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At least 505 records · Page 28Linked to original sources

Toward Class Imbalance and Uncertainty in Powder XRD Analysis: A Dual-Channel Fusion Network for Space Group Classification.

Accurate identification of space groups from powder X-ray diffraction (pXRD) is essential for understanding crystal structures and accelerating materials discovery. However, this task remains highly challenging due to inherent peak overlap, experimental noise, and the complexity of the 230-class classification problem. To address the critical issues of class imbalance and data scarcity, we first design a general physics-informed data augmentation pipeline. We then propose a dual-channel fusion uncertainty-aware network (DFUN) for automated space group classification. The DFUN architecture integrates two complementary feature representations: convolutional features extracted directly from raw diffraction profiles and domain-specific peak descriptors. These distinct representations are adaptively fused through a gating mechanism. Furthermore, to mitigate the inherent long-tailed distribution of crystallographic data, we employ a hybrid loss function that combines Focal Loss with Label Smoothing. Finally, we incorporate Monte Carlo Dropout to provide predictive uncertainty estimation, thereby enabling not only accurate classification but also a crucial assessment of the model's reliability. Evaluated on large-scale simulated data and two public data sets (opXRD and RRUFF), DFUN outperforms the evaluated baseline methods across the reported metrics. The framework also provides uncertainty-aware predictions, establishing DFUN as a robust and interpretable solution for high-throughput automated crystallographic analysis from powder diffraction.

Uncertainty↗

Can sample-specific simulations help detect low base-rate taxonicity?

The authors examined the role of the sample-specific simulations (SSS; A. M. Ruscio & J. Ruscio, 2002; J. Ruscio & A. M. Ruscio, 2004) procedure in detecting low base-rate taxa that might otherwise prove elusive. The procedure preserved key distributional characteristics for moderate to high base-rate taxa, but it performed inadequately for low base-rate taxa, with low to moderate nuisance covariance, decreasing indicator validity, and increasing average nuisance covariance. Visual inspection of the curves produced by the SSS procedure, combined with the expectation that the inchworm test should produce a clear peak for low base-rate taxonic samples, led to inappropriate conclusions about the suitability of data. The authors speculate that examination of low base-rate taxa using SSS may require other algorithms for generating comparison distributions, consideration of the shape of the whole curve, and/or relaxation of the expectation that a clear peak will emerge with the inchworm test.

Algorithms↗

Phenotypic study by numerical taxonomy of strains belonging to the genus Aeromonas.

AIMS: This study was undertaken to cluster and identify a large collection of Aeromonas strains. METHODS AND RESULTS: Numerical taxonomy was used to analyse phenotypic data obtained on 54 new isolates taken from water, fish, snails, sputum and 99 type and reference strains. Each strain was tested for 121 characters but only the data for 71 were analysed using the 'SSM' and 'SJ' coefficients, and the UPGMA clustering algorithm. At SJ values of > or = 81.6% the strains clustered into 22 phenons which were identified as Aer. jandaei, Aer. hydrophila, Aer. encheleia, Aer. veronii biogroup veronii, Aer. trota, Aer. caviae, Aer. eucrenophila, Aer. ichthiosmia, Aer. sobria, Aer. allosaccharophila, Aer. media, Aer. schubertii and Aer. salmonicida. The species Aer. veronii biogroup sobria was represented by several clusters which formed two phenotypic cores, the first related to reference strain CECT 4246 and the second related to CECT 4835. A good correlation was generally observed among this phenotypic clustering and previous genomic and phylogenetic data. In addition, three new phenotypic groups were found, which may represent new Aeromonas species. CONCLUSIONS: The phenetic approach was found to be a necessary tool to delimitate and identify the Aeromonas species. SIGNIFICANCE AND IMPACT OF THE STUDY: Valuable traits for identifying Aeromonas as well as the possible existence of new Aeromonas species or biotypes are indicated.

Aeromonas↗

Chemosensitivity prediction by transcriptional profiling.

In an effort to develop a genomics-based approach to the prediction of drug response, we have developed an algorithm for classification of cell line chemosensitivity based on gene expression profiles alone. Using oligonucleotide microarrays, the expression levels of 6,817 genes were measured in a panel of 60 human cancer cell lines (the NCI-60) for which the chemosensitivity profiles of thousands of chemical compounds have been determined. We sought to determine whether the gene expression signatures of untreated cells were sufficient for the prediction of chemosensitivity. Gene expression-based classifiers of sensitivity or resistance for 232 compounds were generated and then evaluated on independent sets of data. The classifiers were designed to be independent of the cells' tissue of origin. The accuracy of chemosensitivity prediction was considerably better than would be expected by chance. Eighty-eight of 232 expression-based classifiers performed accurately (with P < 0.05) on an independent test set, whereas only 12 of the 232 would be expected to do so by chance. These results suggest that at least for a subset of compounds genomic approaches to chemosensitivity prediction are feasible.

