Semisupervised Deep Learning for the Detection of Foreign Materials on Poultry Meat with Near-Infrared Hyperspectral Imaging.

A novel semisupervised hyperspectral imaging technique was developed to detect foreign materials (FMs) on raw poultry meat. Combining hyperspectral imaging and deep learning has shown promise in identifying food safety and quality attributes. However, the challenge lies in acquiring a large amount of accurately annotated/labeled data for model training. This paper proposes a novel semisupervised hyperspectral deep learning model based on a generative adversarial network, utilizing an improved 1D U-Net as its discriminator, to detect FMs on raw chicken breast fillets. The model was trained by using approximately 879,000 spectral responses from hyperspectral images of clean chicken breast fillets in the near-infrared wavelength range of 1000-1700 nm. Testing involved 30 different types of FMs commonly found in processing plants, prepared in two nominal sizes: 2 × 2 mm2 and 5 × 5 mm2. The FM-detection technique achieved impressive results at both the spectral pixel level and the foreign material object level. At the spectral pixel level, the model achieved a precision of 100%, a recall of over 93%, an F1 score of 96.8%, and a balanced accuracy of 96.9%. When combining the rich 1D spectral data with 2D spatial information, the FM-detection accuracy at the object level reached 96.5%. In summary, the impressive results obtained through this study demonstrate its effectiveness at accurately identifying and localizing FMs. Furthermore, the technique's potential for generalization and application to other agriculture and food-related domains highlights its broader significance.

RTExtract: time-series NMR spectra quantification based on 3D surface ridge tracking.

MOTIVATION: Time-series nuclear magnetic resonance (NMR) has advanced our knowledge about metabolic dynamics. Before analyzing compounds through modeling or statistical methods, chemical features need to be tracked and quantified. However, because of peak overlap and peak shifting, the available protocols are time consuming at best or even impossible for some regions in NMR spectra. RESULTS: We introduce Ridge Tracking-based Extract (RTExtract), a computer vision-based algorithm, to quantify time-series NMR spectra. The NMR spectra of multiple time points were formulated as a 3D surface. Candidate points were first filtered using local curvature and optima, then connected into ridges by a greedy algorithm. Interactive steps were implemented to refine results. Among 173 simulated ridges, 115 can be tracked (RMSD < 0.001). For reproducing previous results, RTExtract took less than 2 h instead of ∼48 h, and two instead of seven parameters need tuning. Multiple regions with overlapping and changing chemical shifts are accurately tracked. AVAILABILITY AND IMPLEMENTATION: Source code is freely available within Metabolomics toolbox GitHub repository (https://github.com/artedison/Edison_Lab_Shared_Metabolomics_UGA/tree/master/metabolomics_toolbox/code/ridge_tracking) and is implemented in MATLAB and R. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks.

Coral reefs are biologically diverse and structurally complex ecosystems, which have been severally affected by human actions. Consequently, there is a need for rapid ecological assessment of coral reefs, but current approaches require time consuming manual analysis, either during a dive survey or on images collected during a survey. Reef structural complexity is essential for ecological function but is challenging to measure and often relegated to simple metrics such as rugosity. Recent advances in computer vision and machine learning offer the potential to alleviate some of these limitations. We developed an approach to automatically classify 3D reconstructions of reef sections and assessed the accuracy of this approach. 3D reconstructions of reef sections were generated using commercial Structure-from-Motion software with images extracted from video surveys. To generate a 3D classified map, locations on the 3D reconstruction were mapped back into the original images to extract multiple views of the location. Several approaches were tested to merge information from multiple views of a point into a single classification, all of which used convolutional neural networks to classify or extract features from the images, but differ in the strategy employed for merging information. Approaches to merging information entailed voting, probability averaging, and a learned neural-network layer. All approaches performed similarly achieving overall classification accuracies of ~96% and >90% accuracy on most classes. With this high classification accuracy, these approaches are suitable for many ecological applications.

Morphological analysis of the left ventricular endocardial surface using a bag-of-features descriptor.

