Deep active learning for suggestive segmentation of biomedical image stacks via optimisation of Dice scores and traced boundary length

Manual segmentation of stacks of 2D biomedical images (e.g., histology) is a time-consuming task which can be sped up with semi-automated techniques. In this article, we present a suggestive deep active learning framework that seeks to minimise the annotation effort required to achieve a certain level of accuracy when labelling such a stack. The framework suggests, at every iteration, a specific region of interest (ROI) in one of the images for manual delineation. Using a deep segmentation neural network and a mixed cross-entropy loss function, we propose a principled strategy to estimate class probabilities for the whole stack, conditioned on heterogeneous partial segmentations of the 2D images, as well as on weak supervision in the form of image indices that bound each ROI. Using the estimated probabilities, we propose a novel active learning criterion based on predictions for the estimated segmentation performance and delineation effort, measured with average Dice scores and total delineated boundary length, respectively, rather than common surrogates such as entropy. The query strategy suggests the ROI that is expected to maximise the ratio between performance and effort, while considering the adjacency of structures that may have already been labelled – which decrease the length of the boundary to trace. We provide quantitative results on synthetically deformed MRI scans and real histological data, showing that our framework can reduce labelling effort by up to 60–70% without compromising accuracy

Active Learning for Text Classification

Text classification approaches are used extensively to solve real-world challenges. The success or failure of text classification systems hangs on the datasets used to train them, without a good dataset it is impossible to build a quality system. This thesis examines the applicability of active learning in text classification for the rapid and economical creation of labelled training data. Four main contributions are made in this thesis. First, we present two novel selection strategies to choose the most informative examples for manually labelling. One is an approach using an advanced aggregated confidence measurement instead of the direct output of classifiers to measure the confidence of the prediction and choose the examples with least confidence for querying. The other is a simple but effective exploration guided active learning selection strategy which uses only the notions of density and diversity, based on similarity, in its selection strategy. Second, we propose new methods of using deterministic clustering algorithms to help bootstrap the active learning process. We first illustrate the problems of using non-deterministic clustering for selecting initial training sets, showing how non-deterministic clustering methods can result in inconsistent behaviour in the active learning process. We then compare various deterministic clustering techniques and commonly used non-deterministic ones, and show that deterministic clustering algorithms are as good as non-deterministic clustering algorithms at selecting initial training examples for the active learning process. More importantly, we show that the use of deterministic approaches stabilises the active learning process. Our third direction is in the area of visualising the active learning process. We demonstrate the use of an existing visualisation technique in understanding active learning selection strategies to show that a better understanding of selection strategies can be achieved with the help of visualisation techniques. Finally, to evaluate the practicality and usefulness of active learning as a general dataset labelling methodology, it is desirable that actively labelled dataset can be reused more widely instead of being only limited to some particular classifier. We compare the reusability of popular active learning methods for text classification and identify the best classifiers to use in active learning for text classification. This thesis is concerned using active learning methods to label large unlabelled textual datasets. Our domain of interest is text classification, but most of the methods proposed are quite general and so are applicable to other domains having large collections of data with high dimensionality