Drug Resistance, Neoplasm↗

Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae).

Phylogenetic analyses of large data sets pose special challenges, including the apparent tendency for the bootstrap support for a clade to decline with increased taxon sampling of that clade. We document this decline in data sets with increasing numbers of taxa in Astragalus, the most species-rich angiosperm genus. Support for one subclade, Neo-Astragalus, declined monotonically with increased sampling of taxa inside Neo-Astragalus, irrespective of whether parsimony or neighbor-joining methods were used or of which particular heuristic search algorithm was used (although more stringent algorithms tended to yield higher support). Three possible explanations for this decline were examined, including (1) mistaken assignment of the most recent common ancestor of the taxon sample (and its bootstrap support) with the most recent common ancestor of the clade from which it was sampled; (2) computational limitations of heuristic search strategies; and (3) statistical bias in bootstrap proportions, especially that from random homoplasy distributed among taxa. The best explanation appears to be (3), although computational shortcomings (2) may explain some of the problem. The bootstrap proportion, as currently used in phylogenetic analysis, does not accurately capture the classical notion of confidence assessments on the null hypothesis of nonmonophyly, especially in large data sets. More accurate assessments of confidence as type I error levels (relying on iterated bootstrap methods) remove most of the monotonic decline in confidence with increasing numbers of taxa.

Algorithms↗

Performance of flip supertree construction with a heuristic algorithm.

Supertree methods are used to assemble separate phylogenetic trees with shared taxa into larger trees (supertrees) in an effort to construct more comprehensive phylogenetic hypotheses. In spite of much recent interest in supertrees, there are still few methods for supertree construction. The flip supertree problem is an error correction approach that seeks to find a minimum number of changes (flips) to the matrix representation of the set of input trees to resolve their incompatibilities. A previous flip supertree algorithm was limited to finding exact solutions and was only feasible for small input trees. We developed a heuristic algorithm for the flip supertree problem suitable for much larger input trees. We used a series of 48- and 96-taxon simulations to compare supertrees constructed with the flip supertree heuristic algorithm with supertrees constructed using other approaches, including MinCut (MC), modified MC (MMC), and matrix representation with parsimony (MRP). Flip supertrees are generally far more accurate than supertrees constructed using MC or MMC algorithms and are at least as accurate as supertrees built with MRP. The flip supertree method is therefore a viable alternative to other supertree methods when the number of taxa is large.

Algorithms↗

Calculating the evolutionary rates of different genes: a fast, accurate estimator with applications to maximum likelihood phylogenetic analysis.

In phylogenetic analyses with combined multigene or multiprotein data sets, accounting for differing evolutionary dynamics at different loci is essential for accurate tree prediction. Existing maximum likelihood (ML) and Bayesian approaches are computationally intensive. We present an alternative approach that is orders of magnitude faster. The method, Distance Rates (DistR), estimates rates based upon distances derived from gene/protein sequence data. Simulation studies indicate that this technique is accurate compared with other methods and robust to missing sequence data. The DistR method was applied to a fungal mitochondrial data set, and the rate estimates compared well to those obtained using existing ML and Bayesian approaches. Inclusion of the protein rates estimated from the DistR method into the ML calculation of trees as a branch length multiplier resulted in a significantly improved fit as measured by the Akaike Information Criterion (AIC). Furthermore, bootstrap support for the ML topology was significantly greater when protein rates were used, and some evident errors in the concatenated ML tree topology (i.e., without protein rates) were corrected. [Bayesian credible intervals; DistR method; multigene phylogeny; PHYML; rate heterogeneity.].

Algorithms↗

Missing the forest for the trees: phylogenetic compression and its implications for inferring complex evolutionary histories.

Phylogenetic tree reconstruction is difficult in the presence of lateral gene transfer and other processes generating conflicting signals. We develop a new approach to this problem using ideas borrowed from algorithmic information theory. It selects the hypothesis that simultaneously minimizes the descriptive complexity of the tree(s) plus the data when encoded using those tree(s). In practice this is the hypothesis that can compress the data the most. We show not only that phylogenetic compression is an efficient method for encoding most phylogenetic data sets and is more efficient than compression schemes designed for single sequences, but also that it provides a clear information theoretic rule for determining when a collection of conflicting trees is a better explanation of the data than a single tree. By casting the parsimony problem in this more general framework, we also conclude that the so-called total-evidence tree--the tree constructed from all the data simultaneously--is not always the most economical explanation of the data.

