Fully Unsupervised Image Denoising, Diversity Denoising and Image Segmentation with Limited Annotations

Understanding the processes of cellular development and the interplay of cell shape changes, division and migration requires investigation of developmental processes at the spatial resolution of single cell. Biomedical imaging experiments enable the study of dynamic processes as they occur in living organisms. While biomedical imaging is essential, a key component of exposing unknown biological phenomena is quantitative image analysis. Biomedical images, especially microscopy images, are usually noisy owing to practical limitations such as available photon budget, sample sensitivity, etc. Additionally, microscopy images often contain artefacts due to the optical aberrations in microscopes or due to imperfections in camera sensor and internal electronics. The noisy nature of images as well as the artefacts prohibit accurate downstream analysis such as cell segmentation. Although countless approaches have been proposed for image denoising, artefact removal and segmentation, supervised Deep Learning (DL) based content-aware algorithms are currently the best performing for all these tasks. Supervised DL based methods are plagued by many practical limitations. Supervised denoising and artefact removal algorithms require paired corrupted and high quality images for training. Obtaining such image pairs can be very hard and virtually impossible in most biomedical imaging applications owing to photosensitivity and the dynamic nature of the samples being imaged. Similarly, supervised DL based segmentation methods need copious amounts of annotated data for training, which is often very expensive to obtain. Owing to these restrictions, it is imperative to look beyond supervised methods. The objective of this thesis is to develop novel unsupervised alternatives for image denoising, and artefact removal as well as semisupervised approaches for image segmentation. The first part of this thesis deals with unsupervised image denoising and artefact removal. For unsupervised image denoising task, this thesis first introduces a probabilistic approach for training DL based methods using parametric models of imaging noise. Next, a novel unsupervised diversity denoising framework is presented which addresses the fundamentally non-unique inverse nature of image denoising by generating multiple plausible denoised solutions for any given noisy image. Finally, interesting properties of the diversity denoising methods are presented which make them suitable for unsupervised spatial artefact removal in microscopy and medical imaging applications. In the second part of this thesis, the problem of cell/nucleus segmentation is addressed. The focus is especially on practical scenarios where ground truth annotations for training DL based segmentation methods are scarcely available. Unsupervised denoising is used as an aid to improve segmentation performance in the presence of limited annotations. Several training strategies are presented in this work to leverage the representations learned by unsupervised denoising networks to enable better cell/nucleus segmentation in microscopy data. Apart from DL based segmentation methods, a proof-of-concept is introduced which views cell/nucleus segmentation from the perspective of solving a label fusion problem. This method, through limited human interaction, learns to choose the best possible segmentation for each cell/nucleus using only a pool of diverse (and possibly faulty) segmentation hypotheses as input. In summary, this thesis seeks to introduce new unsupervised denoising and artefact removal methods as well as semi-supervised segmentation methods which can be easily deployed to directly and immediately benefit biomedical practitioners with their research

Seeing into Darkness: Scotopic Visual Recognition

Images are formed by counting how many photons traveling from a given set of directions hit an image sensor during a given time interval. When photons are few and far in between, the concept of `image' breaks down and it is best to consider directly the flow of photons. Computer vision in this regime, which we call `scotopic', is radically different from the classical image-based paradigm in that visual computations (classification, control, search) have to take place while the stream of photons is captured and decisions may be taken as soon as enough information is available. The scotopic regime is important for biomedical imaging, security, astronomy and many other fields. Here we develop a framework that allows a machine to classify objects with as few photons as possible, while maintaining the error rate below an acceptable threshold. A dynamic and asymptotically optimal speed-accuracy tradeoff is a key feature of this framework. We propose and study an algorithm to optimize the tradeoff of a convolutional network directly from lowlight images and evaluate on simulated images from standard datasets. Surprisingly, scotopic systems can achieve comparable classification performance as traditional vision systems while using less than 0.1% of the photons in a conventional image. In addition, we demonstrate that our algorithms work even when the illuminance of the environment is unknown and varying. Last, we outline a spiking neural network coupled with photon-counting sensors as a power-efficient hardware realization of scotopic algorithms.Comment: 23 pages, 6 figure

