, digital image features detection methodology using bidimensional empirical mode decomposition (BEMD), a sifting process that decomposes a signal into its two-dimensional (2D) bidimensional intrinsic mode functions (BIMFs). The method is further extended to detect corners and curves, and as such, dubbed as BEMDEC, indicating its ability to detect edges, corners and curves. In addition to the application of BEMD, a unique combination of a flexible envelope estimation algorithm, stopping criteria and boundary adjustment made the realization of this multi-feature detector possible. Further application of two morphological operators of binarization and thinning adds to the quality of the operator

A Primer on Seq2Seq Models for Generative Chatbots

The recent spread of Deep Learning-based solutions for Artificial Intelligence and the development of Large Language Models has pushed forwards significantly the Natural Language Processing area. The approach has quickly evolved in the last ten years, deeply affecting NLP, from low-level text pre-processing tasks –such as tokenisation or POS tagging– to high-level, complex NLP applications like machine translation and chatbots. This paper examines recent trends in the development of open-domain data-driven generative chatbots, focusing on the Seq2Seq architectures. Such architectures are compatible with multiple learning approaches, ranging from supervised to reinforcement and, in the last years, allowed to realise very engaging open-domain chatbots. Not only do these architectures allow to directly output the next turn in a conversation but, to some extent, they also allow to control the style or content of the response. To offer a complete view on the subject, we examine possible architecture implementations as well as training and evaluation approaches. Additionally, we provide information about the openly available corpora to train and evaluate such models and about the current and past chatbot competitions. Finally, we present some insights on possible future directions, given the current research status

Brain Tumor Detection and Segmentation in Multisequence MRI

Tato práce se zabývá detekcí a segmentací mozkového nádoru v multisekvenčních MR obrazech se zaměřením na gliomy vysokého a nízkého stupně malignity. Jsou zde pro tento účel navrženy tři metody. První metoda se zabývá detekcí prezence částí mozkového nádoru v axiálních a koronárních řezech. Jedná se o algoritmus založený na analýze symetrie při různých rozlišeních obrazu, který byl otestován na T1, T2, T1C a FLAIR obrazech. Druhá metoda se zabývá extrakcí oblasti celého mozkového nádoru, zahrnující oblast jádra tumoru a edému, ve FLAIR a T2 obrazech. Metoda je schopna extrahovat mozkový nádor z 2D i 3D obrazů. Je zde opět využita analýza symetrie, která je následována automatickým stanovením intenzitního prahu z nejvíce asymetrických částí. Třetí metoda je založena na predikci lokální struktury a je schopna segmentovat celou oblast nádoru, jeho jádro i jeho aktivní část. Metoda využívá faktu, že většina lékařských obrazů vykazuje vysokou podobnost intenzit sousedních pixelů a silnou korelaci mezi intenzitami v různých obrazových modalitách. Jedním ze způsobů, jak s touto korelací pracovat a používat ji, je využití lokálních obrazových polí. Podobná korelace existuje také mezi sousedními pixely v anotaci obrazu. Tento příznak byl využit v predikci lokální struktury při lokální anotaci polí. Jako klasifikační algoritmus je v této metodě použita konvoluční neuronová síť vzhledem k její známe schopnosti zacházet s korelací mezi příznaky. Všechny tři metody byly otestovány na veřejné databázi 254 multisekvenčních MR obrazech a byla dosáhnuta přesnost srovnatelná s nejmodernějšími metodami v mnohem kratším výpočetním čase (v řádu sekund při použitý CPU), což poskytuje možnost manuálních úprav při interaktivní segmetaci.This work deals with the brain tumor detection and segmentation in multisequence MR images with particular focus on high- and low-grade gliomas. Three methods are propose for this purpose. The first method deals with the presence detection of brain tumor structures in axial and coronal slices. This method is based on multi-resolution symmetry analysis and it was tested for T1, T2, T1C and FLAIR images. The second method deals with extraction of the whole brain tumor region, including tumor core and edema, in FLAIR and T2 images and is suitable to extract the whole brain tumor region from both 2D and 3D. It also uses the symmetry analysis approach which is followed by automatic determination of the intensity threshold from the most asymmetric parts. The third method is based on local structure prediction and it is able to segment the whole tumor region as well as tumor core and active tumor. This method takes the advantage of a fact that most medical images feature a high similarity in intensities of nearby pixels and a strong correlation of intensity profiles across different image modalities. One way of dealing with -- and even exploiting -- this correlation is the use of local image patches. In the same way, there is a high correlation between nearby labels in image annotation, a feature that has been used in the ``local structure prediction'' of local label patches. Convolutional neural network is chosen as a learning algorithm, as it is known to be suited for dealing with correlation between features. All three methods were evaluated on a public data set of 254 multisequence MR volumes being able to reach comparable results to state-of-the-art methods in much shorter computing time (order of seconds running on CPU) providing means, for example, to do online updates when aiming at an interactive segmentation.

