Multi-Atlas Segmentation using Partially Annotated Data: Methods and Annotation Strategies

Multi-atlas segmentation is a widely used tool in medical image analysis, providing robust and accurate results by learning from annotated atlas datasets. However, the availability of fully annotated atlas images for training is limited due to the time required for the labelling task. Segmentation methods requiring only a proportion of each atlas image to be labelled could therefore reduce the workload on expert raters tasked with annotating atlas images. To address this issue, we first re-examine the labelling problem common in many existing approaches and formulate its solution in terms of a Markov Random Field energy minimisation problem on a graph connecting atlases and the target image. This provides a unifying framework for multi-atlas segmentation. We then show how modifications in the graph configuration of the proposed framework enable the use of partially annotated atlas images and investigate different partial annotation strategies. The proposed method was evaluated on two Magnetic Resonance Imaging (MRI) datasets for hippocampal and cardiac segmentation. Experiments were performed aimed at (1) recreating existing segmentation techniques with the proposed framework and (2) demonstrating the potential of employing sparsely annotated atlas data for multi-atlas segmentation

What I talk about when I talk about integration of single-cell data

Over the past decade, single-cell technologies evolved from profiling hundreds of cells to millions of cells, and emerged from a single modality of data to cover multiple views at single-cell resolution, including genome, epigenome, transcriptome, and so on. With advance of these single-cell technologies, the booming of multimodal single-cell data creates a valuable resource for us to understand cellular heterogeneity and molecular mechanism at a comprehensive level. However, the large-scale multimodal single-cell data also presents a huge computational challenge for insightful integrative analysis. Here, I will lay out problems in data integration that single-cell research community is interested in and introduce computational principles for solving these integration problems. In the following chapters, I will present four computational methods for data integration under different scenarios. Finally, I will discuss some future directions and potential applications of single-cell data integration

Semi-automated learning strategies for large-scale segmentation of histology and other big bioimaging stacks and volumes

Labelled high-resolution datasets are becoming increasingly common and necessary in different areas of biomedical imaging. Examples include: serial histology and ex-vivo MRI for atlas building, OCT for studying the human brain, and micro X-ray for tissue engineering. Labelling such datasets, typically, requires manual delineation of a very detailed set of regions of interest on a large number of sections or slices. This process is tedious, time-consuming, not reproducible and rather inefficient due to the high similarity of adjacent sections. In this thesis, I explore the potential of a semi-automated slice level segmentation framework and a suggestive region level framework which aim to speed up the segmentation process of big bioimaging datasets. The thesis includes two well validated, published, and widely used novel methods and one algorithm which did not yield an improvement compared to the current state-of the-art. The slice-wise method, SmartInterpol, consists of a probabilistic model for semi-automated segmentation of stacks of 2D images, in which the user manually labels a sparse set of sections (e.g., one every n sections), and lets the algorithm complete the segmentation for other sections automatically. The proposed model integrates in a principled manner two families of segmentation techniques that have been very successful in brain imaging: multi-atlas segmentation and convolutional neural networks. Labelling every structure on a sparse set of slices is not necessarily optimal, therefore I also introduce a region level active learning framework which requires the labeller to annotate one region of interest on one slice at the time. The framework exploits partial annotations, weak supervision, and realistic estimates of class and section-specific annotation effort in order to greatly reduce the time it takes to produce accurate segmentations for large histological datasets. Although both frameworks have been created targeting histological datasets, they have been successfully applied to other big bioimaging datasets, reducing labelling effort by up to 60−70% without compromising accuracy

Semi-Weakly Supervised Learning for Label-efficient Semantic Segmentation in Expert-driven Domains

