Abstract: A computer-implemented method includes generating, by a processor, a set of training data for each phenotype in a database including a set of subjects. The set of training data is generated by dividing genomic information of N subjects selected with or without repetition into windows, computing a distribution of genomic events in the windows for each of N subjects, and extracting, for each window, a tensor that represents the distribution of genomic events for each of N subjects. A set of test data is generated for each phenotype in the database, a distribution of genomic events in windows for each phenotype is computed, and a tensor is extracted for each window that represents a distribution of genomic events for each phenotype. The method includes classifying each phenotype of the test data with a classifier, and assigning a phenotype to a patient.

Abstract: Embodiments of the present invention include method, systems and computer program products for algebraic phasing of polyploids. Aspects of the invention include receiving a matrix including a set of two or more single-nucleotide poloymorphisms (SNPs) for two or more sample organisms. Each row of the matrix is set to a ploidy based on a number of ploidies present in the two or more sample organisms. Each allele in the set of two or more SNPs is represented as a binary number. A set of algebraic rules is received, wherein the set of algebraic rules include an algebraic phasing algorithm. And the set of algebraic rules are applied to the matrix to determine a haplotype of a parent of the two or more sample organisms.

Abstract: Methods and systems for genetic diagnosis include splitting genomes into respective groups of non-overlapping windows. The genomes are sampled into sets, each set being made up of selected genomes. A distribution of events is generated across the sets in each window. A tensor is determined for each window based on statistical properties of the distribution of events for the window. A classifier is generated based on the tensors. One or more phenotypes is diagnosed from an input genome using the classifier.

Abstract: Embodiments of the present invention include method, systems and computer program products for algebraic phasing of polyploids. Aspects of the invention include receiving a matrix including a set of two or more single-nucleotide poloymorphisms (SNPs) for two or more sample organisms. Each row of the matrix is set to a ploidy based on a number of ploidies present in the two or more sample organisms. Each allele in the set of two or more SNPs is represented as a binary number. A set of algebraic rules is received, wherein the set of algebraic rules include an algebraic phasing algorithm. And the set of algebraic rules are applied to the matrix to determine a haplotype of a parent of the two or more sample organisms.

Abstract: Embodiments include methods, systems, and computer program products for identifying content in a metagenomic sample. Aspects include receiving a plurality of metagenomic reads for a sample. Aspects also include comparing a portion of the plurality of metagenomic reads to a genomic database and identifying a plurality of associated nodes, wherein the genomic database includes a plurality of gene sequences having known taxonomies. Aspects also include generating a probabilistic score for each of the associated nodes per metagenomic read. Aspects also include generating an output including a plurality of identifications and a final probability score for each of the identifications based at least in part upon the probabilistic score for each of the associated nodes per metagenomic read.

Abstract: A computer-implemented method, computer program product, and computer processing system are provided for metagenomic pattern classification. The method includes pre-processing, by a processor, a taxonomy tree associated with a genome database to extract taxonomy related information therefrom. The genome database includes a plurality of genome sequences. The method further includes building, by the processor, a suffix tree on the genome database. The method also includes annotating, by the processor, nodes in the suffix tree, using a plurality of right maximal patterns derived from the extracted taxonomy related information as annotations, such that each of the plurality of right maximal patterns in the suffix tree points to a respective one of a plurality of nodes in the taxonomy tree and such that a leaf node in the taxonomy tree represents a respective sample organism. The annotations are configured to function as classifications for the plurality of genome sequences.

Abstract: A computer-implemented method, computer program product, and computer processing system are provided for phasing polyploids. The method includes receiving, by a processor, a n×m matrix including a set of n rows and a set of m columns. Each of the n rows represents a respective one of n samples. Each of the m columns represents a respective one of m SNPs for two or more sample organisms. The method further includes representing, by the processor, each allele in the m SNPs as a binary number. The method also includes phasing, by the processor, the n samples to determine a haplotype of a parent of the two or more sample organisms. The phasing is performed using a trie to process a distribution of alleles in the n-samples that includes homozygous alleles and heterozygous alleles.

