Automatic Lameness Detection in a Milking Robot : Instrumentation, measurement software, algorithms for data analysis and a neural network model

The aim of this thesis is to develop a fully automatic lameness detection system that operates in a milking robot. The instrumentation, measurement software, algorithms for data analysis and a neural network model for lameness detection were developed. Automatic milking has become a common practice in dairy husbandry, and in the year 2006 about 4000 farms worldwide used over 6000 milking robots. There is a worldwide movement with the objective of fully automating every process from feeding to milking. Increase in automation is a consequence of increasing farm sizes, the demand for more efficient production and the growth of labour costs. As the level of automation increases, the time that the cattle keeper uses for monitoring animals often decreases. This has created a need for systems for automatically monitoring the health of farm animals. The popularity of milking robots also offers a new and unique possibility to monitor animals in a single confined space up to four times daily. Lameness is a crucial welfare issue in the modern dairy industry. Limb disorders cause serious welfare, health and economic problems especially in loose housing of cattle. Lameness causes losses in milk production and leads to early culling of animals. These costs could be reduced with early identification and treatment. At present, only a few methods for automatically detecting lameness have been developed, and the most common methods used for lameness detection and assessment are various visual locomotion scoring systems. The problem with locomotion scoring is that it needs experience to be conducted properly, it is labour intensive as an on-farm method and the results are subjective. A four balance system for measuring the leg load distribution of dairy cows during milking in order to detect lameness was developed and set up in the University of Helsinki Research farm Suitia. The leg weights of 73 cows were successfully recorded during almost 10,000 robotic milkings over a period of 5 months. The cows were locomotion scored weekly, and the lame cows were inspected clinically for hoof lesions. Unsuccessful measurements, caused by cows standing outside the balances, were removed from the data with a special algorithm, and the mean leg loads and the number of kicks during milking was calculated. In order to develop an expert system to automatically detect lameness cases, a model was needed. A probabilistic neural network (PNN) classifier model was chosen for the task. The data was divided in two parts and 5,074 measurements from 37 cows were used to train the model. The operation of the model was evaluated for its ability to detect lameness in the validating dataset, which had 4,868 measurements from 36 cows. The model was able to classify 96% of the measurements correctly as sound or lame cows, and 100% of the lameness cases in the validation data were identified. The number of measurements causing false alarms was 1.1%. The developed model has the potential to be used for on-farm decision support and can be used in a real-time lameness monitoring system.

Computing the Stochastic Complexity of Simple Probabilistic Graphical Models

Minimum Description Length (MDL) is an information-theoretic principle that can be used for model selection and other statistical inference tasks. There are various ways to use the principle in practice. One theoretically valid way is to use the normalized maximum likelihood (NML) criterion. Due to computational difficulties, this approach has not been used very often. This thesis presents efficient floating-point algorithms that make it possible to compute the NML for multinomial, Naive Bayes and Bayesian forest models. None of the presented algorithms rely on asymptotic analysis and with the first two model classes we also discuss how to compute exact rational number solutions.

Applicability of Statistical Learning Algorithms for Spatial Variability of Rock Depth

Two algorithms are outlined, each of which has interesting features for modeling of spatial variability of rock depth. In this paper, reduced level of rock at Bangalore, India, is arrived from the 652 boreholes data in the area covering 220 sqa <.km. Support vector machine (SVM) and relevance vector machine (RVM) have been utilized to predict the reduced level of rock in the subsurface of Bangalore and to study the spatial variability of the rock depth. The support vector machine (SVM) that is firmly based on the theory of statistical learning theory uses regression technique by introducing epsilon-insensitive loss function has been adopted. RVM is a probabilistic model similar to the widespread SVM, but where the training takes place in a Bayesian framework. Prediction results show the ability of learning machine to build accurate models for spatial variability of rock depth with strong predictive capabilities. The paper also highlights the capability ofRVM over the SVM model.

Smoothed functional and Quasi-Newton algorithms for routing in multi-stage queueing network with constraints

We consider the problem of optimal routing in a multi-stage network of queues with constraints on queue lengths. We develop three algorithms for probabilistic routing for this problem using only the total end-to-end delays. These algorithms use the smoothed functional (SF) approach to optimize the routing probabilities. In our model all the queues are assumed to have constraints on the average queue length. We also propose a novel quasi-Newton based SF algorithm. Policies like Join Shortest Queue or Least Work Left work only for unconstrained routing. Besides assuming knowledge of the queue length at all the queues. If the only information available is the expected end-to-end delay as with our case such policies cannot be used. We also give simulation results showing the performance of the SF algorithms for this problem.

