399 research outputs found

    A new approach of weighted gradient filter for denoising of medical images in the presence of Poisson noise

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    Predlažemo ponderirani stupnjevani filtar za otklanjanje Poissonova šuma na rendgenskim slikama. U unaprijed definiranom prozoru izračunat je gradijent središnjeg piksela. Za izračunavanje vrijednosti gradijenta primijenjen je Gaussov ponderirani filtar. Predložena metoda je primijenjena na biomedicinske rendgenske slike, a zatim na različite uobičajene slike LENE i paprika. Rezultati pokazuju učinkovitost i bolju jasnoću slika uz primjenu ponderiranog stupnjevanog filtra. Uz to, predložena metoda je računalno vrlo učinkovita i brža od Non Local Mean (NLM) filtra koji predstavlja unaprijeđenu metodu za otklanjanje Poissonova šuma. Rezultati predložene metode su također bolji u odnosu na parametre za mjerenje performanse t.j. korelacije, Peak Signal-to-Noise Ratio (PSNR), Maximum Structural Similarity Index Measure (MSSIM) i Mean Square Error (MSE) nego uobičajeni Median, Wiener i NLM filter.We propose a Weighted Gradient Filter for denoising of Poisson noise in medical images. In a predefined window, gradient of the centre pixel is averaged out. Gaussian Weighted filter is used on all calculated gradient values. Proposed method is applied on biomedical images X-Rays and then on different general images of LENA and Peppers. Recovery results show that the proposed weighted gradient filter is efficient and has better visual appearance. Moreover, proposed method is computationally very efficient and faster than Non Local Mean (NLM) filter which is an advanced technique for Poisson noise removal. Proposed method results are also better in terms of performance measures parameters i.e. correlation, Peak Signal-to-Noise Ratio (PSNR), Maximum Structural Similarity Index Measure (MSSIM) and Mean Square Error (MSE) than the conventional Median, Wiener and NLM filter

    Exploring Linguistic Constraints in Nlp Applications

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    The key argument of this dissertation is that the success of an Natural Language Processing (NLP) application depends on a proper representation of the corresponding linguistic problem. This theme is raised in the context that the recent progress made in our field is widely credited to the effective use of strong engineering techniques. However, the intriguing power of highly lexicalized models shown in many NLP applications is not only an achievement by the development in machine learning, but also impossible without the extensive hand-annotated data resources made available, which are originally built with very deep linguistic considerations. More specifically, we explore three linguistic aspects in this dissertation: the distinction between closed-class vs. open-class words, long-tail distributions in vocabulary study and determinism in language models. The first two aspects are studied in unsupervised tasks, unsupervised part-of-speech (POS) tagging and morphology learning, and the last one is studied in supervised tasks, English POS tagging and Chinese word segmentation. Each linguistic aspect under study manifests itself in a (different) way to help improve performance or efficiency in some NLP application

    Temporal Segmentation of Human Actions in Videos

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    Understanding human actions in videos is of great interest in various scenarios ranging from surveillance over quality control in production processes to content-based video search. Algorithms for automatic temporal action segmentation need to overcome severe difficulties in order to be reliable and provide sufficiently good quality. Not only can human actions occur in different scenes and surroundings, the definition on an action itself is also inherently fuzzy, leading to a significant amount of inter-class variations. Moreover, besides finding the correct action label for a pre-defined temporal segment in a video, localizing an action in the first place is anything but trivial. Different actions not only vary in their appearance and duration but also can have long-range temporal dependencies that span over the complete video. Further, getting reliable annotations of large amounts of video data is time consuming and expensive. The goal of this thesis is to advance current approaches to temporal action segmentation. We therefore propose a generic framework that models the three components of the task explicitly, ie long-range temporal dependencies are handled by a context model, variations in segment durations are represented by a length model, and short-term appearance and motion of actions are addressed with a visual model. While the inspiration for the context model mainly comes from word sequence models in natural language processing, the visual model builds upon recent advances in the classification of pre-segmented action clips. Considering that long-range temporal context is crucial, we avoid local segmentation decisions and find the globally optimal temporal segmentation of a video under the explicit models. Throughout the thesis, we provide explicit formulations and training strategies for the proposed generic action segmentation framework under different supervision conditions. First, we address the task of fully supervised temporal action segmentation, where frame-level annotations are available during training. We show that our approach can outperform early sliding window baselines and recent deep architectures and that explicit length and context modeling leads to substantial improvements. Considering that full frame-level annotation is expensive to obtain, we then formulate a weakly supervised training algorithm that uses ordered sequences of actions occurring in the video as only supervision. While a first approach reduces the weakly supervised setup to a fully supervised setup by generating a pseudo ground-truth during training, we propose a second approach that avoids this intermediate step and allows to directly optimize a loss based on the weak supervision. Closing the gap between the fully and the weakly supervised setup, we moreover evaluate semi-supervised learning, where video frames are sparsely annotated. With the motivation that the vast amount of video data on the Internet only comes with meta-tags or content keywords that do not provide any temporal ordering information, we finally propose a method for action segmentation that learns from unordered sets of actions only. All approaches are evaluated on several commonly used benchmark datasets. With the proposed methods, we reach state-of-the-art performance for both, fully and weakly supervised action segmentation

