International Business Machines Corporation

Mars, Incorporated

Lenovo Limited

James Harvey Kaufman

Tobin Jon Lehman

Matthew Aaron Davis

Robert Glenn Deen

Joann Ruvolo

Mark Kunitomi

Viktors Berstis

Stefan Bengt Edlund

Matthew Hammer

John Daniel Sieron Bethencourt

Kevin Blake Damm

Reiner Kraft

Daniel Alexander Ford

Anthony W Wu

Cameron Shea Miner

Serhat Metin

Sondra Ronee Renly

Kun Hu

Bart C Weimer

Roy E Scheuerlein

Robert Dennis Miller

Christopher Vincent Jahnes

William Joseph Gallagher

Dulce Beatriz Ponceleon

Stuart Stephen Parkin

John Campbell Scott

Mary Frances Doerner

Mohammad Taghi Mirzamaani

Kenneth Lee Clarkson

Jussi Petri Myllymaki

Glenn T Sincerbox

Joseph Grover Gordon, Ii

John T E Timm

Owen R Melroy

Kevin P Roche

Malcolm Slaney

Hu Kun

Martin Kreyenschmidt

Sigfried Friedrich Karg

Toby Lehman

Seyyed Mohammad Mirzamaani

Daniel Dörr

A large collection of sample genomes containing misclassified k-mers and metadata errors from a reference taxonomy was converted to a self-consistent k-mer database comprising a self-consistent taxonomy. The self-consistent taxonomy was based on genetic distances calculated using the MinHash method or the Meier-Koltoff method. An agglomerative clustering algorithm was used to calculate the self-consistent taxonomy. Each k-mer of the sample genomes was assigned to only one node of the self-consistent taxonomy. In another step, each node of the self-consistent taxonomy was mapped to the reference taxonomy, thereby preserving in the self-consistent taxonomy links to the reference taxonomy while correcting for the misclassification errors therein. The self-consistent k-mer database can be used to taxonomically profile sequenced nucleic acids with greater specificity compared to systems relying on the reference taxonomy.

K-mer database for organism identification

Methods are disclosed for reducing the size of a k-mer reference database used for queries and/or taxonomic classifications when available computer storage and/or memory are inadequate. The k-mers of the reference database have been previously classified to a taxonomy, preferably based on genetic distances. In one method, the k-mers are separated into one or more groups followed by removing k-mers common to the groups. In another method, k-mers are removed based on a selected taxonomic threshold level. A third method combines the features of the previous two methods. The methods are adaptable to machine learning.

Optimizing k-mer databases by k-mer subtraction

One embodiment provides for a method including determining, by at least one processor, sequence-sequence distances for a biological sequence collection. The at least one processor generates a matrix Mof the sequence-sequence distances, where i and j are positive integers. The at least one processor further generates clusters for the matrix Mby performing hierarchical clustering. A self-consistent taxonomy is created from the clusters. A visual heat map display of the matrix Mis selectively controlled using metadata, zoom input and opacity input.

Biological sequence distance explorer system providing user visualization of genomic distance between a set of genomes in a dynamic zoomable fashion

A method is described for automatically correcting metadata errors in a k-mer database. A k-mer database having a self-consistent taxonomy based on genome-genome distance was constructed from a set of sample and reference genomes whose metadata included taxonomic labeling from a reference taxonomy (the standard NCBI taxonomy), which is not based on genetic distance. As a result, genomes of a given taxonomic ID of the self-consistent taxonomy could be separated into clusters based on the differences in the metadata. Genomes of the clusters less than a minimum cluster size Cmin were removed and profiled against the remaining genomes, correcting metadata automatically for those genomes that could be mapped back. The resulting k-mer database showed improved specificity for genetic profiling. Another method is described for identifying and handling chimeric genomes using the self-consistent taxonomy. Another method is described for correcting a classification database.

Methods of automatically and self-consistently correcting genome databases

For each unique pair of a complete set of data items, a computing device determines a distance between the data items of the unique pair. The computing device repeats the following until no data items remain in the complete set. For each data item remaining in the complete set, the computing device determines a similarity subset including each other data item that the distance between the data item and the other data item is less than a target difference threshold. The computing device moves a selected data item from a largest similarity subset to a reference database that is a subset of the complete set. The computing device removes each data item from the complete set that the distance between the selected data item and the data item is less than the threshold. A new data item can be classified using the reference database.

Construction of reference database accurately representing complete set of data items for faster and tractable classification usage

Embodiments of the present invention relate to proactive computer simulation of portable product failures, and more specifically, to determining the likely cause of an outbreak of foodborne disease or other geographically distributed symptoms of a failure or contamination of a portable product. In one embodiment, a method of and computer program product for simulating portable product failures is provided. Data regarding the locations of consumers of a portable product within a geographic region is received from a data store. A probability density map is determined from the data, indicating where the portable product is likely to be consumed within the geographical region. For each of a plurality of simulated failures of the portable product, the locations of a plurality of simulated incidents arising from the simulated failure are determined. From the locations of the plurality of simulated incidents and the probability density map, the number of incidents necessary to identify the portable product to a predetermined certainty is determined.