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

Automating the anonymisation of textual corpora

[EU] Gaur egun, testu berriak etengabe sortzen doaz sare sozialetako mezu, osasun-txosten, dokumentu o zial eta halakoen ondorioz. Hala ere, testuok informazio pertsonala baldin badute, ezin dira ikerkuntzarako edota beste helburutarako baliatu, baldin eta aldez aurretik ez badira anonimizatzen. Anonimizatze hori automatikoki egitea erronka handia da eta askotan hutsetik anotatutako domeinukako datuak behar dira, ez baita arrunta helburutzat ditugun testuinguruetarako anotatutako corpusak izatea. Hala, tesi honek bi helburu ditu: (i) Gaztelaniazko elkarrizketa espontaneoz osatutako corpus anonimizatu berri bat konpilatu eta eskura jartzea, eta (ii) sortutako baliabide hau ustiatzea informazio sentiberaren identi kazio-teknikak aztertzeko, helburu gisa dugun domeinuan testu etiketaturik izan gabe. Hala, lehenengo helburuari lotuta, ES-Port izeneko corpusa sortu dugu. Telekomunikazio-ekoizle batek ahoz laguntza teknikoa ematen duenean sortu diren 1170 elkarrizketa espontaneoek osatzen dute corpusa. Ordezkatze-tekniken bidez anonimizatu da, eta ondorioz emaitza testu irakurgarri eta naturala izan da. Hamaika anonimizazio-kategoria landu dira, eta baita hizkuntzakoak eta hizkuntzatik kanpokoak diren beste zenbait anonimizazio-fenomeno ere, hala nola, kode-aldaketa, barrea, errepikapena, ahoskatze okerrak, eta abar. Bigarren helburuari lotuta, berriz, anonimizatu beharreko informazio sentibera identi katzeko, gordailuan oinarritutako Ikasketa Aktiboa erabili da, honek helburutzat baitu ahalik eta testu anotatu gutxienarekin sailkatzaile ahalik eta onena lortzea. Horretaz gain, emaitzak hobetzeko, eta abiapuntuko hautaketarako eta galderen hautaketarako estrategiak aztertzeko, Ezagutza Transferentzian oinarritutako teknikak ustiatu dira, aldez aurretik anotatuta zegoen corpus txiki bat oinarri hartuta. Emaitzek adierazi dute, lan honetan aukeratutako metodoak egokienak izan direla abiapuntuko hautaketa egiteko eta kontsulta-estrategia gisa iturri eta helburu sailkapenen zalantzak konbinatzeak Ikasketa Aktiboa hobetzen duela, ikaskuntza-kurba bizkorragoak eta sailkapen-errendimendu handiagoak lortuz iterazio gutxiagotan.[EN] A huge amount of new textual data are created day by day through social media posts, health records, official documents, and so on. However, if such resources contain personal data, they cannot be shared for research or other purposes without undergoing proper anonymisation. Automating such task is challenging and often requires labelling in-domain data from scratch since anonymised annotated corpora for the target scenarios are rarely available. This thesis has two main objectives: (i) to compile and provide a new corpus in Spanish with annotated anonymised spontaneous dialogue data, and (ii) to exploit the newly provided resource to investigate techniques for automating the sensitive data identification task, in a setting where initially no annotated data from the target domain are available. Following such aims, first, the ES-Port corpus is presented. It is a compilation of 1170 spontaneous spoken human-human dialogues from calls to the technical support service of a telecommunications provider. The corpus has been anonymised using the substitution technique, which implies the result is a readable natural text, and it contains annotations of eleven different anonymisation categories, as well as some linguistic and extra-linguistic phenomena annotations like code-switching, laughter, repetitions, mispronunciations, and so on. Next, the compiled corpus is used to investigate automatic sensitive data identification within a pool-based Active Learning framework, whose aim is to obtain the best possible classifier having to annotate as little data as possible. In order to improve such setting, Knowledge Transfer techniques from another small available anonymisation annotated corpus are explored for seed selection and query selection strategies. Results show that using the proposed seed selection methods obtain the best seeds on which to initialise the base learner's training and that combining source and target classifiers' uncertainties as query strategy improves the Active Learning process, deriving in steeper learning curves and reaching top classifier performance in fewer iterations

A Wholistic View of Continual Learning with Deep Neural Networks: Forgotten Lessons and the Bridge to Active and Open World Learning

Current deep learning research is dominated by benchmark evaluation. A method is regarded as favorable if it empirically performs well on the dedicated test set. This mentality is seamlessly reflected in the resurfacing area of continual learning, where consecutively arriving sets of benchmark data are investigated. The core challenge is framed as protecting previously acquired representations from being catastrophically forgotten due to the iterative parameter updates. However, comparison of individual methods is nevertheless treated in isolation from real world application and typically judged by monitoring accumulated test set performance. The closed world assumption remains predominant. It is assumed that during deployment a model is guaranteed to encounter data that stems from the same distribution as used for training. This poses a massive challenge as neural networks are well known to provide overconfident false predictions on unknown instances and break down in the face of corrupted data. In this work we argue that notable lessons from open set recognition, the identification of statistically deviating data outside of the observed dataset, and the adjacent field of active learning, where data is incrementally queried such that the expected performance gain is maximized, are frequently overlooked in the deep learning era. Based on these forgotten lessons, we propose a consolidated view to bridge continual learning, active learning and open set recognition in deep neural networks. Our results show that this not only benefits each individual paradigm, but highlights the natural synergies in a common framework. We empirically demonstrate improvements when alleviating catastrophic forgetting, querying data in active learning, selecting task orders, while exhibiting robust open world application where previously proposed methods fail.Comment: 32 page