Unter Zuhilfenahme von Deep Learning haben semantische Segmentierungssysteme beeindruckende Ergebnisse erzielt, allerdings auf der Grundlage von überwachtem Lernen, das durch die Verfügbarkeit kostspieliger, pixelweise annotierter Bilder limitiert ist. Bei der Untersuchung der Performance dieser Segmentierungssysteme in Kontexten, in denen kaum Annotationen vorhanden sind, bleiben sie hinter den hohen Erwartungen, die durch die Performance in annotationsreichen Szenarien geschürt werden, zurück. Dieses Dilemma wiegt besonders schwer, wenn die Annotationen von lange geschultem Personal, z.B. Medizinern, Prozessexperten oder Wissenschaftlern, erstellt werden müssen. Um gut funktionierende Segmentierungsmodelle in diese annotationsarmen, Experten-angetriebenen Domänen zu bringen, sind neue Lösungen nötig. Zu diesem Zweck untersuchen wir zunächst, wie schlecht aktuelle Segmentierungsmodelle mit extrem annotationsarmen Szenarien in Experten-angetriebenen Bildgebungsdomänen zurechtkommen. Daran schließt sich direkt die Frage an, ob die kostspielige pixelweise Annotation, mit der Segmentierungsmodelle in der Regel trainiert werden, gänzlich umgangen werden kann, oder ob sie umgekehrt ein Kosten-effektiver Anstoß sein kann, um die Segmentierung in Gang zu bringen, wenn sie sparsam eingestetzt wird. Danach gehen wir auf die Frage ein, ob verschiedene Arten von Annotationen, schwache- und pixelweise Annotationen mit unterschiedlich hohen Kosten, gemeinsam genutzt werden können, um den Annotationsprozess flexibler zu gestalten. Experten-angetriebene Domänen haben oft nicht nur einen Annotationsmangel, sondern auch völlig andere Bildeigenschaften, beispielsweise volumetrische Bild-Daten. Der Übergang von der 2D- zur 3D-semantischen Segmentierung führt zu voxelweisen Annotationsprozessen, was den nötigen Zeitaufwand für die Annotierung mit der zusätzlichen Dimension multipliziert. Um zu einer handlicheren Annotation zu gelangen, untersuchen wir Trainingsstrategien für Segmentierungsmodelle, die nur preiswertere, partielle Annotationen oder rohe, nicht annotierte Volumina benötigen. Dieser Wechsel in der Art der Überwachung im Training macht die Anwendung der Volumensegmentierung in Experten-angetriebenen Domänen realistischer, da die Annotationskosten drastisch gesenkt werden und die Annotatoren von Volumina-Annotationen befreit werden, welche naturgemäß auch eine Menge visuell redundanter Regionen enthalten würden. Schließlich stellen wir die Frage, ob es möglich ist, die Annotations-Experten von der strikten Anforderung zu befreien, einen einzigen, spezifischen Annotationstyp liefern zu müssen, und eine Trainingsstrategie zu entwickeln, die mit einer breiten Vielfalt semantischer Information funktioniert. Eine solche Methode wurde hierzu entwickelt und in unserer umfangreichen experimentellen Evaluierung kommen interessante Eigenschaften verschiedener Annotationstypen-Mixe in Bezug auf deren Segmentierungsperformance ans Licht. Unsere Untersuchungen führten zu neuen Forschungsrichtungen in der semi-weakly überwachten Segmentierung, zu neuartigen, annotationseffizienteren Methoden und Trainingsstrategien sowie zu experimentellen Erkenntnissen, zur Verbesserung von Annotationsprozessen, indem diese annotationseffizient, expertenzentriert und flexibel gestaltet werden

From Constraints to Opportunities: Efficient Object Detection Learning for Humanoid Robots

Reliable perception and efficient adaptation to novel conditions are priority skills for robots that function in ever-changing environments. Indeed, autonomously operating in real world scenarios raises the need of identifying different context\u2019s states and act accordingly. Moreover, the requested tasks might not be known a-priori, requiring the system to update on-line. Robotic platforms allow to gather various types of perceptual information due to the multiple sensory modalities they are provided with. Nonetheless, latest results in computer vision motivate a particular interest in visual perception. Specifically, in this thesis, I mainly focused on the object detection task since it can be at the basis of more sophisticated capabilities. The vast advancements in latest computer vision research, brought by deep learning methods, are appealing in a robotic setting. However, their adoption in applied domains is not straightforward since adapting them to new tasks is strongly demanding in terms of annotated data, optimization time and computational resources. These requirements do not generally meet current robotics constraints. Nevertheless, robotic platforms and especially humanoids present opportunities that can be exploited. The sensors they are provided with represent precious sources of additional information. Moreover, their embodiment in the workspace and their motion capabilities allow for a natural interaction with the environment. Motivated by these considerations, in this Ph.D project, I mainly aimed at devising and developing solutions able to integrate the worlds of computer vision and robotics, by focusing on the task of object detection. Specifically, I dedicated a large amount of effort in alleviating state-of-the-art methods requirements in terms of annotated data and training time, preserving their accuracy by exploiting robotics opportunity

Artificial Intelligence Technology

This open access book aims to give our readers a basic outline of today’s research and technology developments on artificial intelligence (AI), help them to have a general understanding of this trend, and familiarize them with the current research hotspots, as well as part of the fundamental and common theories and methodologies that are widely accepted in AI research and application. This book is written in comprehensible and plain language, featuring clearly explained theories and concepts and extensive analysis and examples. Some of the traditional findings are skipped in narration on the premise of a relatively comprehensive introduction to the evolution of artificial intelligence technology. The book provides a detailed elaboration of the basic concepts of AI, machine learning, as well as other relevant topics, including deep learning, deep learning framework, Huawei MindSpore AI development framework, Huawei Atlas computing platform, Huawei AI open platform for smart terminals, and Huawei CLOUD Enterprise Intelligence application platform. As the world’s leading provider of ICT (information and communication technology) infrastructure and smart terminals, Huawei’s products range from digital data communication, cyber security, wireless technology, data storage, cloud computing, and smart computing to artificial intelligence

Visually-Enabled Active Deep Learning for (Geo) Text and Image Classification: A Review

