How accurate are the marker orders in crop linkage maps generated from large marker datasets?

Marker ordering during linkage map construction is a critical component of QTL mapping research. In recent years, high-throughput genotyping methods have become widely used, and these methods may generate hundreds of markers for a single mapping population. This poses problems for linkage analysis software because the number of possible marker orders increases exponentially as the number of markers increases. In this paper, we tested the accuracy of linkage analyses on simulated recombinant inbred line data using the commonly used Map Manager QTX (Manly et al. 2001: Mammalian Genome 12, 930-932) software and RECORD (Van Os et al. 2005: Theoretical and Applied Genetics 112, 30-40). Accuracy was measured by calculating two scores: % correct marker positions, and a novel, weighted rank-based score derived from the sum of absolute values of true minus observed marker ranks divided by the total number of markers. The accuracy of maps generated using Map Manager QTX was considerably lower than those generated using RECORD. Differences in linkage maps were often observed when marker ordering was performed several times using the identical dataset. In order to test the effect of reducing marker numbers on the stability of marker order, we pruned marker datasets focusing on regions consisting of tightly linked clusters of markers, which included redundant markers. Marker pruning improved the accuracy and stability of linkage maps because a single unambiguous marker order was produced that was consistent across replications of analysis. Marker pruning was also applied to a real barley mapping population and QTL analysis was performed using different map versions produced by the different programs. While some QTLs were identified with both map versions, there were large differences in QTL mapping results. Differences included maximum LOD and R-2 values at QTL peaks and map positions, thus highlighting the importance of marker order for QTL mapping

Automated retinal image quality assessment on the UK Biobank dataset for epidemiological studies

Morphological changes in the retinal vascular network are associated with future risk of many systemic and vascular diseases. However, uncertainty over the presence and nature of some of these associations exists. Analysis of data from large population based studies will help to resolve these uncertainties. The QUARTZ (QUantitative Analysis of Retinal vessel Topology and siZe) retinal image analysis system allows automated processing of large numbers of retinal images. However, an image quality assessment module is needed to achieve full automation. In this paper, we propose such an algorithm, which uses the segmented vessel map to determine the suitability of retinal images for use in the creation of vessel morphometric data suitable for epidemiological studies. This includes an effective 3-dimensional feature set and support vector machine classification. A random subset of 800 retinal images from UK Biobank (a large prospective study of 500,000 middle aged adults; where 68,151 underwent retinal imaging) was used to examine the performance of the image quality algorithm. The algorithm achieved a sensitivity of 95.33% and a specificity of 91.13% for the detection of inadequate images. The strong performance of this image quality algorithm will make rapid automated analysis of vascular morphometry feasible on the entire UK Biobank dataset (and other large retinal datasets), with minimal operator involvement, and at low cost.

Summarizing level-two topological relations in large spatial datasets

Summarizing topological relations is fundamental to many spatial applications including spatial query optimization. In this article, we present several novel techniques to effectively construct cell density based spatial histograms for range (window) summarizations restricted to the four most important level-two topological relations: contains, contained, overlap, and disjoint. We first present a novel framework to construct a multiscale Euler histogram in 2D space with the guarantee of the exact summarization results for aligned windows in constant time. To minimize the storage space in such a multiscale Euler histogram, an approximate algorithm with the approximate ratio 19/12 is presented, while the problem is shown NP-hard generally. To conform to a limited storage space where a multiscale histogram may be allowed to have only k Euler histograms, an effective algorithm is presented to construct multiscale histograms to achieve high accuracy in approximately summarizing aligned windows. Then, we present a new approximate algorithm to query an Euler histogram that cannot guarantee the exact answers; it runs in constant time. We also investigate the problem of nonaligned windows and the problem of effectively partitioning the data space to support nonaligned window queries. Finally, we extend our techniques to 3D space. Our extensive experiments against both synthetic and real world datasets demonstrate that the approximate multiscale histogram techniques may improve the accuracy of the existing techniques by several orders of magnitude while retaining the cost efficiency, and the exact multiscale histogram technique requires only a storage space linearly proportional to the number of cells for many popular real datasets.