Algorithms↗

Phylogenetic diversity and the greedy algorithm.

Given a phylogenetic tree with leaves labeled by a collection of species, and with weighted edges, the "phylogenetic diversity" of any subset of the species is the sum of the edge weights of the minimal subtree connecting the species. This measure is relevant in biodiversity conservation where one may wish to compare different subsets of species according to how much evolutionary variation they encompass. In this note we show that phylogenetic diversity has an attractive mathematical property that ensures that we can solve the following problem easily by the greedy algorithm: find a subset of the species of any given size k of maximal phylogenetic diversity. We also describe an extension of this result that also allows weights to be assigned to species.

Algorithms↗

Reciprocal illumination in the gene content tree of life.

Phylogenies based on gene content rely on statements of primary homology to characterize gene presence or absence. These statements (hypotheses) are usually determined by techniques based on threshold similarity or distance measurements between genes. This fundamental but problematic step can be examined by evaluating each homology hypothesis by the extent to which it is corroborated by the rest of the data. Here we test the effects of varying the stringency for making primary homology statements using a range of similarity (e-value) cutoffs in 166 fully sequenced and annotated genomes spanning the tree of life. By evaluating each resulting data set with tree-based measurements of character consistency and information content, we find a set of homology statements that optimizes overall corroboration. The resulting data set produces well-resolved and well-supported trees of life and greatly ameliorates previously noted inconsistencies such as the misclassification of small genomes. The method presented here, which can be used to test any technique for recognizing primary homology, provides an objective framework for evaluating phylogenetic hypotheses and data sets for the tree of life. It also can serve as a technique for identifying well-corroborated sets of homologous genes for functional genomic applications.

Algorithms↗

Multipolar consensus for phylogenetic trees.

Collections of phylogenetic trees are usually summarized using consensus methods. These methods build a single tree, supposed to be representative of the collection. However, in the case of heterogeneous collections of trees, the resulting consensus may be poorly resolved (strict consensus, majority-rule consensus, ...), or may perform arbitrary choices among mutually incompatible clades, or splits (greedy consensus). Here, we propose an alternative method, which we call the multipolar consensus (MPC). Its aim is to display all the splits having a support above a predefined threshold, in a minimum number of consensus trees, or poles. We show that the problem is equivalent to a graph-coloring problem, and propose an implementation of the method. Finally, we apply the MPC to real data sets. Our results indicate that, typically, all the splits down to a weight of 10% can be displayed in no more than 4 trees. In addition, in some cases, biologically relevant secondary signals, which would not have been present in any of the classical consensus trees, are indeed captured by our method, indicating that the MPC provides a convenient exploratory method for phylogenetic analysis. The method was implemented in a package freely available at http://www.lirmm.fr/~cbonnard/MPC.html

Algorithms↗

GeneTree: comparing gene and species phylogenies using reconciled trees.

SUMMARY: GeneTree is a program for comparing gene and species trees using reconciled trees. The program can compute the cost of embedding a gene tree within a species tree, visually display the location and number of gene duplications and losses, and search for optimal species trees. AVAILABILITY: The program is free and is available at ((http://taxonomy.zoology.gla.ac. uk/rod/genetree/genetree.html)).

Algorithms↗

DOLOP--database of bacterial lipoproteins.

UNLABELLED: Bacterial lipoproteins and lipid modification are gaining importance owing to their essential nature, roles in pathogenesis and interesting commercial applications. We have created an exclusive knowledge base for bacterial lipoproteins by processing information from 510 entries to provide a list of 199 distinct lipoproteins with relevant links to molecular details. Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins from 43 completed bacterial genomes along with interactive information exchange facility. AVAILABILITY: The website called Database Of bacterial LipOProteins (DOLOP) is available at http://www.mrc-lmb.cam.ac.uk/genomes/dolop along with additional information on the biosynthetic pathway, supplementary material and other related figures.

Algorithms↗

A module-based approach for post-omics, post-GWAS network-based gene classification.

