A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

Apprentissage profond de formes manuscrites pour la reconnaissance et le repérage efficace de l'écriture dans les documents numérisés

Malgré les efforts importants de la communauté d’analyse de documents, définir une representation robuste pour les formes manuscrites demeure un défi de taille. Une telle representation ne peut pas être définie explicitement par un ensemble de règles, et doit plutôt être obtenue avec une extraction intelligente de caractéristiques de haut niveau à partir d’images de documents. Dans cette thèse, les modèles d’apprentissage profond sont investigués pour la representation automatique de formes manuscrites. Les représentations proposées par ces modèles sont utilisées pour définir un système de reconnaissance et de repérage de mots individuels dans les documents. Le choix de traiter les mots individuellement est motivé par le fait que n’importe quel texte peut être segmenté en un ensemble de mots séparés. Dans une première contribution, une représentation non supervisée profonde est proposée pour la tâche de repérage de mots manuscrits. Cette représentation se base sur l’algorithme de regroupement spherical k-means, qui est employé pour construire une hiérarchie de fonctions paramétriques encodant les images de documents. Les avantages de cette représentation sont multiples. Tout d’abord, elle est définie de manière non supervisée, ce qui évite la nécessité d’avoir des données annotées pour l’entraînement. Ensuite, elle se calcule rapidement et est de taille compacte, permettant ainsi de repérer des mots efficacement. Dans une deuxième contribution, un modèle de bout en bout est développé pour la reconnaissance de mots manuscrits. Ce modèle est composé d’un réseau de neurones convolutifs qui prend en entrée l’image d’un mot et produit en sortie une représentation du texte reconnu. Ce texte est représenté sous la forme d’un ensemble de sous-sequences bidirectionnelles de caractères formant une hiérarchie. Cette représentation se distingue des approches existantes dans la littérature et offre plusieurs avantages par rapport à celles-ci. Notamment, elle est binaire et a une taille fixe, ce qui la rend robuste à la taille du texte. Par ailleurs, elle capture la distribution des sous-séquences de caractères dans le corpus d’entraînement, et permet donc au modèle entraîné de transférer cette connaissance à de nouveaux mots contenant les memes sous-séquences. Dans une troisième et dernière contribution, un modèle de bout en bout est proposé pour résoudre simultanément les tâches de repérage et de reconnaissance. Ce modèle intègre conjointement les textes et les images de mots dans un seul espace vectoriel. Une image est projetée dans cet espace via un réseau de neurones convolutifs entraîné à détecter les différentes forms de caractères. De même, un mot est projeté dans cet espace via un réseau de neurones récurrents. Le modèle proposé est entraîné de manière à ce que l’image d’un mot et son texte soient projetés au même point. Dans l’espace vectoriel appris, les tâches de repérage et de reconnaissance peuvent être traitées efficacement comme un problème de recherche des plus proches voisins

Exploiting Spatio-Temporal Coherence for Video Object Detection in Robotics

This paper proposes a method to enhance video object detection for indoor environments in robotics. Concretely, it exploits knowledge about the camera motion between frames to propagate previously detected objects to successive frames. The proposal is rooted in the concepts of planar homography to propose regions of interest where to find objects, and recursive Bayesian filtering to integrate observations over time. The proposal is evaluated on six virtual, indoor environments, accounting for the detection of nine object classes over a total of ∼ 7k frames. Results show that our proposal improves the recall and the F1-score by a factor of 1.41 and 1.27, respectively, as well as it achieves a significant reduction of the object categorization entropy (58.8%) when compared to a two-stage video object detection method used as baseline, at the cost of small time overheads (120 ms) and precision loss (0.92).</p

On Improving Generalization of CNN-Based Image Classification with Delineation Maps Using the CORF Push-Pull Inhibition Operator