Multiscale histograms: Summarizing topological relations in large spatial datasets

Summarizing topological relations is fundamental to many spatial applications including spatial query optimization. In this paper, we present several novel techniques to eectively construct cell density based spatial histograms for range (window) summarizations restricted to the four most important topological relations: contains, contained, overlap, and disjoint. We rst present a novel framework to construct a multiscale histogram composed of multiple Euler histograms with the guarantee of the exact summarization results for aligned windows in constant time. Then we present an approximate algorithm, with the approximate ratio 19/12, to minimize the storage spaces of such multiscale Euler histograms, although the problem is generally NP-hard. To conform to a limited storage space where only k Euler histograms are allowed, an effective algorithm is presented to construct multiscale histograms to achieve high accuracy. Finally, we present a new approximate algorithm to query an Euler histogram that cannot guarantee the exact answers; it runs in constant time. Our extensive experiments against both synthetic and real world datasets demonstrated that the approximate mul- tiscale histogram techniques may improve the accuracy of the existing techniques by several orders of magnitude while retaining the cost effciency, and the exact multiscale histogram technique requires only a storage space linearly proportional to the number of cells for the real datasets.

A combined neural network and DEA for measuring efficiency of large scale datasets

Data Envelopment Analysis (DEA) is one of the most widely used methods in the measurement of the efficiency and productivity of Decision Making Units (DMUs). DEA for a large dataset with many inputs/outputs would require huge computer resources in terms of memory and CPU time. This paper proposes a neural network back-propagation Data Envelopment Analysis to address this problem for the very large scale datasets now emerging in practice. Neural network requirements for computer memory and CPU time are far less than that needed by conventional DEA methods and can therefore be a useful tool in measuring the efficiency of large datasets. Finally, the back-propagation DEA algorithm is applied to five large datasets and compared with the results obtained by conventional DEA.

Understanding Uncertainties in Non-Linear Population Trajectories: A Bayesian Semi-Parametric Hierarchical Approach to Large-Scale Surveys of Coral Cover

Recently, attempts to improve decision making in species management have focussed on uncertainties associated with modelling temporal fluctuations in populations. Reducing model uncertainty is challenging; while larger samples improve estimation of species trajectories and reduce statistical errors, they typically amplify variability in observed trajectories. In particular, traditional modelling approaches aimed at estimating population trajectories usually do not account well for nonlinearities and uncertainties associated with multi-scale observations characteristic of large spatio-temporal surveys. We present a Bayesian semi-parametric hierarchical model for simultaneously quantifying uncertainties associated with model structure and parameters, and scale-specific variability over time. We estimate uncertainty across a four-tiered spatial hierarchy of coral cover from the Great Barrier Reef. Coral variability is well described; however, our results show that, in the absence of additional model specifications, conclusions regarding coral trajectories become highly uncertain when considering multiple reefs, suggesting that management should focus more at the scale of individual reefs. The approach presented facilitates the description and estimation of population trajectories and associated uncertainties when variability cannot be attributed to specific causes and origins. We argue that our model can unlock value contained in large-scale datasets, provide guidance for understanding sources of uncertainty, and support better informed decision making

R1SVM: A randomised nonlinear approach to large-scale anomaly detection

The problem of unsupervised anomaly detection arises in a wide variety of practical applications. While one-class support vector machines have demonstrated their effectiveness as an anomaly detection technique, their ability to model large datasets is limited due to their memory and time complexity for training. To address this issue for supervised learning of kernel machines, there has been growing interest in random projection methods as an alternative to the computationally expensive problems of kernel matrix construction and sup-port vector optimisation. In this paper we leverage the theory of nonlinear random projections and propose the Randomised One-class SVM (R1SVM), which is an efficient and scalable anomaly detection technique that can be trained on large-scale datasets. Our empirical analysis on several real-life and synthetic datasets shows that our randomised 1SVM algorithm achieves comparable or better accuracy to deep auto encoder and traditional kernelised approaches for anomaly detection, while being approximately 100 times faster in training and testing.