    Recent Advances in Image Restoration with Applications to Real World Problems

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    In the past few decades, imaging hardware has improved tremendously in terms of resolution, making widespread usage of images in many diverse applications on Earth and planetary missions. However, practical issues associated with image acquisition are still affecting image quality. Some of these issues such as blurring, measurement noise, mosaicing artifacts, low spatial or spectral resolution, etc. can seriously affect the accuracy of the aforementioned applications. This book intends to provide the reader with a glimpse of the latest developments and recent advances in image restoration, which includes image super-resolution, image fusion to enhance spatial, spectral resolution, and temporal resolutions, and the generation of synthetic images using deep learning techniques. Some practical applications are also included

    Three Essays on Enhancing Clinical Trial Subject Recruitment Using Natural Language Processing and Text Mining

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    Patient recruitment and enrollment are critical factors for a successful clinical trial; however, recruitment tends to be the most common problem in most clinical trials. The success of a clinical trial depends on efficiently recruiting suitable patients to conduct the trial. Every clinical trial research has a protocol, which describes what will be done in the study and how it will be conducted. Also, the protocol ensures the safety of the trial subjects and the integrity of the data collected. The eligibility criteria section of clinical trial protocols is important because it specifies the necessary conditions that participants have to satisfy. Since clinical trial eligibility criteria are usually written in free text form, they are not computer interpretable. To automate the analysis of the eligibility criteria, it is therefore necessary to transform those criteria into a computer-interpretable format. Unstructured format of eligibility criteria additionally create search efficiency issues. Thus, searching and selecting appropriate clinical trials for a patient from relatively large number of available trials is a complex task. A few attempts have been made to automate the matching process between patients and clinical trials. However, those attempts have not fully integrated the entire matching process and have not exploited the state-of-the-art Natural Language Processing (NLP) techniques that may improve the matching performance. Given the importance of patient recruitment in clinical trial research, the objective of this research is to automate the matching process using NLP and text mining techniques and, thereby, improve the efficiency and effectiveness of the recruitment process. This dissertation research, which comprises three essays, investigates the issues of clinical trial subject recruitment using state-of-the-art NLP and text mining techniques. Essay 1: Building a Domain-Specific Lexicon for Clinical Trial Subject Eligibility Analysis Essay 2: Clustering Clinical Trials Using Semantic-Based Feature Expansion Essay 3: An Automatic Matching Process of Clinical Trial Subject Recruitment In essay1, I develop a domain-specific lexicon for n-gram Named Entity Recognition (NER) in the breast cancer domain. The domain-specific dictionary is used for selection and reduction of n-gram features in clustering in eassy2. The domain-specific dictionary was evaluated by comparing it with Systematized Nomenclature of Medicine--Clinical Terms (SNOMED CT). The results showed that it add significant number of new terms which is very useful in effective natural language processing In essay 2, I explore the clustering of similar clinical trials using the domain-specific lexicon and term expansion using synonym from the Unified Medical Language System (UMLS). I generate word n-gram features and modify the features with the domain-specific dictionary matching process. In order to resolve semantic ambiguity, a semantic-based feature expansion technique using UMLS is applied. A hierarchical agglomerative clustering algorithm is used to generate clinical trial clusters. The focus is on summarization of clinical trial information in order to enhance trial search efficiency. Finally, in essay 3, I investigate an automatic matching process of clinical trial clusters and patient medical records. The patient records collected from a prior study were used to test our approach. The patient records were pre-processed by tokenization and lemmatization. The pre-processed patient information were then further enhanced by matching with breast cancer custom dictionary described in essay 1 and semantic feature expansion using UMLS Metathesaurus. Finally, I matched the patient record with clinical trial clusters to select the best matched cluster(s) and then with trials within the clusters. The matching results were evaluated by internal expert as well as external medical expert