MOTIVATION: Complex traits and diseases are highly polygenic and understanding the full set of genes involved is a central challenge in biomedicine. However, due to sample size limitations and noise (technical and biological), experimental approaches for disease-gene discovery such as transcriptomics and GWAS result in long, noisy, heterogeneous gene lists, which may be trimmed to a subset of likely relevant genes while leaving several false negatives. Computational gene classification approaches, especially those using genome-scale molecular interaction networks, are promising avenues for complementing such experimental findings by analytically expanding observed gene lists based on the functional relatedness between genes. We previously introduced the network-based gene classification approach, GenePlexus, which was rigorously benchmarked to show state-of-the-art performance, especially for predicting novel genes associated with biological processes and fine-grained phenotypes. Network-based gene classification performance,however, declines for diseases, especially when the inputs are omics and GWAS-based long gene lists. RESULTS: Here, we show that these disease gene lists span multiple biological processes spread across the molecular network, and we propose ModGenePlexus, a new network-based gene classification method that takes a two-stage approach. First, clustering and semi-supervised learning decomposes the input gene list into coherent, denoised network gene modules. Then, ModGenePlexus trains supervised (GenePlexus) classifiers for each module and aggregates predictions to return genome-wide rankings. We benchmarked ModGenePlexus across simulated data, transcriptomic signatures, and GWAS datasets (together spanning hundreds of diseases), showing improved recovery of known disease genes compared to GenePlexus. Beyond improved classification, the results of enrichment analysis of ModGenePlexus outputs are much more interpretable by virtue of revealing nuanced biological processes. Together, these results establish ModGenePlexus as a scalable, interpretable tool for gene classification of GWAS- and omics-derived gene lists across diverse biological contexts. AVAILABILITY AND IMPLEMENTATION: ModGenePlexus is freely available on GitHub at https://github.com/krishnanlab/ModGenePlexus, and the full source code and results supporting this study are available on Zenodo at https://zenodo.org/records/19857910.

Genome-Wide Association Study↗

Comparison of classic statistical methods and machine learning approaches to classify readiness.

MOTIVATION: Predicting physical and cognitive readiness in warfighters is critical for mission success. These predictions can be improved by identifying key biomarkers using multiple omics modalities. The MASTR-E study conducted by McKetney and colleagues is one of the most comprehensive multi-omics studies of saliva samples collected from warfighters, which also applied classic linear statistical (CLS) techniques to discover key biomarkers of readiness. Aligning with McKetney et al.'s assumptions, we operationalize readiness as a binary proxy, where pre-mission samples are labeled as "ready" to reflect a rested, unstressed physiological baseline, while post-mission samples are labeled "not ready" to reflect cumulative physical and cognitive load from the mission. As such, readiness here is not a direct biological or physiological construct, but an inferred state likely dominated by stress-related physiological changes. This assumption and definition is discussed further in the Introduction and Limitations sections. Here, we apply machine learning (ML) analyses to better assess generalizability, consider hidden interactions, and identify nonlinear patterns in the data. We investigated whether ML approaches could predict readiness and identify relevant biomarkers. ML models were trained on proteomics-only or metabolomics-only datasets to classify participants as ready or not ready and important model features were considered as putative biomarkers. Training and testing datasets were curated for two objectives: (i) recognize biomolecular signatures indicative of readiness within the same donor and (ii) assess generalizability across warfighters by withholding donors for testing. RESULTS: Proteomics-based models achieved AUCs of 0.907&#x2009;&#xb1;&#x2009;0.034 and 0.860&#x2009;&#xb1;&#x2009;0.063 for Objectives 1 and 2, respectively. Metabolomics-based models achieved Objective 1 AUC of 0.994&#x2009;&#xb1;&#x2009;0.007 and Objective 2 AUC of 0.993&#x2009;&#xb1;&#x2009;0.010. Comparative analysis with existing literature validates the model's feature importances, but the identified putative biomarkers significantly differ from those discovered through CLS analyses, as only one ML-identified biomarker overlapping with those identified through CLS methods. We show that these ML models and identified features are more robust to noise and generalizable across participants than those identified using CLS methods. AVAILABILITY: The analysis pipelines are provided as Jupyter notebooks, including all code and documentation, and are available publicly on GitHub at {https://github.com/netrias/ReadinessClassification}.

Machine Learning↗

Use of social science research to improve epidemiologic studies of and interventions for diarrhea and dysentery.

The significance of dysentery has not been recognized in community-based programs for the management of diarrhea. Culturally sensitive methods of classification and algorithms for treatment of these diseases must be developed. Considered in this article is the manner in which ethnographic studies of diarrhea can contribute to descriptive epidemiologic data on diarrhea and dysentery and to procedures of health education and evaluation of interventions for the diseases. Indigenous terms for bloody diarrhea exist in many cultures. Local use of such terms must be carefully examined before they are incorporated in health education efforts and epidemiologic surveillance programs.

Culture↗