Robust formulations for clustering-based large-scale classification

Chebyshev-inequality-based convex relaxations of Chance-Constrained Programs (CCPs) are shown to be useful for learning classifiers on massive datasets. In particular, an algorithm that integrates efficient clustering procedures and CCP approaches for computing classifiers on large datasets is proposed. The key idea is to identify high density regions or clusters from individual class conditional densities and then use a CCP formulation to learn a classifier on the clusters. The CCP formulation ensures that most of the data points in a cluster are correctly classified by employing a Chebyshev-inequality-based convex relaxation. This relaxation is heavily dependent on the second-order statistics. However, this formulation and in general such relaxations that depend on the second-order moments are susceptible to moment estimation errors. One of the contributions of the paper is to propose several formulations that are robust to such errors. In particular a generic way of making such formulations robust to moment estimation errors is illustrated using two novel confidence sets. An important contribution is to show that when either of the confidence sets is employed, for the special case of a spherical normal distribution of clusters, the robust variant of the formulation can be posed as a second-order cone program. Empirical results show that the robust formulations achieve accuracies comparable to that with true moments, even when moment estimates are erroneous. Results also illustrate the benefits of employing the proposed methodology for robust classification of large-scale datasets.

Validation of ICDPIC software injury severity scores using a large regional trauma registry.

BACKGROUND: Administrative or quality improvement registries may or may not contain the elements needed for investigations by trauma researchers. International Classification of Diseases Program for Injury Categorisation (ICDPIC), a statistical program available through Stata, is a powerful tool that can extract injury severity scores from ICD-9-CM codes. We conducted a validation study for use of the ICDPIC in trauma research. METHODS: We conducted a retrospective cohort validation study of 40,418 patients with injury using a large regional trauma registry. ICDPIC-generated AIS scores for each body region were compared with trauma registry AIS scores (gold standard) in adult and paediatric populations. A separate analysis was conducted among patients with traumatic brain injury (TBI) comparing the ICDPIC tool with ICD-9-CM embedded severity codes. Performance in characterising overall injury severity, by the ISS, was also assessed. RESULTS: The ICDPIC tool generated substantial correlations in thoracic and abdominal trauma (weighted κ 0.87-0.92), and in head and neck trauma (weighted κ 0.76-0.83). The ICDPIC tool captured TBI severity better than ICD-9-CM code embedded severity and offered the advantage of generating a severity value for every patient (rather than having missing data). Its ability to produce an accurate severity score was consistent within each body region as well as overall. CONCLUSIONS: The ICDPIC tool performs well in classifying injury severity and is superior to ICD-9-CM embedded severity for TBI. Use of ICDPIC demonstrates substantial efficiency and may be a preferred tool in determining injury severity for large trauma datasets, provided researchers understand its limitations and take caution when examining smaller trauma datasets.

Accelerating Large Scale Centroid-based Clustering with Locality Sensitive Hashing

Most traditional data mining algorithms struggle to cope with the sheer scale of data efficiently. In this paper, we propose a general framework to accelerate existing clustering algorithms to cluster large-scale datasets which contain large numbers of attributes, items, and clusters. Our framework makes use of locality sensitive hashing (LSH) to significantly reduce the cluster search space. We also theoretically prove that our framework has a guaranteed error bound in terms of the clustering quality. This framework can be applied to a set of centroid-based clustering algorithms that assign an object to the most similar cluster, and we adopt the popular K-Modes categorical clustering algorithm to present how the framework can be applied. We validated our framework with five synthetic datasets and a real world Yahoo! Answers dataset. The experimental results demonstrate that our framework is able to speed up the existing clustering algorithm between factors of 2 and 6, while maintaining comparable cluster purity.

Towards effective indexing for very large video sequence database

With rapid advances in video processing technologies and ever fast increments in network bandwidth, the popularity of video content publishing and sharing has made similarity search an indispensable operation to retrieve videos of user interests. The video similarity is usually measured by the percentage of similar frames shared by two video sequences, and each frame is typically represented as a high-dimensional feature vector. Unfortunately, high complexity of video content has posed the following major challenges for fast retrieval: (a) effective and compact video representations, (b) efficient similarity measurements, and (c) efficient indexing on the compact representations. In this paper, we propose a number of methods to achieve fast similarity search for very large video database. First, each video sequence is summarized into a small number of clusters, each of which contains similar frames and is represented by a novel compact model called Video Triplet (ViTri). ViTri models a cluster as a tightly bounded hypersphere described by its position, radius, and density. The ViTri similarity is measured by the volume of intersection between two hyperspheres multiplying the minimal density, i.e., the estimated number of similar frames shared by two clusters. The total number of similar frames is then estimated to derive the overall similarity between two video sequences. Hence the time complexity of video similarity measure can be reduced greatly. To further reduce the number of similarity computations on ViTris, we introduce a new one dimensional transformation technique which rotates and shifts the original axis system using PCA in such a way that the original inter-distance between two high-dimensional vectors can be maximally retained after mapping. An efficient B+-tree is then built on the transformed one dimensional values of ViTris' positions. Such a transformation enables B+-tree to achieve its optimal performance by quickly filtering a large portion of non-similar ViTris. Our extensive experiments on real large video datasets prove the effectiveness of our proposals that outperform existing methods significantly.

