Accuracy of MAP segmentation with hidden Potts and Markov mesh prior models via Path Constrained Viterbi Training, Iterated Conditional Modes and Graph Cut based algorithms

In this paper, we study statistical classification accuracy of two different Markov field environments for pixelwise image segmentation, considering the labels of the image as hidden states and solving the estimation of such labels as a solution of the MAP equation. The emission distribution is assumed the same in all models, and the difference lays in the Markovian prior hypothesis made over the labeling random field. The a priori labeling knowledge will be modeled with a) a second order anisotropic Markov Mesh and b) a classical isotropic Potts model. Under such models, we will consider three different segmentation procedures, 2D Path Constrained Viterbi training for the Hidden Markov Mesh, a Graph Cut based segmentation for the first order isotropic Potts model, and ICM (Iterated Conditional Modes) for the second order isotropic Potts model. We provide a unified view of all three methods, and investigate goodness of fit for classification, studying the influence of parameter estimation, computational gain, and extent of automation in the statistical measures Overall Accuracy, Relative Improvement and Kappa coefficient, allowing robust and accurate statistical analysis on synthetic and real-life experimental data coming from the field of Dental Diagnostic Radiography. All algorithms, using the learned parameters, generate good segmentations with little interaction when the images have a clear multimodal histogram. Suboptimal learning proves to be frail in the case of non-distinctive modes, which limits the complexity of usable models, and hence the achievable error rate as well. All Matlab code written is provided in a toolbox available for download from our website, following the Reproducible Research Paradigm

Local Autoencoding for Parameter Estimation in a Hidden Potts-Markov Random Field

A local-autoencoding (LAE) method is proposed for the parameter estimation in a Hidden Potts-Markov random field model. Due to sampling cost, Markov chain Monte Carlo methods are rarely used in real-time applications. Like other heuristic methods, LAE is based on a conditional independence assumption. It adapts, however, the parameters in a block-by-block style with a simple Hebbian learning rule. Experiments with given label fields show that the LAE is able to converge in far less time than required for a scan. It is also possible to derive an estimate for LAE based on a Cramer-Rao bound that is similar to the classical maximum pseudolikelihood method. As a general algorithm, LAE can be used to estimate the parameters in anisotropic label fields. Furthermore, LAE is not limited to the classical Potts model and can be applied to other types of Potts models by simple label field transformations and straightforward learning rule extensions. Experimental results on image segmentations demonstrate the efficiency and generality of the LAE algorithm.</p

Probabilistic Models for Joint Segmentation, Detection and Tracking

Migrace buněk a buněčných částic hraje důležitou roli ve fungování živých organismů. Systematický výzkum buněčné migrace byl umožněn v posledních dvaceti letech rychlým rozvojem neinvazivních zobrazovacích technik a digitálních snímačů. Moderní zobrazovací systémy dovolují studovat chování buněčných populací složených z mnoha ticíců buněk. Manuální analýza takového množství dat by byla velice zdlouhavá, protože některé experimenty vyžadují analyzovat tvar, rychlost a další charakteristiky jednotlivých buněk. Z tohoto důvodu je ve vědecké komunitě velká poptávka po automatických metodách.Migration of cells and subcellular particles plays a crucial role in many processes in living organisms. Despite its importance a systematic research of cell motility has only been possible in last two decades due to rapid development of non-invasive imaging techniques and digital cameras. Modern imaging systems allow to study large populations with thousands of cells. Manual analysis of the acquired data is infeasible, because in order to gain insight into underlying biochemical processes it is sometimes necessary to determine shape, velocity and other characteristics of individual cells. Thus there is a high demand for automatic methods

Statistical methods for biological sequence analysis for DNA binding motifs and protein contacts