Semantics-driven Abstractive Document Summarization

The evolution of the Web over the last three decades has led to a deluge of scientific and news articles on the Internet. Harnessing these publications in different fields of study is critical to effective end user information consumption. Similarly, in the domain of healthcare, one of the key challenges with the adoption of Electronic Health Records (EHRs) for clinical practice has been the tremendous amount of clinical notes generated that can be summarized without which clinical decision making and communication will be inefficient and costly. In spite of the rapid advances in information retrieval and deep learning techniques towards abstractive document summarization, the results of these efforts continue to resemble extractive summaries, achieving promising results predominantly on lexical metrics but performing poorly on semantic metrics. Thus, abstractive summarization that is driven by intrinsic and extrinsic semantics of documents is not adequately explored. Resources that can be used for generating semantics-driven abstractive summaries include: • Abstracts of multiple scientific articles published in a given technical field of study to generate an abstractive summary for topically-related abstracts within the field, thus reducing the load of having to read semantically duplicate abstracts on a given topic. • Citation contexts from different authoritative papers citing a reference paper can be used to generate utility-oriented abstractive summary for a scientific article. • Biomedical articles and the named entities characterizing the biomedical articles along with background knowledge bases to generate entity and fact-aware abstractive summaries. • Clinical notes of patients and clinical knowledge bases for abstractive clinical text summarization using knowledge-driven multi-objective optimization. In this dissertation, we develop semantics-driven abstractive models based on intra- document and inter-document semantic analyses along with facts of named entities retrieved from domain-specific knowledge bases to produce summaries. Concretely, we propose a sequence of frameworks leveraging semantics at various granularity (e.g., word, sentence, document, topic, citations, and named entities) levels, by utilizing external resources. The proposed frameworks have been applied to a range of tasks including 1. Abstractive summarization of topic-centric multi-document scientific articles and news articles. 2. Abstractive summarization of scientific articles using crowd-sourced citation contexts. 3. Abstractive summarization of biomedical articles clustered based on entity-relatedness. 4. Abstractive summarization of clinical notes of patients with heart failure and Chest X-Rays recordings. The proposed approaches achieve impressive performance in terms of preserving semantics in abstractive summarization while paraphrasing. For summarization of topic-centric multiple scientific/news articles, we propose a three-stage approach where abstracts of scientific articles or news articles are clustered based on their topical similarity determined from topics generated using Latent Dirichlet Allocation (LDA), followed by extractive phase and abstractive phase. Then, in the next stage, we focus on abstractive summarization of biomedical literature where we leverage named entities in biomedical articles to 1) cluster related articles; and 2) leverage the named entities towards guiding abstractive summarization. Finally, in the last stage, we turn to external resources such as citation contexts pointing to a scientific article to generate a comprehensive and utility-centric abstractive summary of a scientific article, domain-specific knowledge bases to fill gaps in information about entities in a biomedical article to summarize and clinical notes to guide abstractive summarization of clinical text. Thus, the bottom-up progression of exploring semantics towards abstractive summarization in this dissertation starts with (i) Semantic Analysis of Latent Topics; builds on (ii) Internal and External Knowledge-I (gleaned from abstracts and Citation Contexts); and extends it to make it comprehensive using (iii) Internal and External Knowledge-II (Named Entities and Knowledge Bases)