Parallel geostatistics for sparse and dense datasets

Very large spatially-referenced datasets, for example, those derived from satellite-based sensors which sample across the globe or large monitoring networks of individual sensors, are becoming increasingly common and more widely available for use in environmental decision making. In large or dense sensor networks, huge quantities of data can be collected over small time periods. In many applications the generation of maps, or predictions at specific locations, from the data in (near) real-time is crucial. Geostatistical operations such as interpolation are vital in this map-generation process and in emergency situations, the resulting predictions need to be available almost instantly, so that decision makers can make informed decisions and define risk and evacuation zones. It is also helpful when analysing data in less time critical applications, for example when interacting directly with the data for exploratory analysis, that the algorithms are responsive within a reasonable time frame. Performing geostatistical analysis on such large spatial datasets can present a number of problems, particularly in the case where maximum likelihood. Although the storage requirements only scale linearly with the number of observations in the dataset, the computational complexity in terms of memory and speed, scale quadratically and cubically respectively. Most modern commodity hardware has at least 2 processor cores if not more. Other mechanisms for allowing parallel computation such as Grid based systems are also becoming increasingly commonly available. However, currently there seems to be little interest in exploiting this extra processing power within the context of geostatistics. In this paper we review the existing parallel approaches for geostatistics. By recognising that diffeerent natural parallelisms exist and can be exploited depending on whether the dataset is sparsely or densely sampled with respect to the range of variation, we introduce two contrasting novel implementations of parallel algorithms based on approximating the data likelihood extending the methods of Vecchia [1988] and Tresp [2000]. Using parallel maximum likelihood variogram estimation and parallel prediction algorithms we show that computational time can be significantly reduced. We demonstrate this with both sparsely sampled data and densely sampled data on a variety of architectures ranging from the common dual core processor, found in many modern desktop computers, to large multi-node super computers. To highlight the strengths and weaknesses of the diffeerent methods we employ synthetic data sets and go on to show how the methods allow maximum likelihood based inference on the exhaustive Walker Lake data set.

An improved memory management scheme for large scale graph computing engine GraphChi

GraphChi is the first reported disk-based graph engine that can handle billion-scale graphs on a single PC efficiently. GraphChi is able to execute several advanced data mining, graph mining and machine learning algorithms on very large graphs. With the novel technique of parallel sliding windows (PSW) to load subgraph from disk to memory for vertices and edges updating, it can achieve data processing performance close to and even better than those of mainstream distributed graph engines. GraphChi mentioned that its memory is not effectively utilized with large dataset, which leads to suboptimal computation performances. In this paper we are motivated by the concepts of 'pin ' from TurboGraph and 'ghost' from GraphLab to propose a new memory utilization mode for GraphChi, which is called Part-in-memory mode, to improve the GraphChi algorithm performance. The main idea is to pin a fixed part of data inside the memory during the whole computing process. Part-in-memory mode is successfully implemented with only about 40 additional lines of code to the original GraphChi engine. Extensive experiments are performed with large real datasets (including Twitter graph with 1.4 billion edges). The preliminary results show that Part-in-memory mode memory management approach effectively reduces the GraphChi running time by up to 60% in PageRank algorithm. Interestingly it is found that a larger portion of data pinned in memory does not always lead to better performance in the case that the whole dataset cannot be fitted in memory. There exists an optimal portion of data which should be kept in the memory to achieve the best computational performance.