Automatic speech segmentation using probabilistic latent component modeling

Latent variable methods, such as PLCA (Probabilistic Latent Component Analysis) have been successfully used for analysis of non-negative signal representations. In this paper, we formulate PLCS (Probabilistic Latent Component Segmentation), which models each time frame of a spectrogram as a spectral distribution. Given the signal spectrogram, the segmentation boundaries are estimated using a maximum-likelihood approach. For an efficient solution, the algorithm imposes a hard constraint that each segment is modelled by a single latent component. The hard constraint facilitates the solution of ML boundary estimation using dynamic programming. The PLCS framework does not impose a parametric assumption unlike earlier ML segmentation techniques. PLCS can be naturally extended to model coarticulation between successive phones. Experiments on the TIMIT corpus show that the proposed technique is promising compared to most state of the art speech segmentation algorithms.

Mateda-2.0: Estimation of Distribution Algorithms in MATLAB

This paper describes Mateda-2.0, a MATLAB package for estimation of distribution algorithms (EDAs). This package can be used to solve single and multi-objective discrete and continuous optimization problems using EDAs based on undirected and directed probabilistic graphical models. The implementation contains several methods commonly employed by EDAs. It is also conceived as an open package to allow users to incorporate different combinations of selection, learning, sampling, and local search procedures. Additionally, it includes methods to extract, process and visualize the structures learned by the probabilistic models. This way, it can unveil previously unknown information about the optimization problem domain. Mateda-2.0 also incorporates a module for creating and validating function models based on the probabilistic models learned by EDAs.

Probabilistic amplitude and frequency demodulation

A number of recent scientific and engineering problems require signals to be decomposed into a product of a slowly varying positive envelope and a quickly varying carrier whose instantaneous frequency also varies slowly over time. Although signal processing provides algorithms for so-called amplitude-and frequency-demodulation (AFD), there are well known problems with all of the existing methods. Motivated by the fact that AFD is ill-posed, we approach the problem using probabilistic inference. The new approach, called probabilistic amplitude and frequency demodulation (PAFD), models instantaneous frequency using an auto-regressive generalization of the von Mises distribution, and the envelopes using Gaussian auto-regressive dynamics with a positivity constraint. A novel form of expectation propagation is used for inference. We demonstrate that although PAFD is computationally demanding, it outperforms previous approaches on synthetic and real signals in clean, noisy and missing data settings.

Probabilistic Amplitude Demodulation

Auditory scene analysis is extremely challenging. One approach, perhaps that adopted by the brain, is to shape useful representations of sounds on prior knowledge about their statistical structure. For example, sounds with harmonic sections are common and so time-frequency representations are efficient. Most current representations concentrate on the shorter components. Here, we propose representations for structures on longer time-scales, like the phonemes and sentences of speech. We decompose a sound into a product of processes, each with its own characteristic time-scale. This demodulation cascade relates to classical amplitude demodulation, but traditional algorithms fail to realise the representation fully. A new approach, probabilistic amplitude demodulation, is shown to out-perform the established methods, and to easily extend to representation of a full demodulation cascade.

Probabilistic Solution of Inverse Problems

In this thesis we study the general problem of reconstructing a function, defined on a finite lattice from a set of incomplete, noisy and/or ambiguous observations. The goal of this work is to demonstrate the generality and practical value of a probabilistic (in particular, Bayesian) approach to this problem, particularly in the context of Computer Vision. In this approach, the prior knowledge about the solution is expressed in the form of a Gibbsian probability distribution on the space of all possible functions, so that the reconstruction task is formulated as an estimation problem. Our main contributions are the following: (1) We introduce the use of specific error criteria for the design of the optimal Bayesian estimators for several classes of problems, and propose a general (Monte Carlo) procedure for approximating them. This new approach leads to a substantial improvement over the existing schemes, both regarding the quality of the results (particularly for low signal to noise ratios) and the computational efficiency. (2) We apply the Bayesian appraoch to the solution of several problems, some of which are formulated and solved in these terms for the first time. Specifically, these applications are: teh reconstruction of piecewise constant surfaces from sparse and noisy observationsl; the reconstruction of depth from stereoscopic pairs of images and the formation of perceptual clusters. (3) For each one of these applications, we develop fast, deterministic algorithms that approximate the optimal estimators, and illustrate their performance on both synthetic and real data. (4) We propose a new method, based on the analysis of the residual process, for estimating the parameters of the probabilistic models directly from the noisy observations. This scheme leads to an algorithm, which has no free parameters, for the restoration of piecewise uniform images. (5) We analyze the implementation of the algorithms that we develop in non-conventional hardware, such as massively parallel digital machines, and analog and hybrid networks.