Over the last decades a revolution in novel measurement techniques has permeated the biological sciences filling the databases with unprecedented amounts of data ranging from genomics, transcriptomics, proteomics and metabolomics to structural and ecological data. In order to extract insights from the vast quantity of data, computational and statistical methods are nowadays crucial tools in the toolbox of every biological researcher. In this thesis I summarize my contributions in two data-rich fields in biological sciences: transcription factor binding to DNA and protein structure prediction from protein sequences with shared evolutionary ancestry. In the first part of my thesis I introduce our work towards a web server for analysing transcription factor binding data with Bayesian Markov Models. In contrast to classical PWM or di-nucleotide models, Bayesian Markov models can capture complex inter-nucleotide dependencies that can arise from shape-readout and alternative binding modes. In addition to giving access to our methods in an easy-to-use, intuitive web-interface, we provide our users with novel tools and visualizations to better evaluate the biological relevance of the inferred binding motifs. We hope that our tools will prove useful for investigating weak and complex transcription factor binding motifs which cannot be predicted accurately with existing tools. The second part discusses a statistical attempt to correct out the phylogenetic bias arising in co-evolution methods applied to the contact prediction problem. Co-evolution methods have revolutionized the protein-structure prediction field more than 10 years ago, and, until very recently, have retained their importance as crucial input features to deep neural networks. As the co-evolution information is extracted from evolutionarily related sequences, we investigated whether the phylogenetic bias to the signal can be corrected out in a principled way using a variation of the Felsenstein's tree-pruning algorithm applied in combination with an independent-pair assumption to derive pairwise amino counts that are corrected for the evolutionary history. Unfortunately, the contact prediction derived from our corrected pairwise amino acid counts did not yield a competitive performance.2021-09-2

Part-based recognition of 3-D objects with application to shape modeling in hearing aid manufacturing

In order to meet the needs of people with hearing loss today hearing aids are custom designed. Increasingly accurate 3-D scanning technology has contributed to the transition from conventional production scenarios to software based processes. Nonetheless, there is a tremendous amount of manual work involved to transform an input 3-D surface mesh of the outer ear into a final hearing aid shape. This manual work is often cumbersome and requires lots of experience which is why automatic solutions are of high practical relevance. This work is concerned with the recognition of 3-D surface meshes of ear implants. In particular we present a semantic part-labeling framework which significantly outperforms existing approaches for this task. We make at least three contributions which may also be found useful for other classes of 3-D meshes. Firstly, we validate the discriminative performance of several local descriptors and show that the majority of them performs poorly on our data except for 3-D shape contexts. The reason for this is that many local descriptor schemas are not rich enough to capture subtle variations in form of bends which is typical for organic shapes. Secondly, based on the observation that the left and the right outer ear of an individual look very similar we raised the question how similar the ear shapes among arbitrary individuals are? In this work, we define a notion of distance between ear shapes as building block of a non-parametric shape model of the ear to better handle the anatomical variability in ear implant labeling. Thirdly, we introduce a conditional random field model with a variety of label priors to facilitate the semantic part-labeling of 3-D meshes of ear implants. In particular we introduce the concept of a global parametric transition prior to enforce transition boundaries between adjacent object parts with an a priori known parametric form. In this way we were able to overcome the issue of inadequate geometric cues (e.g., ridges, bumps, concavities) as natural indicators for the presence of part boundaries. The last part of this work offers an outlook to possible extensions of our methods, in particular the development of 3-D descriptors that are fast to compute whilst at the same time rich enough to capture the characteristic differences between objects residing in the same class

On flexible random field models for spatial statistics: Spatial mixture models and deformed SPDE models

Spatial random fields are one of the key concepts in statistical analysis of spatial data. The random field explains the spatial dependency and serves the purpose ofregularizing interpolation of measured values or to act as an explanatory model. In this thesis, models for applications in medical imaging, spatial point pattern analysis, and maritime engineering are developed. They are constructed to be flexible yet interpretable. Since spatial data in several dimensions tend to be large, the methods considered for estimation, prediction, and approximation are focused on reducing computational complexity. The novelty of this work is based on two main ideas. First, the idea of a spatial mixture model, i.e., a stochastic partitioning of the spatial domain using a latent categorically valued random field. This makes it possible to explain discontinuities in otherwise smoothly varying random fields. It also introduces a different perspective that of a spatial classification problem. This idea is used to model the spatial distribution of tissue types in the human head; an application important in reducing cell damage due to ionizing radiation in medical imaging. The idea is also used to introduce an extension of the popular log-Gaussian Cox process. This extension adds an extra layer of a latent random partitioning of the spatial domain. Using this model,it is possible to classify spatial domains based on observed point patterns. The second main idea of this thesis is that of spatially deforming a solution to a stochastic partial differential equation. In this way, a random field with a needed degree of non-stationarity and anisotropy can be acquired. A coupled system of two such stochastic partial differential equations is used to model the joint distribution of significant wave heights and wave periods in the north Atlantic. The model is used to assess risks in naval logistics