Scaling geospatial searches in large spatial databases

Modern geographical databases, which are at the core of geographic information systems (GIS), store a rich set of aspatial attributes in addition to geographic data. Typically, aspatial information comes in textual and numeric format. Retrieving information constrained on spatial and aspatial data from geodatabases provides GIS users the ability to perform more interesting spatial analyses, and for applications to support composite location-aware searches; for example, in a real estate database: “Find the nearest homes for sale to my current location that have backyard and whose prices are between $50,000 and $80,000”. Efficient processing of such queries require combined indexing strategies of multiple types of data. Existing spatial query engines commonly apply a two-filter approach (spatial filter followed by nonspatial filter, or viceversa), which can incur large performance overheads. On the other hand, more recently, the amount of geolocation data has grown rapidly in databases due in part to advances in geolocation technologies (e.g., GPS-enabled smartphones) that allow users to associate location data to objects or events. The latter poses potential data ingestion challenges of large data volumes for practical GIS databases. In this dissertation, we first show how indexing spatial data with R-trees (a typical data pre-processing task) can be scaled in MapReduce—a widely-adopted parallel programming model for data intensive problems. The evaluation of our algorithms in a Hadoop cluster showed close to linear scalability in building R-tree indexes. Subsequently, we develop efficient algorithms for processing spatial queries with aspatial conditions. Novel techniques for simultaneously indexing spatial with textual and numeric data are developed to that end. Experimental evaluations with real-world, large spatial datasets measured query response times within the sub-second range for most cases, and up to a few seconds for a small number of cases, which is reasonable for interactive applications. Overall, the previous results show that the MapReduce parallel model is suitable for indexing tasks in spatial databases, and the adequate combination of spatial and aspatial attribute indexes can attain acceptable response times for interactive spatial queries with constraints on aspatial data.

Datasets, features, learning, and models in visual recognition

Visual recognition is a fundamental research topic in computer vision. This dissertation explores datasets, features, learning, and models used for visual recognition. In order to train visual models and evaluate different recognition algorithms, this dissertation develops an approach to collect object image datasets on web pages using an analysis of text around the image and of image appearance. This method exploits established online knowledge resources (Wikipedia pages for text; Flickr and Caltech data sets for images). The resources provide rich text and object appearance information. This dissertation describes results on two datasets. The first is Berg’s collection of 10 animal categories; on this dataset, we significantly outperform previous approaches. On an additional set of 5 categories, experimental results show the effectiveness of the method. Images are represented as features for visual recognition. This dissertation introduces a text-based image feature and demonstrates that it consistently improves performance on hard object classification problems. The feature is built using an auxiliary dataset of images annotated with tags, downloaded from the Internet. Image tags are noisy. The method obtains the text features of an unannotated image from the tags of its k-nearest neighbors in this auxiliary collection. A visual classifier presented with an object viewed under novel circumstances (say, a new viewing direction) must rely on its visual examples. This text feature may not change, because the auxiliary dataset likely contains a similar picture. While the tags associated with images are noisy, they are more stable when appearance changes. The performance of this feature is tested using PASCAL VOC 2006 and 2007 datasets. This feature performs well; it consistently improves the performance of visual object classifiers, and is particularly effective when the training dataset is small. With more and more collected training data, computational cost becomes a bottleneck, especially when training sophisticated classifiers such as kernelized SVM. This dissertation proposes a fast training algorithm called Stochastic Intersection Kernel Machine (SIKMA). This proposed training method will be useful for many vision problems, as it can produce a kernel classifier that is more accurate than a linear classifier, and can be trained on tens of thousands of examples in two minutes. It processes training examples one by one in a sequence, so memory cost is no longer the bottleneck to process large scale datasets. This dissertation applies this approach to train classifiers of Flickr groups with many group training examples. The resulting Flickr group prediction scores can be used to measure image similarity between two images. Experimental results on the Corel dataset and a PASCAL VOC dataset show the learned Flickr features perform better on image matching, retrieval, and classification than conventional visual features. Visual models are usually trained to best separate positive and negative training examples. However, when recognizing a large number of object categories, there may not be enough training examples for most objects, due to the intrinsic long-tailed distribution of objects in the real world. This dissertation proposes an approach to use comparative object similarity. The key insight is that, given a set of object categories which are similar and a set of categories which are dissimilar, a good object model should respond more strongly to examples from similar categories than to examples from dissimilar categories. This dissertation develops a regularized kernel machine algorithm to use this category dependent similarity regularization. Experiments on hundreds of categories show that our method can make significant improvement for categories with few or even no positive examples.