    Analyzing Authentic Texts for Language Learning: Web-based Technology for Input Enrichment and Question Generation

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    Acquisition of a language largely depends on the learner's exposure to and interaction with it. Our research goal is to explore and implement automatic techniques that help create a richer grammatical intake from a given text input and engage learners in making form-meaning connections during reading. A starting point for addressing this issue is the automatic input enrichment method, which aims to ensure that a target structure is richly represented in a given text. We demonstrate the high performance of our rule-based algorithm, which is able to detect 87 linguistic forms contained in an official curriculum for the English language. Showcasing the algorithm's capability to differentiate between the various functions of the same linguistic form, we establish the task of tense sense disambiguation, which we approach by leveraging machine learning and rule-based methods. Using the aforementioned technology, we develop an online information retrieval system FLAIR that prioritizes texts with a rich representation of selected linguistic forms. It is implemented as a web search engine for language teachers and learners and provides effective input enrichment in a real-life teaching setting. It can also serve as a foundation for empirical research on input enrichment and input enhancement. The input enrichment component of the FLAIR system is evaluated in a web-based study that demonstrates that English teachers prefer automatic input enrichment to standard web search when selecting reading material for class. We then explore automatic question generation for facilitating and testing reading comprehension as well as linguistic knowledge. We give an overview of the types of questions that are usually asked and can be automatically generated from text in the language learning context. We argue that questions can facilitate the acquisition of different linguistic forms by providing functionally driven input enhancement, i.e., by ensuring that the learner notices and processes the form. The generation of well-established and novel types of questions is discussed and examples are provided; moreover, the results from a crowdsourcing study show that automatically generated questions are comparable to human-written ones

    A Graph-Based Approach for the Summarization of Scientific Articles

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    Automatic text summarization is one of the eminent applications in the field of Natural Language Processing. Text summarization is the process of generating a gist from text documents. The task is to produce a summary which contains important, diverse and coherent information, i.e., a summary should be self-contained. The approaches for text summarization are conventionally extractive. The extractive approaches select a subset of sentences from an input document for a summary. In this thesis, we introduce a novel graph-based extractive summarization approach. With the progressive advancement of research in the various fields of science, the summarization of scientific articles has become an essential requirement for researchers. This is our prime motivation in selecting scientific articles as our dataset. This newly formed dataset contains scientific articles from the PLOS Medicine journal, which is a high impact journal in the field of biomedicine. The summarization of scientific articles is a single-document summarization task. It is a complex task due to various reasons, one of it being, the important information in the scientific article is scattered all over it and another reason being, scientific articles contain numerous redundant information. In our approach, we deal with the three important factors of summarization: importance, non-redundancy and coherence. To deal with these factors, we use graphs as they solve data sparsity problems and are computationally less complex. We employ bipartite graphical representation for the summarization task, exclusively. We represent input documents through a bipartite graph that consists of sentence nodes and entity nodes. This bipartite graph representation contains entity transition information which is beneficial for selecting the relevant sentences for a summary. We use a graph-based ranking algorithm to rank the sentences in a document. The ranks are considered as relevance scores of the sentences which are further used in our approach. Scientific articles contain reasonable amount of redundant information, for example, Introduction and Methodology sections contain similar information regarding the motivation and approach. In our approach, we ensure that the summary contains sentences which are non-redundant. Though the summary should contain important and non-redundant information of the input document, its sentences should be connected to one another such that it becomes coherent, understandable and simple to read. If we do not ensure that a summary is coherent, its sentences may not be properly connected. This leads to an obscure summary. Until now, only few summarization approaches take care of coherence. In our approach, we take care of coherence in two different ways: by using the graph measure and by using the structural information. We employ outdegree as the graph measure and coherence patterns for the structural information, in our approach. We use integer programming as an optimization technique, to select the best subset of sentences for a summary. The sentences are selected on the basis of relevance, diversity and coherence measure. The computation of these measures is tightly integrated and taken care of simultaneously. We use human judgements to evaluate coherence of summaries. We compare ROUGE scores and human judgements of different systems on the PLOS Medicine dataset. Our approach performs considerably better than other systems on this dataset. Also, we apply our approach on the standard DUC 2002 dataset to compare the results with the recent state-of-the-art systems. The results show that our graph-based approach outperforms other systems on DUC 2002. In conclusion, our approach is robust, i.e., it works on both scientific and news articles. Our approach has the further advantage of being semi-supervised

