A bag-of-words approach for Drosophila gene expression pattern annotation

abstract: Background Drosophila gene expression pattern images document the spatiotemporal dynamics of gene expression during embryogenesis. A comparative analysis of these images could provide a fundamentally important way for studying the regulatory networks governing development. To facilitate pattern comparison and searching, groups of images in the Berkeley Drosophila Genome Project (BDGP) high-throughput study were annotated with a variable number of anatomical terms manually using a controlled vocabulary. Considering that the number of available images is rapidly increasing, it is imperative to design computational methods to automate this task. Results We present a computational method to annotate gene expression pattern images automatically. The proposed method uses the bag-of-words scheme to utilize the existing information on pattern annotation and annotates images using a model that exploits correlations among terms. The proposed method can annotate images individually or in groups (e.g., according to the developmental stage). In addition, the proposed method can integrate information from different two-dimensional views of embryos. Results on embryonic patterns from BDGP data demonstrate that our method significantly outperforms other methods. Conclusion The proposed bag-of-words scheme is effective in representing a set of annotations assigned to a group of images, and the model employed to annotate images successfully captures the correlations among different controlled vocabulary terms. The integration of existing annotation information from multiple embryonic views improves annotation performance.The electronic version of this article is the complete one and can be found online at: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-11

Selective Compression of Medical Images via Intelligent Segmentation and 3D-SPIHT Coding

ABSTRACT SELECTIVE COMPRESSION OF MEDICAL IMAGES VIA INTELLIGENT SEGMENTATION AND 3D-SPIHT CODING by Bohan Fan The University of Wisconsin-Milwaukee, 2018 Under the Supervision of Professor Zeyun Yu With increasingly high resolutions of 3D volumetric medical images being widely used in clinical patient treatments, efficient image compression techniques have become in great demand due to the cost in storage and time for transmission. While various algorithms are available, the conflicts between high compression rate and the downgraded quality of the images can partially be harmonized by using the region of interest (ROI) coding technique. Instead of compressing the entire image, we can segment the image by critical diagnosis zone (the ROI zone) and background zone, and apply lossless compression or low compression rate to the former and high compression rate to the latter, without losing much clinically important information. In this thesis, we explore a medical image transmitting process that utilizes a deep learning network, called 3D-Unet to segment the region of interest area of volumetric images and 3D-SPIHT algorithm to encode the images for compression, which can be potentially used in medical data sharing scenario. In our experiments, we train a 3D-Unet on a dataset of spine images with their label ground truth, and use the trained model to extract the vertebral bodies of testing data. The segmented vertebral regions are dilated to generate the region of interest, which are subject to the 3D-SPIHT algorithm with low compress ratio while the rest of the image (background) is coded with high compress ratio to achieve an excellent balance of image quality in region of interest and high compression ratio elsewhere

Insights from Classifying Visual Concepts with Multiple Kernel Learning

Combining information from various image features has become a standard technique in concept recognition tasks. However, the optimal way of fusing the resulting kernel functions is usually unknown in practical applications. Multiple kernel learning (MKL) techniques allow to determine an optimal linear combination of such similarity matrices. Classical approaches to MKL promote sparse mixtures. Unfortunately, so-called 1-norm MKL variants are often observed to be outperformed by an unweighted sum kernel. The contribution of this paper is twofold: We apply a recently developed non-sparse MKL variant to state-of-the-art concept recognition tasks within computer vision. We provide insights on benefits and limits of non-sparse MKL and compare it against its direct competitors, the sum kernel SVM and the sparse MKL. We report empirical results for the PASCAL VOC 2009 Classification and ImageCLEF2010 Photo Annotation challenge data sets. About to be submitted to PLoS ONE.Comment: 18 pages, 8 tables, 4 figures, format deviating from plos one submission format requirements for aesthetic reason

Dense Visual Word Spatial Arrangement Dan Penerapannya Pada Pengenalan Gambar Secara Otomatis

Bag of visual word (BoVW) merupakan metode yang menjelaskan isi dari gambar. Metode ini hanya menghitung banyaknya word dan tidak memberikan informasi spatial. Terdapat metode Visual word spatial arrangement (WSA) dimana metode ini memberikan informasi spatial tentang word tertentu pada gambar dengan menggunakan interest point sebagai detektor. WSA kurang dapat memberikan informasi yang penting pada gambar dikarenakan interest point yang dihasilkan oleh detektor dapat memberikan titik-titik yang berpotensi tidak merupakan representasi yang penting dari gambar tersebut. Pada paper ini diusulkan metode dense visual word spatial arrangement (DVSA) yang merupakan modifikasi metode dari WSA. Metode ini tidak menggunakan detektor interest point untuk menghitung deskriptor lokal melainkan dengan menghitung deskriptor lokal pada bagian komponen piksel-piksel yang saling berdekatan. Hasil pengujian pada 4485 gambar dengan 15 jenis kelas menggunakan 10-fold cross validation untuk 2 word metode yang diusulkan memberikan peningkatan performa sebesar 12.68 % dari akurasi BoVW sedangkan akurasi WSA lebih baik 15.62 % dari BoVW. Untuk 4 word metode yang diusulkan memberikan peningkatan performa akurasi sebesar 30.99 % dari akurasi BoVW dan peningkatan performa 18.16 % dari WSA. Sedangkan untuk 6 word metode yang diusulkan memberikan peningkatan performa sebesar 29.98 % dari akurasi BoVW dan peningkatan performa 18.75 % dari WSA. Peningkatan performa akurasi sebesar 36.2 % didapatkan oleh metode yang diusulkan dengan 6 word terhadap BoVW dengan 2 word. Peningkatan performa sampai 18.75 % yang dihasilkan DVSA dibandingkan WSA dan peningkatan performa sampai 30.99 % dibandingkan BoVW dengan jumlah word yang sama menunjukkan metode yang diusulkan kompetitif untuk mengenali jenis gambar