The limitations of conventional imaging techniques have hitherto precluded a thorough and formal investigation of the complex morphology of the left ventricular (LV) endocardial surface and its relation to the severity of coronary artery disease (CAD). However, recent developments in high-resolution multirow-detector computed tomography (MDCT) scanner technology have enabled the imaging of the complex LV endocardial surface morphology in a single heartbeat. Analysis of high-resolution computed tomography images from a 320-MDCT scanner allows for the noninvasive study of the relationship between the percent diameter stenosis (DS) values of the major coronary arteries and localization of the cardiac segments affected by coronary arterial stenosis. In this paper, a novel approach for the analysis of the nonrigid LV endocardial surface from MDCT images, using a combination of rigid body transformation-invariant shape descriptors and a more generalized isometry-invariant Bag-of-Features descriptor, is proposed and implemented. The proposed approach is shown to be successful in identifying, localizing, and quantifying the incidence and extent of CAD and, thus, is seen to have a potentially significant clinical impact. Specifically, the association between the incidence and extent of CAD, determined via the percent DS measurements of the major coronary arteries, and the alterations in the endocardial surface morphology is formally quantified. The results of the proposed approach on 16 normal datasets and 16 abnormal datasets exhibiting CAD with varying levels of severity are presented. A multivariable regression test is employed to test the effectiveness of the proposed morphological analysis approach. Experiments performed on a strictly leave-one-out basis are shown to exhibit a distinct and interesting pattern in terms of the correlation coefficient values within the cardiac segments, where the incidence of coronary arterial stenosis is localized.

Morphological analysis of the left ventricular endocardial surface and its clinical implications.

The complex morphological structure of the left ventricular endocardial surface and its relation to the severity of arterial stenosis has not yet been thoroughly investigated due to the limitations of conventional imaging techniques. By exploiting the recent developments in Multirow-Detector Computed Tomography (MDCT) scanner technology, the complex endocardial surface morphology of the left ventricle is studied and the cardiac segments affected by coronary arterial stenosis localized via analysis of Computed Tomography (CT) image data obtained from a 320-MDCT scanner. The non-rigid endocardial surface data is analyzed using an isometry-invariant Bag-of-Words (BOW) feature-based approach. The clinical significance of the analysis in identifying, localizing and quantifying the incidence and extent of coronary artery disease is investigated. Specifically, the association between the incidence and extent of coronary artery disease and the alterations in the endocardial surface morphology is studied. The results of the proposed approach on 15 normal data sets, and 12 abnormal data sets exhibiting coronary artery disease with varying levels of severity are presented. Based on the characterization of the endocardial surface morphology using the Bag-of-Words features, a neural network-based classifier is implemented to test the effectiveness of the proposed morphological analysis approach. Experiments performed on a strict leave-one-out basis are shown to exhibit a distinct pattern in terms of classification accuracy within the cardiac segments where the incidence of coronary arterial stenosis is localized.

Virtual multi-fracture craniofacial reconstruction using computer vision and graph matching.

The problem of computer vision-guided reconstruction of a fractured human mandible from a computed tomography (CT) image sequence exhibiting multiple broken fragments is addressed. The problem resembles 3D jigsaw puzzle assembly and hence is of general interest for a variety of applications dealing with automated reconstruction or assembly. The specific problem of automated multi-fracture craniofacial reconstruction is particularly challenging since the identification of opposable fracture surfaces followed by their pairwise registration needs to be performed expeditiously in order to minimize the operative trauma to the patient and also limit the operating costs. A polynomial time solution using graph matching is proposed. In the first phase of the proposed solution, the opposable fracture surfaces are identified using the Maximum Weight Graph Matching algorithm. The pairs of opposable fracture surfaces, identified in the first stage, are registered in the second phase using the Iterative Closest Point (ICP) algorithm. Correspondence for a given pair of fracture surfaces, needed for the Closest Set computation in the ICP algorithm, is established using the Maximum Cardinality Minimum Weight bipartite graph matching algorithm. The correctness of the reconstruction is constantly monitored by using constraints derived from a volumetric matching procedure guided by the computation of the Tanimoto Coefficient.

