Patents Assigned to ILLUMINA SOFTWARE, INC.
  • Publication number: 20230015945
    Abstract: The technology disclosed extracts intensities from sequencing images for base calling target clusters and attenuates spatial crosstalk from neighboring clusters. The technology disclosed accesses a particular section from a plurality of sections of an image output by a sensor, the particular section of the image including at least one pixel depicting intensity emission values from a target cluster and neighboring clusters located across the sensor, and convolves the particular section of the image with a corresponding convolution kernel in a plurality of convolution kernels, to generate a feature map comprising a plurality of feature values. The technology disclosed further assigns a corresponding feature value to the target cluster based on feature values in the plurality of feature values adjoining a center of the target cluster, and processes the corresponding feature value assigned to the target cluster, to base call the target cluster.
    Type: Application
    Filed: September 2, 2022
    Publication date: January 19, 2023
    Applicant: ILLUMINA SOFTWARE, INC.
    Inventors: Abde Ali Hunaid KAGALWALL, Eric Jon OJARD, Rami MEHIO, Gavin Derek PARNABY, Nitin UDPA, Bo LU, John S. VIECELI
  • Publication number: 20230018469
    Abstract: We disclose a system. The system comprises a memory and a runtime logic. The memory stores a plurality of specialist signal profilers. Each specialist signal profiler in the plurality of specialist signal profilers is trained to maximize signal-to-noise ratio of sequenced signals in a particular signal profile detected for analytes in a particular analyte class and characterized in a particular training data set. The runtime logic, having access to the memory, is configured to execute a base calling operation by applying respective specialist signal profilers in the plurality of specialist signal profilers to sequenced signals in respective signal profiles detected for analytes in respective analyte classes during the base calling operation.
    Type: Application
    Filed: June 13, 2022
    Publication date: January 19, 2023
    Applicant: ILLUMINA SOFTWARE, INC.
    Inventors: Abde Ali Hunaid KAGALWALLA, Eric Jon OJARD, Rami MEHIO, Gavin Derek PARNABY, Nitin UDPA, John S. VIECELI
  • Patent number: 11455487
    Abstract: The technology disclosed attenuates spatial crosstalk from sequencing images for base calling. The technology disclosed accesses a section of an image output by a biosensor, where the section of the image includes a plurality of pixels depicting intensity emission values from a plurality of clusters within the biosensor and from locations within the biosensor that are adjacent to the plurality of clusters. The plurality of clusters includes a target cluster. The section of the image is convolved with a convolution kernel, to generate a feature map comprising a plurality of features having a corresponding plurality of feature values. A weighted feature value is assigned to the target cluster, where the weighted feature value is based on one or more features values of the plurality of feature values of the feature map. The weighted feature value assigned to the target cluster is processed, to base call the target cluster.
    Type: Grant
    Filed: October 26, 2021
    Date of Patent: September 27, 2022
    Assignee: Illumina Software, Inc.
    Inventors: Abde Ali Hunaid Kagalwalla, Eric Jon Ojard, Rami Mehio, Gavin Derek Parnaby, Nitin Udpa, Bo Lu, John S. Vieceli
  • Publication number: 20220300811
    Abstract: A method of quantizing parameters of a neural network includes grouping a plurality of parameters of a neural network in a plurality of groups. Each group of the plurality of groups includes corresponding two or more parameters of the plurality of parameters. In an example, for each group, a corresponding quantization format is selected from a plurality of available quantization formats, such that a first quantization format selected for at least a first group is different from a second quantization format selected for at least a second group. For each group, individual parameters within the corresponding group are quantized using the quantization format selected for the corresponding group. The quantized parameters of the plurality of groups are stored in a memory.
    Type: Application
    Filed: March 4, 2022
    Publication date: September 22, 2022
    Applicant: ILLUMINA SOFTWARE, INC.
    Inventor: Gavin Derek PARNABY