Pre-processing for approximate Bayesian computation in image analysis

Most of the existing algorithms for approximate Bayesian computation (ABC) assume that it is feasible to simulate pseudo-data from the model at each iteration. However, the computational cost of these simulations can be prohibitive for high dimensional data. An important example is the Potts model, which is commonly used in image analysis. Images encountered in real world applications can have millions of pixels, therefore scalability is a major concern. We apply ABC with a synthetic likelihood to the hidden Potts model with additive Gaussian noise. Using a pre-processing step, we fit a binding function to model the relationship between the model parameters and the synthetic likelihood parameters. Our numerical experiments demonstrate that the precomputed binding function dramatically improves the scalability of ABC, reducing the average runtime required for model fitting from 71 hours to only 7 minutes. We also illustrate the method by estimating the smoothing parameter for remotely sensed satellite imagery. Without precomputation, Bayesian inference is impractical for datasets of that scale.

Scalable Bayesian Computation for intractable likelihoods in image analysis

The inverse temperature hyperparameter of the hidden Potts model governs the strength of spatial cohesion and therefore has a substantial influence over the resulting model fit. The difficulty arises from the dependence of an intractable normalising constant on the value of the inverse temperature, thus there is no closed form solution for sampling from the distribution directly. We review three computational approaches for addressing this issue, namely pseudolikelihood, path sampling, and the approximate exchange algorithm. We compare the accuracy and scalability of these methods using a simulation study.

Structure matters: Adoption of structured classification Approach in the context of cognitive presence classification

Within online learning communities, receiving timely and meaningful insights into the quality of learning activities is an important part of an effective educational experience. Commonly adopted methods – such as the Community of Inquiry framework – rely on manual coding of online discussion transcripts, which is a costly and time consuming process. There are several efforts underway to enable the automated classification of online discussion messages using supervised machine learning, which would enable the real-time analysis of interactions occurring within online learning communities. This paper investigates the importance of incorporating features that utilise the structure of on-line discussions for the classification of "cognitive presence" – the central dimension of the Community of Inquiry framework focusing on the quality of students' critical thinking within online learning communities. We implemented a Conditional Random Field classification solution, which incorporates structural features that may be useful in increasing classification performance over other implementations. Our approach leads to an improvement in classification accuracy of 5.8% over current existing techniques when tested on the same dataset, with a precision and recall of 0.630 and 0.504 respectively.

On Visual Detection of Highly-occluded Objects for Harvesting Automation in Horticulture

Developing accurate and reliable crop detection algorithms is an important step for harvesting automation in horticulture. This paper presents a novel approach to visual detection of highly-occluded fruits. We use a conditional random field (CRF) on multi-spectral image data (colour and Near-Infrared Reflectance, NIR) to model two classes: crop and background. To describe these two classes, we explore a range of visual-texture features including local binary pattern, histogram of oriented gradients, and learn auto-encoder features. The pro-posed methods are evaluated using hand-labelled images from a dataset captured on a commercial capsicum farm. Experimental results are presented, and performance is evaluated in terms of the Area Under the Curve (AUC) of the precision-recall curves.Our current results achieve a maximum performance of 0.81AUC when combining all of the texture features in conjunction with colour information.

Constraining uncertainty in regional hydrologic impacts of climate change: Nonstationarity in downscaling

Regional impacts of climate change remain subject to large uncertainties accumulating from various sources, including those due to choice of general circulation models (GCMs), scenarios, and downscaling methods. Objective constraints to reduce the uncertainty in regional predictions have proven elusive. In most studies to date the nature of the downscaling relationship (DSR) used for such regional predictions has been assumed to remain unchanged in a future climate. However,studies have shown that climate change may manifest in terms of changes in frequencies of occurrence of the leading modes of variability, and hence, stationarity of DSRs is not really a valid assumption in regional climate impact assessment. This work presents an uncertainty modeling framework where, in addition to GCM and scenario uncertainty, uncertainty in the nature of the DSR is explored by linking downscaling with changes in frequencies of such modes of natural variability. Future projections of the regional hydrologic variable obtained by training a conditional random field (CRF) model on each natural cluster are combined using the weighted Dempster-Shafer (D-S) theory of evidence combination. Each projection is weighted with the future projected frequency of occurrence of that cluster (''cluster linking'') and scaled by the GCM performance with respect to the associated cluster for the present period (''frequency scaling''). The D-S theory was chosen for its ability to express beliefs in some hypotheses, describe uncertainty and ignorance in the system, and give a quantitative measurement of belief and plausibility in results. The methodology is tested for predicting monsoon streamflow of the Mahanadi River at Hirakud Reservoir in Orissa, India. The results show an increasing probability of extreme, severe, and moderate droughts due to limate change. Significantly improved agreement between GCM predictions owing to cluster linking and frequency scaling is seen, suggesting that by linking regional impacts to natural regime frequencies, uncertainty in regional predictions can be realistically quantified. Additionally, by using a measure of GCM performance in simulating natural regimes, this uncertainty can be effectively constrained.