Nearest-neighbor Queries in Probabilistic Graphs

Large probabilistic graphs arise in various domains spanning from social networks to biological and communication networks. An important query in these graphs is the k nearest-neighbor query, which involves finding and reporting the k closest nodes to a specific node. This query assumes the existence of a measure of the "proximity" or the "distance" between any two nodes in the graph. To that end, we propose various novel distance functions that extend well known notions of classical graph theory, such as shortest paths and random walks. We argue that many meaningful distance functions are computationally intractable to compute exactly. Thus, in order to process nearest-neighbor queries, we resort to Monte Carlo sampling and exploit novel graph-transformation ideas and pruning opportunities. In our extensive experimental analysis, we explore the trade-offs of our approximation algorithms and demonstrate that they scale well on real-world probabilistic graphs with tens of millions of edges.

Probabilistic logic with independence

This paper investigates probabilistic logics endowed with independence relations. We review propositional probabilistic languages without and with independence. We then consider graph-theoretic representations for propositional probabilistic logic with independence; complexity is analyzed, algorithms are derived, and examples are discussed. Finally, we examine a restricted first-order probabilistic logic that generalizes relational Bayesian networks.

Algorithms for Hidden Markov Models With Imprecisely Specified Parameters

Hidden Markov models (HMMs) are widely used models for sequential data. As with other probabilistic graphical models, they require the specification of precise probability values, which can be too restrictive for some domains, especially when data are scarce or costly to acquire. We present a generalized version of HMMs, whose quantification can be done by sets of, instead of single, probability distributions. Our models have the ability to suspend judgment when there is not enough statistical evidence, and can serve as a sensitivity analysis tool for standard non-stationary HMMs. Efficient inference algorithms are developed to address standard HMM usage such as the computation of likelihoods and most probable explanations. Experiments with real data show that the use of imprecise probabilities leads to more reliable inferences without compromising efficiency.

Propositional and Relational Bayesian Networks Associated with Imprecise and Qualitative Probabilistic Assessments

This paper investigates a representation language with flexibility inspired by probabilistic logic and compactness inspired by relational Bayesian networks. The goal is to handle propositional and first-order constructs together with precise, imprecise, indeterminate and qualitative probabilistic assessments. The paper shows how this can be achieved through the theory of credal networks. New exact and approximate inference algorithms based on multilinear programming and iterated/loopy propagation of interval probabilities are presented; their superior performance, compared to existing ones, is shown empirically.

Anytime Algorithms for Solving Possibilistic MDPs and Hybrid MDPs

The ability of an agent to make quick, rational decisions in an uncertain environment is paramount for its applicability in realistic settings. Markov Decision Processes (MDP) provide such a framework, but can only model uncertainty that can be expressed as probabilities. Possibilistic counterparts of MDPs allow to model imprecise beliefs, yet they cannot accurately represent probabilistic sources of uncertainty and they lack the efficient online solvers found in the probabilistic MDP community. In this paper we advance the state of the art in three important ways. Firstly, we propose the first online planner for possibilistic MDP by adapting the Monte-Carlo Tree Search (MCTS) algorithm. A key component is the development of efficient search structures to sample possibility distributions based on the DPY transformation as introduced by Dubois, Prade, and Yager. Secondly, we introduce a hybrid MDP model that allows us to express both possibilistic and probabilistic uncertainty, where the hybrid model is a proper extension of both probabilistic and possibilistic MDPs. Thirdly, we demonstrate that MCTS algorithms can readily be applied to solve such hybrid models.

Probabilistic Egomotion for Stereo Visual Odometry

We present a novel approach of Stereo Visual Odometry for vehicles equipped with calibrated stereo cameras. We combine a dense probabilistic 5D egomotion estimation method with a sparse keypoint based stereo approach to provide high quality estimates of vehicle’s angular and linear velocities. To validate our approach, we perform two sets of experiments with a well known benchmarking dataset. First, we assess the quality of the raw velocity estimates in comparison to classical pose estimation algorithms. Second, we added to our method’s instantaneous velocity estimates a Kalman Filter and compare its performance with a well known open source stereo Visual Odometry library. The presented results compare favorably with state-of-the-art approaches, mainly in the estimation of the angular velocities, where significant improvements are achieved.