Abstract: A computer-implemented method is provided for phasing polyploids. The method includes assembling, by a processor, haplotypes in polyploid genomes of two or more sample organisms. The method further includes performing, by the processor, haplotype phasing on the haplotypes using a haplotype phasing process having multiple phases applied to ploid samples corresponding to the haplotypes to determine which parent chromosomes possess which of the haplotypes. The step of performing haplotype phasing includes (i) reducing, in each of the multiple phases, a ploidy p to a floor value (p/2), (ii) assigning variables in at least some of the multiple phases such that resulting intermediate ones of the ploid samples co-occur multiple times in the at least some of the multiple phases, and (iii) linking, in each of the multiple phases, the ploid samples together using one or more daisy chain models and daisy chain linkage criteria.

Abstract: Embodiments include methods, systems, and computer program products for identifying a metagenomic read. Aspects include receiving a metagenomic read of a sample. Aspects also include comparing the metagenomic read to a genomic database including a plurality of gene sequences. Aspects also include randomly fragmenting the metagenomic read into two read fragments. Aspects also include comparing the read fragments to the genomic database including a plurality of gene sequences. Aspects also include generating an identification based at least in part on a determination that a read fragment exactly matches a gene sequence.

Abstract: Embodiments of the present invention include method, systems and computer program products for algebraic phasing of polyploids. Aspects of the invention include receiving a matrix including a set of two or more single-nucleotide poloymorphisms (SNPs) for two or more sample organisms. Each row of the matrix is set to a ploidy based on a number of ploidies present in the two or more sample organisms. Each allele in the set of two or more SNPs is represented as a binary number. A set of algebraic rules is received, wherein the set of algebraic rules include an algebraic phasing algorithm. And the set of algebraic rules are applied to the matrix to determine a haplotype of a parent of the two or more sample organisms.

Abstract: Embodiments of the present invention include method, systems and computer program products for algebraic phasing of polyploids. Aspects of the invention include receiving a matrix including a set of two or more single-nucleotide poloymorphisms (SNPs) for two or more sample organisms. Each row of the matrix is set to a ploidy based on a number of ploidies present in the two or more sample organisms. Each allele in the set of two or more SNPs is represented as a binary number. A set of algebraic rules is received, wherein the set of algebraic rules include an algebraic phasing algorithm. And the set of algebraic rules are applied to the matrix to determine a haplotype of a parent of the two or more sample organisms.

Abstract: Embodiments of the present invention are directed to a computer-implemented method for positive OTU identification. A non-limiting example of the computer-implemented method includes receiving, by a processor, a plurality of sequencing reads for a metagenome sample and, for each of the plurality of sequencing reads, a corresponding OTU set comprising a plurality of OTUs. The method also includes determining, by the processor, a true positive score for each of the plurality of OTUs based upon a C?ech Complex and generating a plurality of preliminary OTUs. The method also includes determining a threshold score for the preliminary OTUs. The method also includes removing one of the preliminary OTUs based at least in part upon a determination that the true positive score is less than a threshold. The method also includes retaining one of the preliminary OTUs based at least in part upon a determination that the true positive score is greater than or equal to the threshold.

Abstract: Embodiments of the present invention are directed to a computer-implemented method for positive OTU identification. A non-limiting example of the computer-implemented method includes receiving, by a processor, a plurality of sequencing reads for a metagenome sample and, for each of the plurality of sequencing reads, a corresponding OTU set comprising a plurality of OTUs. The method also includes determining, by the processor, a true positive score for each of the plurality of OTUs based upon a ?ech Complex and generating a plurality of preliminary OTUs. The method also includes determining a threshold score for the preliminary OTUs. The method also includes removing one of the preliminary OTUs based at least in part upon a determination that the true positive score is less than a threshold. The method also includes retaining one of the preliminary OTUs based at least in part upon a determination that the true positive score is greater than or equal to the threshold.