Hydrologic drought prediction under climate change: Uncertainty modeling with Dempster-Shafer and Bayesian approaches

Representation and quantification of uncertainty in climate change impact studies are a difficult task. Several sources of uncertainty arise in studies of hydrologic impacts of climate change, such as those due to choice of general circulation models (GCMs), scenarios and downscaling methods. Recently, much work has focused on uncertainty quantification and modeling in regional climate change impacts. In this paper, an uncertainty modeling framework is evaluated, which uses a generalized uncertainty measure to combine GCM, scenario and downscaling uncertainties. The Dempster-Shafer (D-S) evidence theory is used for representing and combining uncertainty from various sources. A significant advantage of the D-S framework over the traditional probabilistic approach is that it allows for the allocation of a probability mass to sets or intervals, and can hence handle both aleatory or stochastic uncertainty, and epistemic or subjective uncertainty. This paper shows how the D-S theory can be used to represent beliefs in some hypotheses such as hydrologic drought or wet conditions, describe uncertainty and ignorance in the system, and give a quantitative measurement of belief and plausibility in results. The D-S approach has been used in this work for information synthesis using various evidence combination rules having different conflict modeling approaches. A case study is presented for hydrologic drought prediction using downscaled streamflow in the Mahanadi River at Hirakud in Orissa, India. Projections of n most likely monsoon streamflow sequences are obtained from a conditional random field (CRF) downscaling model, using an ensemble of three GCMs for three scenarios, which are converted to monsoon standardized streamflow index (SSFI-4) series. This range is used to specify the basic probability assignment (bpa) for a Dempster-Shafer structure, which represents uncertainty associated with each of the SSFI-4 classifications. These uncertainties are then combined across GCMs and scenarios using various evidence combination rules given by the D-S theory. A Bayesian approach is also presented for this case study, which models the uncertainty in projected frequencies of SSFI-4 classifications by deriving a posterior distribution for the frequency of each classification, using an ensemble of GCMs and scenarios. Results from the D-S and Bayesian approaches are compared, and relative merits of each approach are discussed. Both approaches show an increasing probability of extreme, severe and moderate droughts and decreasing probability of normal and wet conditions in Orissa as a result of climate change. (C) 2010 Elsevier Ltd. All rights reserved.

A comparison of three methods for downscaling daily precipitation in the Punjab region

Many downscaling techniques have been developed in the past few years for projection of station-scale hydrological variables from large-scale atmospheric variables simulated by general circulation models (GCMs) to assess the hydrological impacts of climate change. This article compares the performances of three downscaling methods, viz. conditional random field (CRF), K-nearest neighbour (KNN) and support vector machine (SVM) methods in downscaling precipitation in the Punjab region of India, belonging to the monsoon regime. The CRF model is a recently developed method for downscaling hydrological variables in a probabilistic framework, while the SVM model is a popular machine learning tool useful in terms of its ability to generalize and capture nonlinear relationships between predictors and predictand. The KNN model is an analogue-type method that queries days similar to a given feature vector from the training data and classifies future days by random sampling from a weighted set of K closest training examples. The models are applied for downscaling monsoon (June to September) daily precipitation at six locations in Punjab. Model performances with respect to reproduction of various statistics such as dry and wet spell length distributions, daily rainfall distribution, and intersite correlations are examined. It is found that the CRF and KNN models perform slightly better than the SVM model in reproducing most daily rainfall statistics. These models are then used to project future precipitation at the six locations. Output from the Canadian global climate model (CGCM3) GCM for three scenarios, viz. A1B, A2, and B1 is used for projection of future precipitation. The projections show a change in probability density functions of daily rainfall amount and changes in the wet and dry spell distributions of daily precipitation. Copyright (C) 2011 John Wiley & Sons, Ltd.