Deployed image classification pipelines are typically dependent on the images captured in real-world environments. This means that images might be affected by different sources of perturbations (e.g. sensor noise in low-light environments). The main challenge arises by the fact that image quality directly impacts the reliability and consistency of classification tasks. This challenge has, hence, attracted wide interest within the computer vision communities. We propose a transformation step that attempts to enhance the generalization ability of CNN models in the presence of unseen noise in the test set. Concretely, the delineation maps of given images are determined using the CORF push-pull inhibition operator. Such an operation transforms an input image into a space that is more robust to noise before being processed by a CNN. We evaluated our approach on the Fashion MNIST data set with an AlexNet model. It turned out that the proposed CORF-augmented pipeline achieved comparable results on noise-free images to those of a conventional AlexNet classification model without CORF delineation maps, but it consistently achieved significantly superior performance on test images perturbed with different levels of Gaussian and uniform noise

FIAS Scientific Report 2011

In the year 2010 the Frankfurt Institute for Advanced Studies has successfully continued to follow its agenda to pursue theoretical research in the natural sciences. As stipulated in its charter, FIAS closely collaborates with extramural research institutions, like the Max Planck Institute for Brain Research in Frankfurt and the GSI Helmholtz Center for Heavy Ion Research, Darmstadt and with research groups at the science departments of Goethe University. The institute also engages in the training of young researchers and the education of doctoral students. This Annual Report documents how these goals have been pursued in the year 2010. Notable events in the scientific life of the Institute will be presented, e.g., teaching activities in the framework of the Frankfurt International Graduate School for Science (FIGSS), colloquium schedules, conferences organized by FIAS, and a full bibliography of publications by authors affiliated with FIAS. The main part of the Report consists of short one-page summaries describing the scientific progress reached in individual research projects in the year 2010..

Signal Processing Methods for Music Synchronization, Audio Matching, and Source Separation

The field of music information retrieval (MIR) aims at developing techniques and tools for organizing, understanding, and searching multimodal information in large music collections in a robust, efficient and intelligent manner. In this context, this thesis presents novel, content-based methods for music synchronization, audio matching, and source separation. In general, music synchronization denotes a procedure which, for a given position in one representation of a piece of music, determines the corresponding position within another representation. Here, the thesis presents three complementary synchronization approaches, which improve upon previous methods in terms of robustness, reliability, and accuracy. The first approach employs a late-fusion strategy based on multiple, conceptually different alignment techniques to identify those music passages that allow for reliable alignment results. The second approach is based on the idea of employing musical structure analysis methods in the context of synchronization to derive reliable synchronization results even in the presence of structural differences between the versions to be aligned. Finally, the third approach employs several complementary strategies for increasing the accuracy and time resolution of synchronization results. Given a short query audio clip, the goal of audio matching is to automatically retrieve all musically similar excerpts in different versions and arrangements of the same underlying piece of music. In this context, chroma-based audio features are a well-established tool as they possess a high degree of invariance to variations in timbre. This thesis describes a novel procedure for making chroma features even more robust to changes in timbre while keeping their discriminative power. Here, the idea is to identify and discard timbre-related information using techniques inspired by the well-known MFCC features, which are usually employed in speech processing. Given a monaural music recording, the goal of source separation is to extract musically meaningful sound sources corresponding, for example, to a melody, an instrument, or a drum track from the recording. To facilitate this complex task, one can exploit additional information provided by a musical score. Based on this idea, this thesis presents two novel, conceptually different approaches to source separation. Using score information provided by a given MIDI file, the first approach employs a parametric model to describe a given audio recording of a piece of music. The resulting model is then used to extract sound sources as specified by the score. As a computationally less demanding and easier to implement alternative, the second approach employs the additional score information to guide a decomposition based on non-negative matrix factorization (NMF)

Entropy in Image Analysis II

Image analysis is a fundamental task for any application where extracting information from images is required. The analysis requires highly sophisticated numerical and analytical methods, particularly for those applications in medicine, security, and other fields where the results of the processing consist of data of vital importance. This fact is evident from all the articles composing the Special Issue "Entropy in Image Analysis II", in which the authors used widely tested methods to verify their results. In the process of reading the present volume, the reader will appreciate the richness of their methods and applications, in particular for medical imaging and image security, and a remarkable cross-fertilization among the proposed research areas