    Detection of crack-like indications in digital radiography by global optimisation of a probabilistic estimation function

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    A new algorithm for detection of longitudinal crack-like indications in radiographic images is developed in this work. Conventional local detection techniques give unsatisfactory results for this task due to the low signal to noise ratio (SNR ~ 1) of crack-like indications in radiographic images. The usage of global features of crack-like indications provides the necessary noise resistance, but this is connected with prohibitive computational complexities of detection and difficulties in a formal description of the indication shape. Conventionally, the excessive computational complexity of the solution is reduced by usage of heuristics. The heuristics to be used, are selected on a trial and error basis, are problem dependent and do not guarantee the optimal solution. Not following this way is a distinctive feature of the algorithm developed here. Instead, a global characteristic of crack-like indication (the estimation function) is used, whose maximum in the space of all possible positions, lengths and shapes can be found exactly, i.e. without any heuristics. The proposed estimation function is defined as a sum of a posteriori information gains about hypothesis of indication presence in each point along the whole hypothetical indication. The gain in the information about hypothesis of indication presence results from the analysis of the underlying image in the local area. Such an estimation function is theoretically justified and exhibits a desirable behaviour on changing signals. The developed algorithm is implemented in the C++ programming language and testet on synthetic as well as on real images. It delivers good results (high correct detection rate by given false alarm rate) which are comparable to the performance of trained human inspectors.In dieser Arbeit wurde ein neuer Algorithmus zur Detektion rissartiger Anzeigen in der digitalen Radiographie entwickelt. Klassische lokale Detektionsmethoden versagen wegen des geringen Signal-Rausch-Verhältnisses (von ca. 1) der Rissanzeigen in den Radiographien. Die notwendige Resistenz gegen Rauschen wird durch die Benutzung von globalen Merkmalen dieser Anzeigen erzielt. Das ist aber mit einem undurchführbaren Rechenaufwand sowie Problemen bei der formalen Beschreibung der Rissform verbunden. Üblicherweise wird ein übermäßiger Rechenaufwand bei der Lösung vergleichbarer Probleme durch Anwendung von Heuristisken reduziert. Dazu benuzte Heuristiken werden mit der Versuchs-und-Irrtums-Methode ermittelt, sind stark problemangepasst und können die optimale Lösung nicht garantieren. Das Besondere dieser Arbeit ist anderer Lösungsansatz, der jegliche Heuristik bei der Suche nach Rissanzeigen vermeidet. Ein globales wahrscheinlichkeitstheoretisches Merkmal, hier Schätzfunktion genannt, wird konstruiert, dessen Maximum unter allen möglichen Formen, Längen und Positionen der Rissanzeige exakt (d.h. ohne Einsatz jeglicher Heuristik) gefunden werden kann. Diese Schätzfunktion wird als die Summe des a posteriori Informationsgewinns bezüglich des Vorhandenseins eines Risses im jeden Punkt entlang der hypothetischen Rissanzeige definiert. Der Informationsgewinn entsteht durch die Überprüfung der Hypothese der Rissanwesenheit anhand der vorhandenen Bildinformation. Eine so definierte Schätzfunktion ist theoretisch gerechtfertigt und besitzt die gewünschten Eigenschaften bei wechselnder Anzeigenintensität. Der Algorithmus wurde in der Programmiersprache C++ implementiert. Seine Detektionseigenschaften wurden sowohl mit simulierten als auch mit realen Bildern untersucht. Der Algorithmus liefert gute Ergenbise (hohe Detektionsrate bei einer vorgegebenen Fehlalarmrate), die jeweils vergleichbar mit den Ergebnissen trainierter menschlicher Auswerter sind
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