CROWD FLOW SEGMENTATION IN COMPRESSED DOMAIN USING CRF

Crowd flow segmentation is an important step in many video surveillance tasks. In this work, we propose an algorithm for segmenting flows in H.264 compressed videos in a completely unsupervised manner. Our algorithm works on motion vectors which can be obtained by partially decoding the compressed video without extracting any additional features. Our approach is based on modelling the motion vector field as a Conditional Random Field (CRF) and obtaining oriented motion segments by finding the optimal labelling which minimises the global energy of CRF. These oriented motion segments are recursively merged based on gradient across their boundaries to obtain the final flow segments. This work in compressed domain can be easily extended to pixel domain by substituting motion vectors with motion based features like optical flow. The proposed algorithm is experimentally evaluated on a standard crowd flow dataset and its superior performance in both accuracy and computational time are demonstrated through quantitative results.

Combining information sources for confidence estimation with CRF models

Obtaining accurate confidence measures for automatic speech recognition (ASR) transcriptions is an important task which stands to benefit from the use of multiple information sources. This paper investigates the application of conditional random field (CRF) models as a principled technique for combining multiple features from such sources. A novel method for combining suitably defined features is presented, allowing for confidence annotation using lattice-based features of hypotheses other than the lattice 1-best. The resulting framework is applied to different stages of a state-of-the-art large vocabulary speech recognition pipeline, and consistent improvements are shown over a sophisticated baseline system. Copyright © 2011 ISCA.

A confidence-based approach for improving keyword hypothesis scores

The task in keyword spotting (KWS) is to hypothesise times at which any of a set of key terms occurs in audio. An important aspect of such systems are the scores assigned to these hypotheses, the accuracy of which have a significant impact on performance. Estimating these scores may be formulated as a confidence estimation problem, where a measure of confidence is assigned to each key term hypothesis. In this work, a set of discriminative features is defined, and combined using a conditional random field (CRF) model for improved confidence estimation. An extension to this model to directly address the problem of score normalisation across key terms is also introduced. The implicit score normalisation which results from applying this approach to separate systems in a hybrid configuration yields further benefits. Results are presented which show notable improvements in KWS performance using the techniques presented in this work. © 2013 IEEE.

Design And Development Of A Named Entity Based Question Answering System For Malayalam Language

This is a Named Entity Based Question Answering System for Malayalam Language. Although a vast amount of information is available today in digital form, no effective information access mechanism exists to provide humans with convenient information access. Information Retrieval and Question Answering systems are the two mechanisms available now for information access. Information systems typically return a long list of documents in response to a user’s query which are to be skimmed by the user to determine whether they contain an answer. But a Question Answering System allows the user to state his/her information need as a natural language question and receives most appropriate answer in a word or a sentence or a paragraph. This system is based on Named Entity Tagging and Question Classification. Document tagging extracts useful information from the documents which will be used in finding the answer to the question. Question Classification extracts useful information from the question to determine the type of the question and the way in which the question is to be answered. Various Machine Learning methods are used to tag the documents. Rule-Based Approach is used for Question Classification. Malayalam belongs to the Dravidian family of languages and is one of the four major languages of this family. It is one of the 22 Scheduled Languages of India with official language status in the state of Kerala. It is spoken by 40 million people. Malayalam is a morphologically rich agglutinative language and relatively of free word order. Also Malayalam has a productive morphology that allows the creation of complex words which are often highly ambiguous. Document tagging tools such as Parts-of-Speech Tagger, Phrase Chunker, Named Entity Tagger, and Compound Word Splitter are developed as a part of this research work. No such tools were available for Malayalam language. Finite State Transducer, High Order Conditional Random Field, Artificial Immunity System Principles, and Support Vector Machines are the techniques used for the design of these document preprocessing tools. This research work describes how the Named Entity is used to represent the documents. Single sentence questions are used to test the system. Overall Precision and Recall obtained are 88.5% and 85.9% respectively. This work can be extended in several directions. The coverage of non-factoid questions can be increased and also it can be extended to include open domain applications. Reference Resolution and Word Sense Disambiguation techniques are suggested as the future enhancements

Improved cerebellar tissue classification on magnetic resonance images of brain.

