Brain tumor segmentation with missing modalities via latent multi-source correlation representation

Multimodal MR images can provide complementary information for accurate brain tumor segmentation. However, it's common to have missing imaging modalities in clinical practice. Since there exists a strong correlation between multi modalities, a novel correlation representation block is proposed to specially discover the latent multi-source correlation. Thanks to the obtained correlation representation, the segmentation becomes more robust in the case of missing modalities. The model parameter estimation module first maps the individual representation produced by each encoder to obtain independent parameters, then, under these parameters, the correlation expression module transforms all the individual representations to form a latent multi-source correlation representation. Finally, the correlation representations across modalities are fused via the attention mechanism into a shared representation to emphasize the most important features for segmentation. We evaluate our model on BraTS 2018 datasets, it outperforms the current state-of-the-art method and produces robust results when one or more modalities are missing.Comment: 9 pages, 6 figures, accepted by MICCAI 202

Uncertainty-based image segmentation with unsupervised mixture models

In this thesis, a contribution to explainable artificial intelligence is made. More specifically, the aspect of artificial intelligence which focusses on recreating the human perception is tackled from a previously neglected direction. A variant of human perception is building a mental model of the extents of semantic objects which appear in the field of view. If this task is performed by an algorithm, it is termed image segmentation. Recent methods in this area are mostly trained in a supervised fashion by exploiting an as extensive as possible data set of ground truth segmentations. Further, semantic segmentation is almost exclusively tackled by Deep Neural Networks (DNNs). Both trends pose several issues. First, the annotations have to be acquired somehow. This is especially inconvenient if, for instance, a new sensor becomes available, new domains are explored, or different quantities become of interest. In each case, the cumbersome and potentially costly labelling of the raw data has to be redone. While annotating keywords to an image can be achieved in a reasonable amount of time, annotating every pixel of an image with its respective ground truth class is an order of magnitudes more time-consuming. Unfortunately, the quality of the labels is an issue as well because fine-grained structures like hair, grass, or the boundaries of biological cells have to be outlined exactly in image segmentation in order to derive meaningful conclusions. Second, DNNs are discriminative models. They simply learn to separate the features of the respective classes. While this works exceptionally well if enough data is provided, quantifying the uncertainty with which a prediction is made is then not directly possible. In order to allow this, the models have to be designed differently. This is achieved through generatively modelling the distribution of the features instead of learning the boundaries between classes. Hence, image segmentation is tackled from a generative perspective in this thesis. By utilizing mixture models which belong to the set of generative models, the quantification of uncertainty is an implicit property. Additionally, the dire need of annotations can be reduced because mixture models are conveniently estimated in the unsupervised setting. Starting with the computation of the upper bounds of commonly used probability distributions, this knowledge is used to build a novel probability distribution. It is based on flexible marginal distributions and a copula which models the dependence structure of multiple features. This modular approach allows great flexibility and shows excellent performance at image segmentation. After deriving the upper bounds, different ways to reach them in an unsupervised fashion are presented. Including the probable locations of edges in the unsupervised model estimation greatly increases the performance. The proposed models surpass state-of-the-art accuracies in the generative and unsupervised setting and are on-par with many discriminative models. The analyses are conducted following the Bayesian paradigm which allows computing uncertainty estimates of the model parameters. Finally, a novel approach combining a discriminative DNN and a local appearance model in a weakly supervised setting is presented. This combination yields a generative semantic segmentation model with minimal annotation effort

Connected image processing with multivariate attributes: an unsupervised Markovian classification approach

International audienceThis article presents a new approach for constructing connected operators for image processing and analysis. It relies on a hierarchical Markovian unsupervised algorithm in order to classify the nodes of the traditional Max-Tree. This approach enables to naturally handle multivariate attributes in a robust non-local way. The technique is demonstrated on several image analysis tasks: filtering, segmentation, and source detection, on astronomical and biomedical images. The obtained results show that the method is competitive despite its general formulation. This article provides also a new insight in the field of hierarchical Markovian image processing showing that morphological trees can advantageously replace traditional quadtrees