This paper investigates recent research on active learning for (geo) text and image classification, with an emphasis on methods that combine visual analytics and/or deep learning. Deep learning has attracted substantial attention across many domains of science and practice, because it can find intricate patterns in big data; but successful application of the methods requires a big set of labeled data. Active learning, which has the potential to address the data labeling challenge, has already had success in geospatial applications such as trajectory classification from movement data and (geo) text and image classification. This review is intended to be particularly relevant for extension of these methods to GISience, to support work in domains such as geographic information retrieval from text and image repositories, interpretation of spatial language, and related geo-semantics challenges. Specifically, to provide a structure for leveraging recent advances, we group the relevant work into five categories: active learning, visual analytics, active learning with visual analytics, active deep learning, plus GIScience and Remote Sensing (RS) using active learning and active deep learning. Each category is exemplified by recent influential work. Based on this framing and our systematic review of key research, we then discuss some of the main challenges of integrating active learning with visual analytics and deep learning, and point out research opportunities from technical and application perspectives-for application-based opportunities, with emphasis on those that address big data with geospatial components

Visual Analytics for the Exploratory Analysis and Labeling of Cultural Data

Cultural data can come in various forms and modalities, such as text traditions, artworks, music, crafted objects, or even as intangible heritage such as biographies of people, performing arts, cultural customs and rites. The assignment of metadata to such cultural heritage objects is an important task that people working in galleries, libraries, archives, and museums (GLAM) do on a daily basis. These rich metadata collections are used to categorize, structure, and study collections, but can also be used to apply computational methods. Such computational methods are in the focus of Computational and Digital Humanities projects and research. For the longest time, the digital humanities community has focused on textual corpora, including text mining, and other natural language processing techniques. Although some disciplines of the humanities, such as art history and archaeology have a long history of using visualizations. In recent years, the digital humanities community has started to shift the focus to include other modalities, such as audio-visual data. In turn, methods in machine learning and computer vision have been proposed for the specificities of such corpora. Over the last decade, the visualization community has engaged in several collaborations with the digital humanities, often with a focus on exploratory or comparative analysis of the data at hand. This includes both methods and systems that support classical Close Reading of the material and Distant Reading methods that give an overview of larger collections, as well as methods in between, such as Meso Reading. Furthermore, a wider application of machine learning methods can be observed on cultural heritage collections. But they are rarely applied together with visualizations to allow for further perspectives on the collections in a visual analytics or human-in-the-loop setting. Visual analytics can help in the decision-making process by guiding domain experts through the collection of interest. However, state-of-the-art supervised machine learning methods are often not applicable to the collection of interest due to missing ground truth. One form of ground truth are class labels, e.g., of entities depicted in an image collection, assigned to the individual images. Labeling all objects in a collection is an arduous task when performed manually, because cultural heritage collections contain a wide variety of different objects with plenty of details. A problem that arises with these collections curated in different institutions is that not always a specific standard is followed, so the vocabulary used can drift apart from another, making it difficult to combine the data from these institutions for large-scale analysis. This thesis presents a series of projects that combine machine learning methods with interactive visualizations for the exploratory analysis and labeling of cultural data. First, we define cultural data with regard to heritage and contemporary data, then we look at the state-of-the-art of existing visualization, computer vision, and visual analytics methods and projects focusing on cultural data collections. After this, we present the problems addressed in this thesis and their solutions, starting with a series of visualizations to explore different facets of rap lyrics and rap artists with a focus on text reuse. Next, we engage in a more complex case of text reuse, the collation of medieval vernacular text editions. For this, a human-in-the-loop process is presented that applies word embeddings and interactive visualizations to perform textual alignments on under-resourced languages supported by labeling of the relations between lines and the relations between words. We then switch the focus from textual data to another modality of cultural data by presenting a Virtual Museum that combines interactive visualizations and computer vision in order to explore a collection of artworks. With the lessons learned from the previous projects, we engage in the labeling and analysis of medieval illuminated manuscripts and so combine some of the machine learning methods and visualizations that were used for textual data with computer vision methods. Finally, we give reflections on the interdisciplinary projects and the lessons learned, before we discuss existing challenges when working with cultural heritage data from the computer science perspective to outline potential research directions for machine learning and visual analytics of cultural heritage data

Artificial Intelligence Technology

This open access book aims to give our readers a basic outline of today’s research and technology developments on artificial intelligence (AI), help them to have a general understanding of this trend, and familiarize them with the current research hotspots, as well as part of the fundamental and common theories and methodologies that are widely accepted in AI research and application. This book is written in comprehensible and plain language, featuring clearly explained theories and concepts and extensive analysis and examples. Some of the traditional findings are skipped in narration on the premise of a relatively comprehensive introduction to the evolution of artificial intelligence technology. The book provides a detailed elaboration of the basic concepts of AI, machine learning, as well as other relevant topics, including deep learning, deep learning framework, Huawei MindSpore AI development framework, Huawei Atlas computing platform, Huawei AI open platform for smart terminals, and Huawei CLOUD Enterprise Intelligence application platform. As the world’s leading provider of ICT (information and communication technology) infrastructure and smart terminals, Huawei’s products range from digital data communication, cyber security, wireless technology, data storage, cloud computing, and smart computing to artificial intelligence