PURPOSE: To develop and implement a method for improved cerebellar tissue classification on the MRI of brain by automatically isolating the cerebellum prior to segmentation. MATERIALS AND METHODS: Dual fast spin echo (FSE) and fluid attenuation inversion recovery (FLAIR) images were acquired on 18 normal volunteers on a 3 T Philips scanner. The cerebellum was isolated from the rest of the brain using a symmetric inverse consistent nonlinear registration of individual brain with the parcellated template. The cerebellum was then separated by masking the anatomical image with individual FLAIR images. Tissues in both the cerebellum and rest of the brain were separately classified using hidden Markov random field (HMRF), a parametric method, and then combined to obtain tissue classification of the whole brain. The proposed method for tissue classification on real MR brain images was evaluated subjectively by two experts. The segmentation results on Brainweb images with varying noise and intensity nonuniformity levels were quantitatively compared with the ground truth by computing the Dice similarity indices. RESULTS: The proposed method significantly improved the cerebellar tissue classification on all normal volunteers included in this study without compromising the classification in remaining part of the brain. The average similarity indices for gray matter (GM) and white matter (WM) in the cerebellum are 89.81 (+/-2.34) and 93.04 (+/-2.41), demonstrating excellent performance of the proposed methodology. CONCLUSION: The proposed method significantly improved tissue classification in the cerebellum. The GM was overestimated when segmentation was performed on the whole brain as a single object.

Interactive Segmentation of MR Images from Brain Tumor Patients

Medical doctors often do not trust the result of fully automatic segmentations because they have no possibility to make corrections if necessary. On the other hand, manual corrections can introduce a user bias. In this work, we propose to integrate the possibility for quick manual corrections into a fully automatic segmentation method for brain tumor images. This allows for necessary corrections while maintaining a high objectiveness. The underlying idea is similar to the well-known Grab-Cut algorithm, but here we combine decision forest classification with conditional random field regularization for interactive segmentation of 3D medical images. The approach has been evaluated by two different users on the BraTS2012 dataset. Accuracy and robustness improved compared to a fully automatic method and our interactive approach was ranked among the top performing methods. Time for computation including manual interaction was less than 10 minutes per patient, which makes it attractive for clinical use.

Temporally Coherent Disparity Maps Using CRFs with Fast 4D Filtering

State of the art methods for disparity estimation achieve good results for single stereo frames, but temporal coherence in stereo videos is often neglected. In this paper we present a method to compute temporally coherent disparity maps. We define an energy over whole stereo sequences and optimize their Conditional Random Field (CRF) distributions using mean-field approximation. We introduce novel terms for smoothness and consistency between the left and right views, and perform CRF optimization by fast, iterative spatio-temporal filtering with linear complexity in the total number of pixels. Our results rank among the state of the art while having significantly less flickering artifacts in stereo sequences.

MBIS: Multivariate Bayesian Image Segmentation Tool

We present MBIS (Multivariate Bayesian Image Segmentation tool), a clustering tool based on the mixture of multivariate normal distributions model. MBIS supports multi-channel bias field correction based on a B-spline model. A second methodological novelty is the inclusion of graph-cuts optimization for the stationary anisotropic hidden Markov random field model. Along with MBIS, we release an evaluation framework that contains three different experiments on multi-site data. We first validate the accuracy of segmentation and the estimated bias field for each channel. MBIS outperforms a widely used segmentation tool in a cross-comparison evaluation. The second experiment demonstrates the robustness of results on atlas-free segmentation of two image sets from scan-rescan protocols on 21 healthy subjects. Multivariate segmentation is more replicable than the monospectral counterpart on T1-weighted images. Finally, we provide a third experiment to illustrate how MBIS can be used in a large-scale study of tissue volume change with increasing age in 584 healthy subjects. This last result is meaningful as multivariate segmentation performs robustly without the need for prior knowledge.