Computational Approaches to Drug Profiling and Drug-Protein Interactions

Despite substantial increases in R&D spending within the pharmaceutical industry, denovo drug design has become a time-consuming endeavour. High attrition rates led to a long period of stagnation in drug approvals. Due to the extreme costs associated with introducing a drug to the market, locating and understanding the reasons for clinical failure is key to future productivity. As part of this PhD, three main contributions were made in this respect. First, the web platform, LigNFam enables users to interactively explore similarity relationships between ‘drug like’ molecules and the proteins they bind. Secondly, two deep-learning-based binding site comparison tools were developed, competing with the state-of-the-art over benchmark datasets. The models have the ability to predict offtarget interactions and potential candidates for target-based drug repurposing. Finally, the open-source ScaffoldGraph software was presented for the analysis of hierarchical scaffold relationships and has already been used in multiple projects, including integration into a virtual screening pipeline to increase the tractability of ultra-large screening experiments. Together, and with existing tools, the contributions made will aid in the understanding of drug-protein relationships, particularly in the fields of off-target prediction and drug repurposing, helping to design better drugs faster

Data-driven Representation Learning from Histopathology Image Databases to Support Digital Pathology Analysis

Cancer research is a major public health priority in the world due to its high incidence, diversity and mortality. Despite great advances in this area during recent decades, the high incidence and lack of specialists have proven that one of the major challenges is to achieve early diagnosis. Improved early diagnosis, especially in developing countries, plays a crucial role in timely treatment and patient survival. Recent advances in scanner technology for the digitization of pathology slides and the growth of global initiatives to build databases for cancer research have enabled the emergence of digital pathology as a new approach to support pathology workflows. This has led to the development of many computational methods for automatic histopathology image analysis, which in turn has raised new computational challenges due to the high visual variability of histopathology slides, the difficulty in assessing the effectiveness of methods (considering the lack of annotated data from different pathologists and institutions), and the need of interpretable, efficient and feasible methods for practical use. On the other hand, machine learning techniques have focused on exploiting large databases to automatically extract and induce information and knowledge, in the form of patterns and rules, that allow to connect low-level content with its high-level meaning. Several approaches have emerged as opposed to traditional schemes based on handcrafted features for data representation, which nowadays are known as representation learning. The objective of this thesis is the exploration, development and validation of precise, interpretable and efficient computational machine learning methods for automatic representation learning from histopathology image databases to support diagnosis tasks of different types of cancer. The validation of the proposed methods during the thesis development allowed to corroborate their capability in several histopathology image analysis tasks of different types of cancer. These methods achieve good results in terms of accuracy, robustness, reproducibility, interpretability and feasibility suggesting their potential practical application towards translational and personalized medicine.Resumen. La investigación en cáncer es una de las principales prioridades de salud pública en el mundo debido a su alta incidencia, diversidad y mortalidad. A pesar de los grandes avances en el área en las últimas décadas, la alta incidencia y la falta de especialistas ha llevado a que una de las principales problemáticas sea lograr su detección temprana, en especial en países en vías de desarrollo, como quiera a que de ello depende las posibilidades de un tratamiento oportuno y las oportunidades de supervivencia de los pacientes. Los recientes avances en tecnología de escáneres para digitalización de láminas de patología y el crecimiento de iniciativas mundiales para la construcción de bases de datos para la investigación en cáncer, han permitido el surgimiento de la patología digital como un nuevo enfoque para soportar los flujos de trabajo en patología. Esto ha llevado al desarrollo de una gran variedad de métodos computacionales para el análisis automático de imágenes de histopatología, lo cual ha planteado nuevos desafíos computacionales debido a la alta variabilidad visual de las láminas de histopatología; la dificultad para evaluar la efectividad de los métodos por la falta de datos de diferentes instituciones que cuenten con anotaciones por parte de los patólogos, y la necesidad de métodos interpretables, eficientes y factibles para su uso práctico. Por otro lado, el aprendizaje de máquina se ha enfocado en explotar las grandes bases de datos para extraer e inducir de manera automática información y conocimiento, en forma de patrones y reglas, que permita conectar el contenido de bajo nivel con su significado. Diferentes técnicas han surgido en contraposición a los esquemas tradicionales basados en diseño manual de la representación de los datos, en lo que se conoce como aprendizaje de la representación. El propósito de esta tesis fue la exploración, desarrollo y validación de métodos computacionales de aprendizaje de máquina precisos, interpretables y eficientes a partir de bases de datos de imágenes de histopatología para el aprendizaje automático de la representación en tareas de apoyo al diagnóstico de distintos tipos de cáncer. La validación de los distintos métodos propuestos durante el desarrollo de la tesis permitieron corroborar la capacidad de cada uno de ellos en distintivas tareas de análisis de imágenes de histopatología, en diferentes tipos de cáncer, con buenos resultados en términos de exactitud, robustez, reproducibilidad, interpretabilidad y factibilidad, lo cual sugiere su potencial aplicación práctica hacia la medicina traslacional y personalizada.Doctorad