Exploring Hidden Networks Yields Important Insights in Disparate Fields of Study

Network science captures a broad range of problems related to things (nodes) and relationships between them (edges). This dissertation explores real-world network problems in disparate domain applications where exploring less obvious hidden networks reveals important dynamics of the original network. The power grid is an explicit network of buses (e.g., generators) connected by branches (e.g., transmission lines). In rare cases, if k branches (a k-set) fail simultaneously, a cascading blackout may ensue; we refer to such k-sets as defective . We calculate system risk of cascading failure due to defective 2-sets and 3-sets in synthetic test cases of the Polish and Western US power grids. A stochastic group testing algorithm (Random Chemistry) is used to efficiently sample defective k-sets in the hidden network of all possible k-sets, and new methods are proposed to derive bounds on the total number of defective sets from the obtained sample. We use copula analysis, with a custom distance metric, to estimate risk when the k initiating outages are spatially correlated and show that this realistic assumption increases the relative contribution to risk of 3-sets over 2-sets. In the power systems application, among others, computational costs vary when testing defective vs. non-defective k-sets, a consideration that has not previously been made when evaluating group testing algorithms. We develop a domain-independent test problem generator that enables us to vary the number of defective k-sets, with a tunable parameter to control the cost ratio of testing defective vs. non-defective k-sets. We introduce a deterministic group-testing algorithm (SIGHT) capable of sampling from this space, and show that both the number of defective sets and the test cost ratio affect the relative efficiency of Random Chemistry vs. SIGHT. We discuss various applications where each algorithm is expected to outperform the other. Conversations can also be viewed as explicit networks of dialog (edges) between speakers (nodes). We propose using second and third order Markov models based on the sequence of speaker turn lengths to elucidate hidden networks of information flow and reveal patterns of information sharing between participants. The proposed method is demonstrated on a corpus of conversations between patients with advanced cancer and palliative care clinicians. We demonstrate the efficacy of the model by confirming known patterns of conversational discourse, identifying normative patterns of information flow in serious illness conversation, and showing how these patterns differ under a variety of contexts, including the expression of distressing emotion

A comparison of the CAR and DAGAR spatial random effects models with an application to diabetics rate estimation in Belgium

When hierarchically modelling an epidemiological phenomenon on a finite collection of sites in space, one must always take a latent spatial effect into account in order to capture the correlation structure that links the phenomenon to the territory. In this work, we compare two autoregressive spatial models that can be used for this purpose: the classical CAR model and the more recent DAGAR model. Differently from the former, the latter has a desirable property: its ρ parameter can be naturally interpreted as the average neighbor pair correlation and, in addition, this parameter can be directly estimated when the effect is modelled using a DAGAR rather than a CAR structure. As an application, we model the diabetics rate in Belgium in 2014 and show the adequacy of these models in predicting the response variable when no covariates are available

A Statistical Approach to the Alignment of fMRI Data

Multi-subject functional Magnetic Resonance Image studies are critical. The anatomical and functional structure varies across subjects, so the image alignment is necessary. We define a probabilistic model to describe functional alignment. Imposing a prior distribution, as the matrix Fisher Von Mises distribution, of the orthogonal transformation parameter, the anatomical information is embedded in the estimation of the parameters, i.e., penalizing the combination of spatially distant voxels. Real applications show an improvement in the classification and interpretability of the results compared to various functional alignment methods

