US 12,277,998 B2
Artificial intelligence-based base calling
Kishore Jaganathan, San Francisco, CA (US); John Randall Gobbel, Brisbane, CA (US); and Amirali Kia, San Mateo, CA (US)
Assigned to Illumina, Inc., San Diego, CA (US)
Filed by Illumina, Inc., San Diego, CA (US)
Filed on Feb. 2, 2023, as Appl. No. 18/163,794.
Application 18/163,794 is a continuation of application No. 16/826,126, filed on Mar. 20, 2020, granted, now 11,783,917.
Claims priority of provisional application 62/821,681, filed on Mar. 21, 2019.
Claims priority of provisional application 62/821,602, filed on Mar. 21, 2019.
Claims priority of provisional application 62/821,618, filed on Mar. 21, 2019.
Claims priority of provisional application 62/821,766, filed on Mar. 21, 2019.
Claims priority of provisional application 62/821,724, filed on Mar. 21, 2019.
Prior Publication US 2023/0268033 A1, Aug. 24, 2023
This patent is subject to a terminal disclaimer.
Int. Cl. G06V 10/82 (2022.01); G06F 16/907 (2019.01); G06F 18/21 (2023.01); G06F 18/214 (2023.01); G06F 18/23 (2023.01); G06F 18/23211 (2023.01); G06F 18/24 (2023.01); G06F 18/2415 (2023.01); G06F 18/2431 (2023.01); G06N 3/04 (2023.01); G06N 3/08 (2023.01); G06N 3/084 (2023.01); G06N 7/01 (2023.01); G06V 10/26 (2022.01); G06V 10/44 (2022.01); G06V 10/75 (2022.01); G06V 10/762 (2022.01); G06V 10/764 (2022.01); G06V 10/77 (2022.01); G06V 10/778 (2022.01); G06V 10/98 (2022.01); G06V 20/69 (2022.01); G16B 40/00 (2019.01); G16B 40/20 (2019.01); G06N 5/046 (2023.01); G06V 20/40 (2022.01)
CPC G16B 40/20 (2019.02) [G06F 16/907 (2019.01); G06F 18/214 (2023.01); G06F 18/217 (2023.01); G06F 18/23 (2023.01); G06F 18/23211 (2023.01); G06F 18/24 (2023.01); G06F 18/2415 (2023.01); G06F 18/2431 (2023.01); G06N 3/04 (2013.01); G06N 3/08 (2013.01); G06N 3/084 (2013.01); G06N 7/01 (2023.01); G06V 10/267 (2022.01); G06V 10/454 (2022.01); G06V 10/751 (2022.01); G06V 10/763 (2022.01); G06V 10/764 (2022.01); G06V 10/7715 (2022.01); G06V 10/7784 (2022.01); G06V 10/82 (2022.01); G06V 10/993 (2022.01); G06V 20/69 (2022.01); G16B 40/00 (2019.02); G06N 5/046 (2013.01); G06V 20/47 (2022.01)] 20 Claims
OG exemplary drawing
 
9. A non-transitory computer readable storage medium storing computer instructions that, when executed by at least one processor, cause a system to:
receive a set of per-cycle images depicting intensity emissions from a target cluster and one or more adjacent clusters at different positions within a region of a flow cell and at different sequencing cycles;
receive supplemental input that provides information in addition to the intensity emissions depicted in the set of per-cycle images, the supplemental input comprising at least one of distance information indicating distances between pixels within the set of per-cycle images, scaling information indicating at least one of cluster sizes or illumination conditions, cluster center coordinate information, or pixel attribution information indicating classifications of pixels as background, cluster center, or cluster interior;
generate, utilizing convolutional layers of a neural network, an alternative representation of the set of per-cycle images and the supplemental input;
determine, utilizing an output layer of the neural network and based on the alternative representation, classification scores indicating likelihoods that the target cluster incorporated each of four bases at a target sequencing cycle; and
determine a base call for the target cluster at the target sequencing cycle based on the classification scores.