Computer vision guided virtual craniofacial reconstruction.

The problem of virtual craniofacial reconstruction from a sequence of computed tomography (CT) images is addressed and is modeled as a rigid surface registration problem. Two different classes of surface matching algorithms, namely the data aligned rigidity constrained exhaustive search (DARCES) algorithm and the iterative closest point (ICP) algorithm are first used in isolation. Since the human bone can be reasonably approximated as a rigid body, 3D rigid surface registration techniques such as the DARCES and ICP algorithms are deemed to be well suited for the purpose of aligning the fractured bone fragments. A synergistic combination of these two algorithms, termed as the hybrid DARCES-ICP algorithm, is proposed. The hybrid algorithm is shown to result in a more accurate mandibular reconstruction when compared to the individual algorithms used in isolation. The proposed scheme for virtual reconstructive surgery would prove to be of tremendous benefit to the operating surgeons as it would allow them to pre-visualize the reconstructed mandible (i.e., the end-product of their work), before performing the actual surgical procedure. Experimental results on both phantom and real (human) patient datasets are presented.

Human motion capture data compression by model-based indexing: a power aware approach.

Human Motion Capture (MoCap) data can be used for animation of virtual human-like characters in distributed virtual reality applications and networked games. MoCap data compressed using the standard MPEG-4 encoding pipeline comprising of predictive encoding (and/or DCT decorrelation), quantization, and arithmetic/Huffman encoding, entails significant power consumption for the purpose of decompression. In this paper, we propose a novel algorithm for compression of MoCap data, which is based on smart indexing of the MoCap data by exploiting structural information derived from the skeletal virtual human model. The indexing algorithm can be fine-controlled using three predefined quality control parameters (QCPs). We demonstrate how an efficient combination of the three QCPs results in a lower network bandwidth requirement and reduced power consumption for data decompression at the client end when compared to standard MPEG-4 compression. Since the proposed algorithm exploits structural information derived from the skeletal virtual human model, it is observed to result in virtual human animation of visually acceptable quality upon decompression.

A comparison of physical mapping algorithms based on the maximum likelihood model.

MOTIVATION: Physical mapping of chromosomes using the maximum likelihood (ML) model is a problem of high computational complexity entailing both discrete optimization to recover the optimal probe order as well as continuous optimization to recover the optimal inter-probe spacings. In this paper, two versions of the genetic algorithm (GA) are proposed, one with heuristic crossover and deterministic replacement and the other with heuristic crossover and stochastic replacement, for the physical mapping problem under the maximum likelihood model. The genetic algorithms are compared with two other discrete optimization approaches, namely simulated annealing (SA) and large-step Markov chains (LSMC), in terms of solution quality and runtime efficiency. RESULTS: The physical mapping algorithms based on the GA, SA and LSMC have been tested using synthetic datasets and real datasets derived from cosmid libraries of the fungus Neurospora crassa. The GA, especially the version with heuristic crossover and stochastic replacement, is shown to consistently outperform the SA-based and LSMC-based physical mapping algorithms in terms of runtime and final solution quality. Experimental results on real datasets and simulated datasets are presented. Further improvements to the GA in the context of physical mapping under the maximum likelihood model are proposed. AVAILABILITY: The software is available upon request from the first author.

Parallel Monte Carlo methods for physical mapping of chromosomes.

Reconstructing a physical map of a chromosome from a genomic library presents a central computational problem in genetics. Physical map reconstruction in the presence of errors is a problem of high computational complexity. Parallel Monte Carlo methods for a maximum likelihood estimation-based approach to physical map reconstruction are presented. The estimation procedure entails gradient descent search for determining the optimal spacings between probes for a given probe ordering. The optimal probe ordering is determined using a simulated Monte Carlo algorithm. A two-tier parallelization strategy is proposed wherein the gradient descent search is parallelized at the lower level and the simulated Monte Carlo algorithm is simultaneously parallelized at the higher level. Implementation and experimental results on a network of shared-memory symmetric multiprocessors (SMPs) are presented.