Scalable Tools for Information Extraction and Causal Modeling of Neural Data

Systems neuroscience has entered in the past 20 years into an era that one might call "large scale systems neuroscience". From tuning curves and single neuron recordings there has been a conceptual shift towards a more holistic understanding of how the neural circuits work and as a result how their representations produce neural tunings. With the introduction of a plethora of datasets in various scales, modalities, animals, and systems; we as a community have witnessed invaluable insights that can be gained from the collective view of a neural circuit which was not possible with small scale experimentation. The concurrency of the advances in neural recordings such as the production of wide field imaging technologies and neuropixels with the developments in statistical machine learning and specifically deep learning has brought system neuroscience one step closer to data science. With this abundance of data, the need for developing computational models has become crucial. We need to make sense of the data, and thus we need to build models that are constrained up to the acceptable amount of biological detail and probe those models in search of neural mechanisms. This thesis consists of sections covering a wide range of ideas from computer vision, statistics, machine learning, and dynamical systems. But all of these ideas share a common purpose, which is to help automate neuroscientific experimentation process in different levels. In chapters 1, 2, and 3, I develop tools that automate the process of extracting useful information from raw neuroscience data in the model organism C. elegans. The goal of this is to avoid manual labor and pave the way for high throughput data collection aiming at better quantification of variability across the population of worms. Due to its high level of structural and functional stereotypy, and its relative simplicity, the nematode C. elegans has been an attractive model organism for systems and developmental research. With 383 neurons in males and 302 neurons in hermaphrodites, the positions and function of neurons is remarkably conserved across individuals. Furthermore, C. elegans remains the only organism for which a complete cellular, lineage, and anatomical map of the entire nervous system has been described for both sexes. Here, I describe the analysis pipeline that we developed for the recently proposed NeuroPAL technique in C. elegans. Our proposed pipeline consists of atlas building (chapter 1), registration, segmentation, neural tracking (chapter 2), and signal extraction (chapter 3). I emphasize that categorizing the analysis techniques as a pipeline consisting of the above steps is general and can be applied to virtually every single animal model and emerging imaging modality. I use the language of probabilistic generative modeling and graphical models to communicate the ideas in a rigorous form, therefore some familiarity with those concepts could help the reader navigate through the chapters of this thesis more easily. In chapters 4 and 5 I build models that aim to automate hypothesis testing and causal interrogation of neural circuits. The notion of functional connectivity (FC) has been instrumental in our understanding of how information propagates in a neural circuit. However, an important limitation is that current techniques do not dissociate between causal connections and purely functional connections with no mechanistic correspondence. I start chapter 4 by introducing causal inference as a unifying language for the following chapters. In chapter 4 I define the notion of interventional connectivity (IC) as a way to summarize the effect of stimulation in a neural circuit providing a more mechanistic description of the information flow. I then investigate which functional connectivity metrics are best predictive of IC in simulations and real data. Following this framework, I discuss how stimulations and interventions can be used to improve fitting and generalization properties of time series models. Building on the literature of model identification and active causal discovery I develop a switching time series model and a method for finding stimulation patterns that help the model to generalize to the vicinity of the observed neural trajectories. Finally in chapter 5 I develop a new FC metric that separates the transferred information from one variable to the other into unique and synergistic sources. In all projects, I have abstracted out concepts that are specific to the datasets at hand and developed the methods in the most general form. This makes the presented methods applicable to a broad range of datasets, potentially leading to new findings. In addition, all projects are accompanied with extensible and documented code packages, allowing theorists to repurpose the modules for novel applications and experimentalists to run analysis on their datasets efficiently and scalably. In summary my main contribution in this thesis are the following: 1) Building the first atlases of hermaphrodite and male C. elegans and developing a generic statistical framework for constructing atlases for a broad range of datasets. 2) Developing a semi-automated analysis pipeline for neural registration, segmentation, and tracking in C. elegans. 3) Extending the framework of non-negative matrix factorization to datasets with deformable motion and developing algorithms for joint tracking and signal demixing from videos of semi-immobilized C. elegans. 4) Defining the notion of interventional connectivity (IC) as a way to summarize the effect of stimulation in a neural circuit and investigating which functional connectivity metrics are best predictive of IC in simulations and real data. 5) Developing a switching time series model and a method for finding stimulation patterns that help the model to generalize to the vicinity of the observed neural trajectories. 6) Developing a new functional connectivity metric that separates the transferred information from one variable to the other into unique and synergistic sources. 7) Implementing extensible, well documented, open source code packages for each of the above contributions