IST Austria Thesis

The human ability to recognize objects in complex scenes has driven research in the computer vision field over couple of decades. This thesis focuses on the object recognition task in images. That is, given the image, we want the computer system to be able to predict the class of the object that appears in the image. A recent successful attempt to bridge semantic understanding of the image perceived by humans and by computers uses attribute-based models. Attributes are semantic properties of the objects shared across different categories, which humans and computers can decide on. To explore the attribute-based models we take a statistical machine learning approach, and address two key learning challenges in view of object recognition task: learning augmented attributes as mid-level discriminative feature representation, and learning with attributes as privileged information. Our main contributions are parametric and non-parametric models and algorithms to solve these frameworks. In the parametric approach, we explore an autoencoder model combined with the large margin nearest neighbor principle for mid-level feature learning, and linear support vector machines for learning with privileged information. In the non-parametric approach, we propose a supervised Indian Buffet Process for automatic augmentation of semantic attributes, and explore the Gaussian Processes classification framework for learning with privileged information. A thorough experimental analysis shows the effectiveness of the proposed models in both parametric and non-parametric views

Semantic-enriched visual vocabulary construction in a weakly supervised context

© 2015 - IOS Press and the authors. All rights reserved. One of the prevalent learning tasks involving images is content-based image classification. This is a difficult task especially because the low-level features used to digitally describe images usually capture little information about the semantics of the images. In this paper, we tackle this difficulty by enriching the semantic content of the image representation by using external knowledge. The underlying hypothesis of our work is that creating a more semantically rich representation for images would yield higher machine learning performances, without the need to modify the learning algorithms themselves. The external semantic information is presented under the form of non-positional image labels, therefore positioning our work in a weakly supervised context. Two approaches are proposed: the first one leverages the labels into the visual vocabulary construction algorithm, the result being dedicated visual vocabularies. The second approach adds a filtering phase as a pre-processing of the vocabulary construction. Known positive and known negative sets are constructed and features that are unlikely to be associated with the objects denoted by the labels are filtered. We apply our proposition to the task of content-based image classification and we show that semantically enriching the image representation yields higher classification performances than the baseline representation

Analyzing Granger causality in climate data with time series classification methods

Attribution studies in climate science aim for scientifically ascertaining the influence of climatic variations on natural or anthropogenic factors. Many of those studies adopt the concept of Granger causality to infer statistical cause-effect relationships, while utilizing traditional autoregressive models. In this article, we investigate the potential of state-of-the-art time series classification techniques to enhance causal inference in climate science. We conduct a comparative experimental study of different types of algorithms on a large test suite that comprises a unique collection of datasets from the area of climate-vegetation dynamics. The results indicate that specialized time series classification methods are able to improve existing inference procedures. Substantial differences are observed among the methods that were tested

Understanding Heterogeneous EO Datasets: A Framework for Semantic Representations

Earth observation (EO) has become a valuable source of comprehensive, reliable, and persistent information for a wide number of applications. However, dealing with the complexity of land cover is sometimes difficult, as the variety of EO sensors reflects in the multitude of details recorded in several types of image data. Their properties dictate the category and nature of the perceptible land structures. The data heterogeneity hampers proper understanding, preventing the definition of universal procedures for content exploitation. The main shortcomings are due to the different human and sensor perception on objects, as well as to the lack of coincidence between visual elements and similarities obtained by computation. In order to bridge these sensory and semantic gaps, the paper presents a compound framework for EO image information extraction. The proposed approach acts like a common ground between the user's understanding, who is visually shortsighted to the visible domain, and the machines numerical interpretation of a much wider information. A hierarchical data representation is considered. At first, basic elements are automatically computed. Then, users can enforce their judgement on the data processing results until semantic structures are revealed. This procedure completes a user-machine knowledge transfer. The interaction is formalized as a dialogue, where communication is determined by a set of parameters guiding the computational process at each level of representation. The purpose is to maintain the data-driven observable connected to the level of semantics and to human awareness. The proposed concept offers flexibility and interoperability to users, allowing them to generate those results that best fit their application scenario. The experiments performed on different satellite images demonstrate the ability to increase the performances in case of semantic annotation by adjusting a set of parameters to the particularities of the analyzed data