Machine learning approaches for lung cancer diagnosis.

The enormity of changes and development in the field of medical imaging technology is hard to fathom, as it does not just represent the technique and process of constructing visual representations of the body from inside for medical analysis and to reveal the internal structure of different organs under the skin, but also it provides a noninvasive way for diagnosis of various disease and suggest an efficient ways to treat them. While data surrounding all of our lives are stored and collected to be ready for analysis by data scientists, medical images are considered a rich source that could provide us with a huge amount of data, that could not be read easily by physicians and radiologists, with valuable information that could be used in smart ways to discover new knowledge from these vast quantities of data. Therefore, the design of computer-aided diagnostic (CAD) system, that can be approved for use in clinical practice that aid radiologists in diagnosis and detecting potential abnormalities, is of a great importance. This dissertation deals with the development of a CAD system for lung cancer diagnosis, which is the second most common cancer in men after prostate cancer and in women after breast cancer. Moreover, lung cancer is considered the leading cause of cancer death among both genders in USA. Recently, the number of lung cancer patients has increased dramatically worldwide and its early detection doubles a patient’s chance of survival. Histological examination through biopsies is considered the gold standard for final diagnosis of pulmonary nodules. Even though resection of pulmonary nodules is the ideal and most reliable way for diagnosis, there is still a lot of different methods often used just to eliminate the risks associated with the surgical procedure. Lung nodules are approximately spherical regions of primarily high density tissue that are visible in computed tomography (CT) images of the lung. A pulmonary nodule is the first indication to start diagnosing lung cancer. Lung nodules can be benign (normal subjects) or malignant (cancerous subjects). Large (generally defined as greater than 2 cm in diameter) malignant nodules can be easily detected with traditional CT scanning techniques. However, the diagnostic options for small indeterminate nodules are limited due to problems associated with accessing small tumors. Therefore, additional diagnostic and imaging techniques which depends on the nodules’ shape and appearance are needed. The ultimate goal of this dissertation is to develop a fast noninvasive diagnostic system that can enhance the accuracy measures of early lung cancer diagnosis based on the well-known hypotheses that malignant nodules have different shape and appearance than benign nodules, because of the high growth rate of the malignant nodules. The proposed methodologies introduces new shape and appearance features which can distinguish between benign and malignant nodules. To achieve this goal a CAD system is implemented and validated using different datasets. This CAD system uses two different types of features integrated together to be able to give a full description to the pulmonary nodule. These two types are appearance features and shape features. For the appearance features different texture appearance descriptors are developed, namely the 3D histogram of oriented gradient, 3D spherical sector isosurface histogram of oriented gradient, 3D adjusted local binary pattern, 3D resolved ambiguity local binary pattern, multi-view analytical local binary pattern, and Markov Gibbs random field. Each one of these descriptors gives a good description for the nodule texture and the level of its signal homogeneity which is a distinguishable feature between benign and malignant nodules. For the shape features multi-view peripheral sum curvature scale space, spherical harmonics expansions, and different group of fundamental geometric features are utilized to describe the nodule shape complexity. Finally, the fusion of different combinations of these features, which is based on two stages is introduced. The first stage generates a primary estimation for every descriptor. Followed by the second stage that consists of an autoencoder with a single layer augmented with a softmax classifier to provide us with the ultimate classification of the nodule. These different combinations of descriptors are combined into different frameworks that are evaluated using different datasets. The first dataset is the Lung Image Database Consortium which is a benchmark publicly available dataset for lung nodule detection and diagnosis. The second dataset is our local acquired computed tomography imaging data that has been collected from the University of Louisville hospital and the research protocol was approved by the Institutional Review Board at the University of Louisville (IRB number 10.0642). These frameworks accuracy was about 94%, which make the proposed frameworks demonstrate promise to be valuable tool for the detection of lung cancer

Proceedings of the 10th International Conference on Ecological Informatics: translating ecological data into knowledge and decisions in a rapidly changing world: ICEI 2018

The Conference Proceedings are an impressive display of the current scope of Ecological Informatics. Whilst Data Management, Analysis, Synthesis and Forecasting have been lasting popular themes over the past nine biannual ICEI conferences, ICEI 2018 addresses distinctively novel developments in Data Acquisition enabled by cutting edge in situ and remote sensing technology. The here presented ICEI 2018 abstracts captures well current trends and challenges of Ecological Informatics towards: • regional, continental and global sharing of ecological data, • thorough integration of complementing monitoring technologies including DNA-barcoding, • sophisticated pattern recognition by deep learning, • advanced exploration of valuable information in ‘big data’ by means of machine learning and process modelling, • decision-informing solutions for biodiversity conservation and sustainable ecosystem management in light of global changes

Proceedings of the 10th International Conference on Ecological Informatics: translating ecological data into knowledge and decisions in a rapidly changing world: ICEI 2018