Proactive simulation and detection of outbreaks based on product data

Embodiments relate to implementing a query-driven virtual social media network group. An aspect includes providing, through a social media network, a search function option incorporated into a user interface that is configured for access by a user of the social media network. Another aspect includes receiving, at the social media network, a query from the user through the search function option of the user interface and searching a database of user profiles and content history for information that satisfies the query. The user profiles and the content history include content received from users as members of the social media network. A further aspect includes creating a virtual social media network group from results of the searching and providing access to a view of the virtual social media network group via the user interface for the user.

Query-driven virtual social network group

Embodiments relate to method and program product enabling collaborative social coding. Social networking functionality is embedded and via that social networking functionality information relating to a particular function across a computing network is tracked. The tracked information is then accumulating and organized as relating to a particular function. Upon request receipt, information is then provided relating to the particular function including a list of those accessing that function.

Techniques to facilitate collaborative social coding

A system facilitates management of public health data. The system includes an input interface, a policy data structure, a notification compliance engine, and a data translator. The input interface receives input data content descriptive of a public health event. The policy data structure stores reporting conditions for a plurality of public health jurisdictions. The notification compliance engine reviews at least some of the reporting conditions of the policy data structure and identifies a relevant reporting condition for the input data content. The data translator derives and arranges output data content based on the input data content according to the relevant reporting condition identified by the notification compliance engine.

Public health data exchange bridge and post office

The initial partitioning of a distributed computing problem can be critical, and is often a source of tedium for the user. A method is provided that automatically segments the problem into fixed sized collections of original program cells (OPCs) based on the complexity of the problem specified, and the combination of computing agents of various caliber available for the overall job. The OPCs that are on the edge of a collection can communicate with OPCs on the edges of neighboring collections, and are indexed separately from OPCs that are within the 'core' or inner non-edge portion of a collection. Consequently, core OPCs can iterate independently of whether any communication occurs between collections and groups of collections (VPPs). All OPCs on an edge have common dependencies on remote information (i.e., their neighbors are all on the same edge of a neighboring collection).

System and method for automatically segmenting and populating a distributed computing problem

Embodiments herein present a system, method, etc. for an efficient super cluster implementation for solving connected problems in a distributed environment. More specifically, the system adapts computing latency to communication latency, wherein the system comprises VPPs wrapped within OCW layers. The VPPs represent a subset of an overall computer task; and, the OCW layers are adapted to enclose the VPPs. Specifically, the number of OCWs that enclose a VPP correspond to the number of computing iterations that may be locally executed by the VPP during an inter-VPP communication cycle. In addition, each VPP comprises collections of OPCs, wherein the OPCs comprise data, methods, and pointers to neighbors. The OPCs are indexed separately based on whether the OPC is part of an OCW layer.

Efficient super cluster implementation for solving connected problems in a distributed environment

The disclosed massive multi-player on-line gaming environment and method eliminate the coordination and synchronization problems between servers by assigning each game user to a specific client proxy server for game duration and utilizing a space information distribution center to indicate client specific changes in game space. Such configuration eliminates the need to use 'grey' areas around partitioning boundaries and servers having to 'own' client objects thereby improving massive multi-player on-line gaming scalability.

Handling of players and objects in massive multi-player on-line games

A message pathway selection system dynamically selects an optimum message pathway for transmitting messages. The system dynamically optimizes a message pathway according to various criteria such as, for example, efficiency, economy, data requirements, auditing requirements, security, data size, etc. The system can direct a message to bypass an infrastructure messaging server, using a direct message pathway. The system can also switch from an infrastructure messaging server to a direct method. The system can also utilize an infrastructure messaging pathway either as an alternative or in parallel with the direct message pathway. The system allows an application to use a single communication system for both a direct mode and an infrastructure mode of data transfer. The present system can bypass the infrastructure message pathway, thus reducing message latency, number of messages sent, and improving overall bandwidth.

System, method, and service for dynamically selecting an optimum message pathway

A method for providing location dependent information to a user for selective colleague assistance. The method on a Client Wireless Component includes the steps of receiving location data from a plurality of Global Positioning System GPS satellites and transmitting the location data to an Active Calendar Component. The method further includes on an Active Calendar Component the steps of receiving Client Wireless Component location data and determining if within a threshold distance a Colleague item list exists for user completion.

Cooperative location based tasks

Embodiments herein present a virtual memory technique for efficiently solving connected problems in a distributed environment. An exemplary method begins by selectively loading computing task segments into a first node, wherein the number of computing task segments is the maximum number of computing task segments that will fit within the first node. The computing task segments are enclosed within wrappers, wherein the wrappers are streamed into the first node at a maximum rate that a disk can read and write data. Further, the wrappers comprise priority wrappers that must be computed in order to process the computing task segments; and thus, the priority wrappers are loaded into the first node first. In addition, the computing task segments comprise computing task segment block collections, wherein the method creates a list of computing task segment block collection jobs that must be completed in order to process one of the computing task segments.

Virtual memory technique for efficiently solving connected problems in a distributed environment

Growing community of inventors

San Jose, CA, United States of America

James Harvey Kaufman