Abstract: Embodiments of the present invention include method, systems and computer program products for algebraic phasing of polyploids. Aspects of the invention include receiving a matrix including a set of two or more single-nucleotide poloymorphisms (SNPs) for two or more sample organisms. Each row of the matrix is set to a ploidy based on a number of ploidies present in the two or more sample organisms. Each allele in the set of two or more SNPs is represented as a binary number. A set of algebraic rules is received, wherein the set of algebraic rules include an algebraic phasing algorithm. And the set of algebraic rules are applied to the matrix to determine a haplotype of a parent of the two or more sample organisms.

Abstract: Embodiments of the present invention include method, systems and computer program products for algebraic phasing of polyploids. Aspects of the invention include receiving a matrix including a set of two or more single-nucleotide polymorphisms (SNPs) for two or more sample organisms. Each row of the matrix is set to a ploidy based on a number of ploidies present in the two or more sample organisms. Each allele in the set of two or more SNPs is represented as a binary number. A set of algebraic rules is received, wherein the set of algebraic rules include an algebraic phasing algorithm. And the set of algebraic rules are applied to the matrix to determine a haplotype of a parent of the two or more sample organisms.

Abstract: Embodiments are directed to a computer implemented method of assessing a relevancy of a drug to a disease state of a patient. The method includes assessing an impact of the drug on driver genes (DGs) of the disease state of the patient, assessing an impact of the drug on druggable target genes (DTs) of the drug, and assessing the relationship between the DGs and DTs that are in one of a plurality of biological pathways of the disease state of the patient. The method further includes combining the impact of the drug on the DGs, the impact of the drug on the DTs, and the relationship between the DGs and DTs that are in the one of the biological pathways, wherein the combining results in an assessment of the relevancy of the drug to the disease state of the patient.

Abstract: Embodiments are directed to a computer-based system for analyzing genotype data of a set of multiple progeny to estimate information about unknown parents of the multiple progeny. The system includes a memory and a processor system communicatively coupled to the memory. The processor system is configured to receive data representing markers of each genotype of each of the multiple progeny, compare the data to identify compatible genotypes having compatible markers, and label the compatible genotypes as having at least one parent in common.

Abstract: Embodiments are directed to a computer-based system for analyzing genotype data of a set of multiple progeny to estimate information about unknown parents of the multiple progeny. The system includes a memory and a processor system communicatively coupled to the memory. The processor system is configured to receive data representing markers of each genotype of each of the multiple progeny, compare the data to identify compatible genotypes having compatible markers, and label the compatible genotypes as having at least one parent in common.

Abstract: Embodiments are directed to computer implemented method of assessing a relevancy of a pathway to a disease of interest, the pathway having a source and a target. The method includes developing an impact of the source on the pathway. The method further includes developing a value of targeting, based at least in part on an alteration of the pathway, the pathway with a drug of interest. The method further includes identifying a relationship between the source and the target within the pathway. The method further includes combining: the impact of the source on the pathway; the value of targeting, based at least in part on the alteration of the pathway, the pathway with a drug of interest; and the relationship between the source and the target within the pathway, wherein the combining results in an assessment that represents the relevancy of the pathway to the disease of interest.

Abstract: Embodiments are directed to computer implemented method of assessing a relevancy of a pathway to a disease of interest, the pathway having a source and a target. The method includes developing an impact of the source on the pathway. The method further includes developing a value of targeting, based at least in part on an alteration of the pathway, the pathway with a drug of interest. The method further includes identifying a relationship between the source and the target within the pathway. The method further includes combining: the impact of the source on the pathway; the value of targeting, based at least in part on the alteration of the pathway, the pathway with a drug of interest; and the relationship between the source and the target within the pathway, wherein the combining results in an assessment that represents the relevancy of the pathway to the disease of interest.