The Conference Proceedings are an impressive display of the current scope of Ecological Informatics. Whilst Data Management, Analysis, Synthesis and Forecasting have been lasting popular themes over the past nine biannual ICEI conferences, ICEI 2018 addresses distinctively novel developments in Data Acquisition enabled by cutting edge in situ and remote sensing technology. The here presented ICEI 2018 abstracts captures well current trends and challenges of Ecological Informatics towards: • regional, continental and global sharing of ecological data, • thorough integration of complementing monitoring technologies including DNA-barcoding, • sophisticated pattern recognition by deep learning, • advanced exploration of valuable information in ‘big data’ by means of machine learning and process modelling, • decision-informing solutions for biodiversity conservation and sustainable ecosystem management in light of global changes

A picture is worth a thousand words : content-based image retrieval techniques

In my dissertation I investigate techniques for improving the state of the art in content-based image retrieval. To place my work into context, I highlight the current trends and challenges in my field by analyzing over 200 recent articles. Next, I propose a novel paradigm called __artificial imagination__, which gives the retrieval system the power to imagine and think along with the user in terms of what she is looking for. I then introduce a new user interface for visualizing and exploring image collections, empowering the user to navigate large collections based on her own needs and preferences, while simultaneously providing her with an accurate sense of what the database has to offer. In the later chapters I present work dealing with millions of images and focus in particular on high-performance techniques that minimize memory and computational use for both near-duplicate image detection and web search. Finally, I show early work on a scene completion-based image retrieval engine, which synthesizes realistic imagery that matches what the user has in mind.LEI Universiteit LeidenNWOImagin

Laboratory Directed Research and Development Program FY 2004 Annual Report

The Oak Ridge National Laboratory (ORNL) Laboratory Directed Research and Development (LDRD) Program reports its status to the U.S. Department of Energy (DOE) in March of each year. The program operates under the authority of DOE Order 413.2A, 'Laboratory Directed Research and Development' (January 8, 2001), which establishes DOE's requirements for the program while providing the Laboratory Director broad flexibility for program implementation. LDRD funds are obtained through a charge to all Laboratory programs. This report describes all ORNL LDRD research activities supported during FY 2004 and includes final reports for completed projects and shorter progress reports for projects that were active, but not completed, during this period. The FY 2004 ORNL LDRD Self-Assessment (ORNL/PPA-2005/2) provides financial data about the FY 2004 projects and an internal evaluation of the program's management process. ORNL is a DOE multiprogram science, technology, and energy laboratory with distinctive capabilities in materials science and engineering, neutron science and technology, energy production and end-use technologies, biological and environmental science, and scientific computing. With these capabilities ORNL conducts basic and applied research and development (R&D) to support DOE's overarching national security mission, which encompasses science, energy resources, environmental quality, and national nuclear security. As a national resource, the Laboratory also applies its capabilities and skills to the specific needs of other federal agencies and customers through the DOE Work For Others (WFO) program. Information about the Laboratory and its programs is available on the Internet at <http://www.ornl.gov/>. LDRD is a relatively small but vital DOE program that allows ORNL, as well as other multiprogram DOE laboratories, to select a limited number of R&D projects for the purpose of: (1) maintaining the scientific and technical vitality of the Laboratory; (2) enhancing the Laboratory's ability to address future DOE missions; (3) fostering creativity and stimulating exploration of forefront science and technology; (4) serving as a proving ground for new research; and (5) supporting high-risk, potentially high-value R&D. Through LDRD the Laboratory is able to improve its distinctive capabilities and enhance its ability to conduct cutting-edge R&D for its DOE and WFO sponsors. To meet the LDRD objectives and fulfill the particular needs of the Laboratory, ORNL has established a program with two components: the Director's R&D Fund and the Seed Money Fund. As outlined in Table 1, these two funds are complementary. The Director's R&D Fund develops new capabilities in support of the Laboratory initiatives, while the Seed Money Fund is open to all innovative ideas that have the potential for enhancing the Laboratory's core scientific and technical competencies. Provision for multiple routes of access to ORNL LDRD funds maximizes the likelihood that novel and seminal ideas with scientific and technological merit will be recognized and supported

Handle Local Optimum Traps In Cbir Systems

Existing CBIR systems, designed around query refinement based on relevance feedback, suffer from local optimum traps. That is, when the user is examining a relevant cluster surrounded by less relevant images, essentially the same set of images will be returned for the user to provide relevance feedback. Since the user would select the same query images again, the relevance feedback process gets trapped in a local optimum. This local-optimum trap problem may severely impair the overall retrieval performance of today\u27s CBIR systems. In this paper, we therefore propose a simulated annealing-based approach to address this important issue. When a stuck-at-a-local-optimum occurs, we employ a neighborhood search technique (i.e., simulated annealing) to escape from the local optimum. We also propose an index structure to speed up such neighborhood search. Our experimental study confirms that our approach can efficiently address the local-optimum trap problem, and therefore can improve the effectiveness of existing CBIR systems. Copyright 2008 ACM

Guidelines for the use and interpretation of assays for monitoring autophagy (2nd edition)

In 2008 we published the first set of guidelines for standardiz- ing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new tech- nologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in differ- ent organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes..