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Classifiability-based omnivariate decision trees.

Top-down induction of decision trees is a simple and powerful method of pattern classification. In a decision tree, each node partitions the available patterns into two or more sets. New nodes are created to handle each of the resulting partitions and the process continues. A node is considered terminal if it satisfies some stopping criteria (for example, purity, i.e., all patterns at the node are from a single class). Decision trees may be univariate, linear multivariate, or nonlinear multivariate depending on whether a single attribute, a linear function of all the attributes, or a nonlinear function of all the attributes is used for the partitioning at each node of the decision tree. Though nonlinear multivariate decision trees are the most powerful, they are more susceptible to the risks of overfitting. In this paper, we propose to perform model selection at each decision node to build omnivariate decision trees. The model selection is done using a novel classifiability measure that captures the possible sources of misclassification with relative ease and is able to accurately reflect the complexity of the subproblem at each node. The proposed approach is fast and does not suffer from as high a computational burden as that incurred by typical model selection algorithms. Empirical results over 26 data sets indicate that our approach is faster and achieves better classification accuracy compared to statistical model select algorithms.

Algorithms↗

Three-dimensional reconstruction of partially 3D-digitized peach tree canopies.

A simplified method for building three-dimensional (3D) mock-ups of peach trees is presented. The method combines partial digitizing of tree structure with reconstruction rules for non-digitized organs. Reconstruction was applied at two scales: leaves on current-year shoots (CYS) and shoots on 1-year-old shoots (OYOS). Reconstruction rules make use of allometric relationships, random sampling of shoot attribute distribution and additional hypotheses (e.g., constant internode length). The method was quantitatively assessed for two training systems (tight goblet and wide-double-Y), at a range of spatial scales. For this purpose, light interception properties of reference and reconstructed mock-ups were compared. Mock-up quality depended on scale. Foliage reconstruction on CYS was unsuitable for generating a given CYS. Similarly, CYS reconstruction on OYOS was unsuitable for generating a given OYOS. This is because generic rules derived at the population scale do not consider specific foliage or shoot attributes of a given CYS or OYOS. In contrast, foliage reconstruction on CYS was able to generate OYOS mock-ups having light properties similar to the reference mock-ups. The same held for CYS reconstruction on OYOS for light capture properties at the tree scale. The CYS reconstruction on OYOS was also suitable for deriving OYOS distribution as a function of light interception ability. Reconstruction rules were successfully used to build the vegetation neighborhood of a reference shoot. The proposed method could therefore be used to make 3D tree mock-ups usable for a range of some, but not all, light computations. Because the simplified method allows large time savings, it could be used in virtual experiments requiring large numbers of replicates, such as comparative studies of tree genotypes or training systems.

Image Processing, Computer-Assisted↗

Metabolic rate and body size: a new view on the 'surface law' for basic metabolic rate.

In larger animals a considerable part of the total body mass (e.g. body water, dissolved substances, mineral and organic deposits) does not consume significant amounts of oxygen. These materials can be considered to form a metabolically inert infrastructure which mainly serves three functions: (1) structural support to the organism, (2) storage of nutrients (building material and energy stores) and (3) transport and distribution of these materials. Considering the transport and support function of the metabolically inert structures and their interconnections it is likely that the infrastructure will basically show some tree-like, branching building plan. The weight of the metabolically inert infrastructure of an organism, can be given by bW/(c+W), in which W = body weight, b and c are constants. With increasing size the weight of the metabolic inert infrastructure increases disproportionably. Experimental data concerning basic metabolic rate (M) in relation to body weight (W) better fit the equation M = a W (1-bW/(c+W), (a = constant) than the conventional power law.

Animals↗

Supporting medical decisions with vector decision trees.

The article presents the extension of a common decision tree concept to a multidimensional - vector - decision tree constructed with the help of evolutionary techniques. In contrary to the common decision tree the vector decision tree can make more than just one suggestion per input sample. It has the functionality of many separate decision trees acting on a same set of training data and answering different questions. Vector decision tree is therefore simple in its form, is easy to use and analyse and can express some relationships between decisions not visible before. To explore and test the possibilities of this concept we developed a software tool--DecRain--for building vector decision trees using the ideas of evolutionary computing. Generated vector decision trees showed good results in comparison to classical decision trees. The concept of vector decision trees can be safely and effectively used in any decision making process.

Algorithms↗

A tree-based model for homogeneous groupings of multinomials.

The motivation of this paper is to provide a tree-based method for grouping multinomial data according to their classification probability vectors. We produce an initial tree by binary recursive partitioning whereby multinomials are successively split into two subsets and the splits are determined by maximizing the likelihood function. If the number of multinomials k is too large, we propose to order the multinomials, and then build the initial tree based on a dramatically smaller number k-1 of possible splits. The tree is then pruned from the bottom up. The pruning process involves a sequence of hypothesis tests of a single homogeneous group against the alternative that there are two distinct, internally homogeneous groups. As pruning criteria, the Bayesian information criterion and the Wilcoxon rank-sum test are proposed. The tree-based model is illustrated on genetic sequence data. Homogeneous groupings of genetic sequences present new opportunities to understand and align these sequences.

Animals↗

Haplotype fine mapping by evolutionary trees.

To refine the location of a disease gene within the bounds provided by linkage analysis, many scientists use the pattern of linkage disequilibrium between the disease allele and alleles at nearby markers. We describe a method that seeks to refine location by analysis of "disease" and "normal" haplotypes, thereby using multivariate information about linkage disequilibrium. Under the assumption that the disease mutation occurs in a specific gap between adjacent markers, the method first combines parsimony and likelihood to build an evolutionary tree of disease haplotypes, with each node (haplotype) separated, by a single mutational or recombinational step, from its parent. If required, latent nodes (unobserved haplotypes) are incorporated to complete the tree. Once the tree is built, its likelihood is computed from probabilities of mutation and recombination. When each gap between adjacent markers is evaluated in this fashion and these results are combined with prior information, they yield a posterior probability distribution to guide the search for the disease mutation. We show, by evolutionary simulations, that an implementation of these methods, called "FineMap," yields substantial refinement and excellent coverage for the true location of the disease mutation. Moreover, by analysis of hereditary hemochromatosis haplotypes, we show that FineMap can be robust to genetic heterogeneity.

Algorithms↗

Selection of orthogonal reversed-phase HPLC systems by univariate and auto-associative multivariate regression trees.

In order to select chromatographic starting conditions to be optimized during further method development of the separation of a given mixture, so-called generic orthogonal chromatographic systems could be explored in parallel. In this paper the use of univariate and multivariate regression trees (MRT) was studied to define the most orthogonal subset from a given set of chromatographic systems. Two data sets were considered, which contain the retention data of 68 structurally diversive drugs on sets of 32 and 38 chromatographic systems, respectively. For both the univariate and multivariate approaches no other data but the measured retention factors are needed to build the decision trees. Since multivariate regression trees are used in an unsupervised way, they are called auto-associative multivariate regression trees (AAMRT). For all decision trees used, a variable importance list of the predictor variables can be derived. It was concluded that based on these ranked lists, both for univariate and multivariate regression trees, a selection of the most orthogonal systems from a given set of systems can be obtained in a user-friendly and fast way.

Chromatography, High Pressure Liquid↗

An empirical comparison of expert-derived and data-derived classification trees.

Classification trees provide an attractively transparent discrimination technique, and may be derived from both expert opinion and from data analysis. We consider a real and complex problem concerning the diagnosis of babies with suspected critical congenital heart disease into one of 27 classes. A full loss matrix for all possible misclassifications was obtained from clinical assessments. A tree derived from expert opinion was compared with those derived from analysis of 571 past cases, both for the full problem and for a subset of 6 diseases. Automatic methods for tree creation and pruning were found to have problems for rare diseases, and hand-pruning was carried out. Inclusion of costs led to much improved clinical performance, even for trees that had originally been constructed to minimize classification errors. The expert tree showed a specific building strategy that could not be reproduced automatically. The expert tree generally outperformed those derived from data, particularly in the ability to identify important composite features.

Algorithms↗

Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle.

The Minimum Evolution (ME) approach to phylogeny estimation has been shown to be statistically consistent when it is used in conjunction with ordinary least-squares (OLS) fitting of a metric to a tree structure. The traditional approach to using ME has been to start with the Neighbor Joining (NJ) topology for a given matrix and then do a topological search from that starting point. The first stage requires O(n(3)) time, where n is the number of taxa, while the current implementations of the second are in O(p n(3)) or more, where p is the number of swaps performed by the program. In this paper, we examine a greedy approach to minimum evolution which produces a starting topology in O(n(2)) time. Moreover, we provide an algorithm that searches for the best topology using nearest neighbor interchanges (NNIs), where the cost of doing p NNIs is O(n(2) + p n), i.e., O(n(2)) in practice because p is always much smaller than n. The Greedy Minimum Evolution (GME) algorithm, when used in combination with NNIs, produces trees which are fairly close to NJ trees in terms of topological accuracy. We also examine ME under a balanced weighting scheme, where sibling subtrees have equal weight, as opposed to the standard "unweighted" OLS, where all taxa have the same weight so that the weight of a subtree is equal to the number of its taxa. The balanced minimum evolution scheme (BME) runs slower than the OLS version, requiring O(n(2) x diam(T)) operations to build the starting tree and O(p n x diam(T)) to perform the NNIs, where diam(T) is the topological diameter of the output tree. In the usual Yule-Harding distribution on phylogenetic trees, the diameter expectation is in log(n), so our algorithms are in practice faster that NJ. Moreover, this BME scheme yields a very significant improvement over NJ and other distance-based algorithms, especially with large trees, in terms of topological accuracy.

Algorithms↗

Selecting a decision model for economic evaluation: a case study and review.

The increased use of modelling techniques as a methodological tool in the economic evaluation of health care technologies has, in the main, been limited to two approaches--decision trees and Markov chain models. The former are suited to modelling simple scenarios that occur over a short time period, whilst Markov chain models allow longer time periods to be modelled, in continuous time, where the timing of an event is uncertain. In the context of economic evaluation, a less well developed technique is discrete event simulation, which may allow even greater flexibility. Taking the economic evaluation of adjuvant therapies for breast cancer as an illustrative example, the process of building a decision tree, a Markov chain model, and a discrete event simulation model are described. The potential benefits and problems of each approach are discussed. The suitability of the modelling techniques to economic evaluations of health care programmes in general is then discussed. This section aims to illustrate the areas in which the alternative modelling methods may be most appropriately employed.

Adult↗

Diagnostic potential of serum proteomic patterns in prostate cancer.

PURPOSE: The serum prostate specific antigen test has been widely used in the last decade as an effective screening tool for prostate cancer (CaP). However, the high false-positive rate of the serum prostate specific antigen test necessitates the development of more accurate diagnostic and prognostic biomarkers for CaP. Promising diagnostic potential of serum protein patterns detected by surface enhanced laser desorption/ionization time of flight mass spectrometry for CaP has recently been reported. Independent evaluation of this new technology is warranted to realize its translational utility. We determined whether serum protein profiling by surface enhanced laser desorption/ionization time of flight mass spectrometry and a decision tree algorithm classification system could accurately discriminate between patients with CaP and unaffected individuals. MATERIALS AND METHODS: Proteomic spectra of crude serum were generated using the Ciphergen ProteinChip System and pattern detection was performed using Biomarker Patterns Software (Ciphergen Biosystems, Inc., Fremont, California). A total of 106 patients with CaP and 56 controls were randomly allocated to a training set and a test set. The training set, which consisted of 44 patients with cancer and 30 controls, was used to build a decision tree algorithm. The test set, which consisted of 62 patients with cancer and 26 controls, was used in blinded fashion to validate the decision tree. RESULTS: Accuracy of classification using the test set was 67% and 42% for the weak cation exchange array and the copper metal affinity capture array, respectively. Combined spectral data from the weak cation exchange and copper metal affinity capture arrays generated an algorithm that achieved 85% sensitivity and 85% specificity for the detection of CaP. CONCLUSIONS: These preliminary findings support recent observations that complex protein profiles have promising potential for the early detection of CaP and warrant future studies with streamlined technology. Furthermore, the combined effect of using 2 array types can greatly enhance the ability of protein profile patterns, suggesting the potential usefulness of alternative approaches to evaluate this new emerging technology.

Algorithms↗

[Serum proteomic profiles of the subjects with esophageal precancerous and cancerous lesions from Linzhou, an area with high incidence of esophageal cancer in Henan Province, Northern China].

BACKGROUND & OBJECTIVE: Some molecular changes occurred in esophageal precancerous and cancerous lesions could be reflected in the serum, but the clinical application is limited because of their low sensitivity and specificity. Serum proteomic profiling is much desirable in identifying the proteins closely related to esophageal carcinogenesis. This study was to characterize the serum protein profiles of the subjects with normal esophagus, esophageal precancerous and cancerous lesions from Linzhou, the area with the highest incidence of esophageal carcinoma (EC) in Henan Province, Northern China. METHODS: Proteomic spectra were generated with surface-enhanced laser desorption/inionation-time of flight-mass spectra (SELDI-TOF-MS) and weak cation exchange (WCX2) protein chip system, and analyzed by bioinformatics like decision tree classification algorithm on a set of serum from 130 symptom-free subjects [including 63 cases with normal esophageal epithelia, 40 with basal cell hyperplasia (BCH), and 27 with dysplasia (DYS)] and 30 EC patients from Linzhou. RESULTS: One protein in BCH group with a ratio of mass to charge (M/Z) of M9 306.61 u, 1 in DYS group with a M/Z ratio of M13 765.9 u, and 2 in EC group with M/Z ratios of M2 942.15 u and M15 953.4 u were selected to build 3 decision tree classification models to identify the subjects with BCH, DYS, and EC, respectively. With these classification models, the sensitivities of identifying BCH, DYS and EC were 57.5% (23/40), 88.8% (24/27) and 96.6% (29/30), respectively, in the training sets, and 57.5% (23/40), 66.6% (18/27) and 60.0% (18/30), respectively, in the test sets; the specificities of identifying BCH, DYS and EC were 96.8% (61/63), 63.4% (40/63) and 92.0% (58/63), respectively, in the training sets, and 95.2% (60/63), 71.4% (45/63) and 84.1% (53/63), respectively, in the test sets. CONCLUSION: The protein sets with M/Z ratios of M9 306.61 u, M13 765.9 u, M2 942.15 u, and M15 953.4 u may contain promising serum biomarkers for screening the subjects with high-risk of EC.

Adult↗

PoInTree: a polar and interactive phylogenetic tree.

PoInTree (Polar and Interactive Tree) is an application that allows to build, visualize and customize phylogenetic trees in a polar interactive and highly flexible view. It takes as input a FASTA file or multiple alignment formats. Phylogenetic tree calculation is based on a sequence distance method and utilizes the Neighbor Joining (NJ) algorithm. It also allows displaying precalculated trees of the major protein families based on Pfam classification. In PoInTree, nodes can be dynamically opened and closed and distances between genes are graphically represented. Tree root can be centered on a selected leaf. Text search mechanism, color-coding and labeling display are integrated. The visualizer can be connected to an Oracle database containing information on sequences and other biological data, helping to guide their interpretation within a given protein family across multiple species. The application is written in Borland Delphi and based on VCL Teechart Pro 6 graphical component (Steema software).

Algorithms↗

Phylogeny for the faint of heart: a tutorial.

Phylogenetic trees seem to be finding ever broader applications, and researchers from very different backgrounds are becoming interested in what they might have to say. This tutorial aims to introduce the basics of building and interpreting phylogenetic trees. It is intended for those wanting to understand better what they are looking at when they look at someone else's trees or to begin learning how to build their own. Topics covered include: how to read a tree, assembling a dataset, multiple sequence alignment (how it works and when it does not), phylogenetic methods, bootstrap analysis and long-branch artefacts, and software and resources.

Amino Acid Sequence↗

Towards reconstruction of gene networks from expression data by supervised learning.

BACKGROUND: Microarray experiments are generating datasets that can help in reconstructing gene networks. One of the most important problems in network reconstruction is finding, for each gene in the network, which genes can affect it and how. We use a supervised learning approach to address this question by building decision-tree-related classifiers, which predict gene expression from the expression data of other genes. RESULTS: We present algorithms that work for continuous expression levels and do not require a priori discretization. We apply our method to publicly available data for the budding yeast cell cycle. The obtained classifiers can be presented as simple rules defining gene interrelations. In most cases the extracted rules confirm the existing knowledge about cell-cycle gene expression, while hitherto unknown relationships can be treated as new hypotheses. CONCLUSIONS: All the relations between the considered genes are consistent with the facts reported in the literature. This indicates that the approach presented here is valid and that the resulting rules can be used as elements for building and explaining gene networks.

Algorithms↗

Parallel evolution of virulence in pathogenic Escherichia coli.

The mechanisms underlying the evolution and emergence of new bacterial pathogens are not well understood. To elucidate the evolution of pathogenic Escherichia coli strains, here we sequenced seven housekeeping genes to build a phylogenetic tree and trace the history of the acquisition of virulence genes. Compatibility analysis indicates that more than 70% of the informative sites agree with a single phylogeny, suggesting that recombination has not completely obscured the remnants of ancestral chromosomes. On the basis of the rate of synonymous substitution for E. coli and Salmonella enterica (4.7 x 10(-9) per site per year), the radiation of clones began about 9 million years ago and the highly virulent pathogen responsible for epidemics of food poisoning, E. coli O157:H7, separated from a common ancestor of E. coli K-12 as long as 4.5 million years ago. Phylogenetic analysis reveals that old lineages of E. coli have acquired the same virulence factors in parallel, including a pathogenicity island involved in intestinal adhesion, a plasmid-borne haemolysin, and phage-encoded Shiga toxins. Such parallel evolution indicates that natural selection has favoured an ordered acquisition of genes and the progressive build-up of molecular mechanisms that increase virulence.

DNA, Bacterial↗

An approach to identifying osteopenic women at increased short-term risk of fracture.

BACKGROUND: Identification and management of women to reduce fractures is often limited to T scores less than -2.5, although many fractures occur with higher T scores. We developed a classification algorithm that identifies women with osteopenia (T scores of -2.5 to -1.0) who are at increased risk of fracture within 12 months of peripheral bone density testing. METHODS: A total of 57 421 postmenopausal white women with baseline peripheral T scores of -2.5 to -1.0 and 1-year information on new fractures were included. Thirty-two risk factors for fracture were entered into a classification and regression tree analysis to build an algorithm that best predicted future fracture events. RESULTS: A total of 1130 women had new fractures in 1 year. Previous fracture, T score at a peripheral site of -1.8 or less, self-rated poor health status, and poor mobility were identified as the most important determinants of short-term fracture. Fifty-five percent of the women were identified as being at increased fracture risk. Women with previous fracture, regardless of T score, had a risk of 4.1%, followed by 2.2% in women with T scores of -1.8 or less or with poor health status, and 1.9% for women with poor mobility. The algorithm correctly classified 74% of the women who experienced a fracture. CONCLUSIONS: This classification tool accurately identified postmenopausal women with peripheral T scores of -2.5 to -1.0 who are at increased risk of fracture within 12 months. It can be used in clinical practice to guide assessment and treatment decisions.

Age Distribution↗

Application of the StrOligo algorithm for the automated structure assignment of complex N-linked glycans from glycoproteins using tandem mass spectrometry.

Oligosaccharides associated with proteins are known to give these molecules specific conformations and functions. Analysis of proteins would not be complete without studying the glycans. However, high-throughput techniques in proteomics will soon overwhelm the current capacity of methods if no automation is incorporated into glycomics. New capabilities of the StrOligo algorithm introduced for this purpose (Ethier et al., Rapid Commun. Mass Spectrom., 2002; 16: 1743) will be discussed here. Experimental tandem mass spectra were acquired to test the algorithm using a hybrid quadrupole-time-of-flight (QqTOF) instrument with a matrix-assisted laser desorption/ionization (MALDI) source. The samples were N-linked oligosaccharides from monoclonal antibody IgG, beta interferon and fetuin, detached by enzymatic deglycosylation and labeled at the reducing end. Improvements to the program were made in order to reduce the need for user intervention. StrOligo strips the spectra down to monoisotopic peaks only. The algorithm first builds a relationship tree, accounting for each observed loss of a monosaccharide moiety, and then analyzes the tree and proposes possible structures from combinations of adducts and fragment ion types. A score, which reflects agreement with experimental results, is then given to each proposed structure. The program then decides which combination is the best one and labels relevant peaks in the experimental mass spectrum using a modified nomenclature. The usefulness of the algorithm has been demonstrated by assigning structures to several glycans released from glycoproteins. The analysis was completed in less than 2 minutes for any glycan, which is a substantial improvement over manual interpretation.

Algorithms↗