Domain-informed Language Models for Process Systems Engineering

Process systems engineering (PSE) involves a systems-level approach to solving problems in chemical engineering related to process modeling, design, control, and optimization and involves modeling interactions between various systems (and subsystems) governing the process. This requires using a combination of mathematical methods, physical intuition, and recently machine learning techniques. Recently, language models have seen tremendous advances due to new and more efficient model architectures (such as transformers), computing power, and large volumes of training data. Many of these language models could be appropriately adapted to solve several PSE-related problems. However, language models are inherently complex and are often characterized by several million parameters, which could only be trained efficiently in data-rich areas, unlike PSE. Moreover, PSE is characterized by decades of rich process knowledge that must be utilized during model training to avoid mismatch between process knowledge and data-driven language models. This thesis presents a framework for building domain-informed language models for several central problems in PSE spanning multiple scales. Specifically, the frameworks presented include molecular property prediction, forward and retrosynthesis reaction outcome prediction, chemical flowsheet representation and generation, pharmaceutical information extraction, and reaction classification. Domain knowledge is integrated with language models using custom model architectures, standard and custom-built ontologies, linguistics-inspired chemistry and process flowsheet grammar, adapted problem formulations, graph theory techniques, and so on. This thesis is intended to provide a path for future developments of domain-informed language models in process systems engineering that respect domain knowledge, but leverage their computational advantages

Article Segmentation in Digitised Newspapers

Digitisation projects preserve and make available vast quantities of historical text. Among these, newspapers are an invaluable resource for the study of human culture and history. Article segmentation identifies each region in a digitised newspaper page that contains an article. Digital humanities, information retrieval (IR), and natural language processing (NLP) applications over digitised archives improve access to text and allow automatic information extraction. The lack of article segmentation impedes these applications. We contribute a thorough review of the existing approaches to article segmentation. Our analysis reveals divergent interpretations of the task, and inconsistent and often ambiguously defined evaluation metrics, making comparisons between systems challenging. We solve these issues by contributing a detailed task definition that examines the nuances and intricacies of article segmentation that are not immediately apparent. We provide practical guidelines on handling borderline cases and devise a new evaluation framework that allows insightful comparison of existing and future approaches. Our review also reveals that the lack of large datasets hinders meaningful evaluation and limits machine learning approaches. We solve these problems by contributing a distant supervision method for generating large datasets for article segmentation. We manually annotate a portion of our dataset and show that our method produces article segmentations over characters nearly as well as costly human annotators. We reimplement the seminal textual approach to article segmentation (Aiello and Pegoretti, 2006) and show that it does not generalise well when evaluated on a large dataset. We contribute a framework for textual article segmentation that divides the task into two distinct phases: block representation and clustering. We propose several techniques for block representation and contribute a novel highly-compressed semantic representation called similarity embeddings. We evaluate and compare different clustering techniques, and innovatively apply label propagation (Zhu and Ghahramani, 2002) to spread headline labels to similar blocks. Our similarity embeddings and label propagation approach substantially outperforms Aiello and Pegoretti but still falls short of human performance. Exploring visual approaches to article segmentation, we reimplement and analyse the state-of-the-art Bansal et al. (2014) approach. We contribute an innovative 2D Markov model approach that captures reading order dependencies and reduces the structured labelling problem to a Markov chain that we decode with Viterbi (1967). Our approach substantially outperforms Bansal et al., achieves accuracy as good as human annotators, and establishes a new state of the art in article segmentation. Our task definition, evaluation framework, and distant supervision dataset will encourage progress in the task of article segmentation. Our state-of-the-art textual and visual approaches will allow sophisticated IR and NLP applications over digitised newspaper archives, supporting research in the digital humanities