Customized Sequential Designs for Random Simulation Experiments: Kriging Metamodelling and Bootstrapping

This paper proposes a novel method to select an experimental design for interpolation in random simulation.(Though the paper focuses on Kriging, this method may also apply to other types of metamodels such as linear regression models.)Assuming that simulation requires much computer time, it is important to select a design with a small number of observations (or simulation runs).The proposed method is therefore sequential.Its novelty is that it accounts for the specific input/output behavior (or response function) of the particular simulation at hand; i.e., the method is customized or application-driven.A tool for this customization is bootstrapping, which enables the estimation of the variances of predictions for inputs not yet simulated.The new method is tested through the classic M/M/1 queueing simulation.For this simulation the novel design indeed gives better results than a Latin Hypercube Sampling (LHS) with a prefixed sample of the same size.simulation;statistical methods;bootstrap

Feature Selection For The Fuzzy Artmap Neural Network Using A Hybrid Genetic Algorithm And Tabu Search

Prestasi pengelas rangkaian neural amat bergantung kepada set data yang digunakan dalam process pembelajaran. The performance of Neural-Network (NN)-based classifiers is strongly dependent on the data set used for learning

Normative Evidence Accumulation in Unpredictable Environments

In our dynamic world, decisions about noisy stimuli can require temporal accumulation of evidence to identify steady signals, differentiation to detect unpredictable changes in those signals, or both. Normative models can account for learning in these environments but have not yet been applied to faster decision processes. We present a novel, normative formulation of adaptive learning models that forms decisions by acting as a leaky accumulator with non-absorbing bounds. These dynamics, derived for both discrete and continuous cases, depend on the expected rate of change of the statistics of the evidence and balance signal identification and change detection. We found that, for two different tasks, human subjects learned these expectations, albeit imperfectly, then used them to make decisions in accordance with the normative model. The results represent a unified, empirically supported account of decision-making in unpredictable environments that provides new insights into the expectation-driven dynamics of the underlying neural signals

Identifying the Complete Correlation Structure in Large-Scale High-Dimensional Data Sets with Local False Discovery Rates

The identification of the dependent components in multiple data sets is a fundamental problem in many practical applications. The challenge in these applications is that often the data sets are high-dimensional with few observations or available samples and contain latent components with unknown probability distributions. A novel mathematical formulation of this problem is proposed, which enables the inference of the underlying correlation structure with strict false positive control. In particular, the false discovery rate is controlled at a pre-defined threshold on two levels simultaneously. The deployed test statistics originate in the sample coherence matrix. The required probability models are learned from the data using the bootstrap. Local false discovery rates are used to solve the multiple hypothesis testing problem. Compared to the existing techniques in the literature, the developed technique does not assume an a priori correlation structure and work well when the number of data sets is large while the number of observations is small. In addition, it can handle the presence of distributional uncertainties, heavy-tailed noise, and outliers.Comment: Preliminary versio

Feature Selection For The Fuzzy Artmap Neural Network Using A Hybrid Genetic Algorithm And Tabu Search [QA76.87. T164 2007 f rb].

Prestasi pengelas rangkaian neural amat bergantung kepada set data yang digunakan dalam process pembelajaran. Secara praktik, set data berkemungkinan mengandungi maklumat yang tidak diperlukan. Dengan itu, pencarian ciri merupakan suatu langkah yang penting dalam pembinaan suatu pengelas berdasarkan rangkaian neural yang efektif. The performance of Neural-Network (NN)-based classifiers is strongly dependent on the data set used for learning. In practice, a data set may contain noisy or redundant data items. Thus, feature selection is an important step in building an effective and efficient NN-based classifier