公开(公告)号：US11756649B2

公开(公告)日：2023-09-12

申请号：US16640214

申请日：2018-10-16

Applicant: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

Inventor： Xin Gao ,  Yu Li

IPC: G16B5/20 ,  G06N3/044 ,  G06N3/045 ,  G16B20/00 ,  G06N3/08 ,  G16B15/20 ,  G06N3/084

CPC classification number: G16B5/20 ,  G06N3/044 ,  G06N3/045 ,  G06N3/08 ,  G16B15/20 ,  G16B20/00 ,  G06N3/084

Abstract: An apparatus, computer program product, and method are provided for the determination of one or more components of an EC number through the application of a level-by-level modeling approach capable of conducting feature reconstruction and classifier training simultaneously, based on encoded aspects of a sequence listing for a protein with an unknown function. The method includes receiving a sequence source data object associated with an enzyme; extracting a sequence data set from the sequence source data object; encoding the sequence data set into a first and second encoded sequence; generating a first predicted characteristic of the enzyme by applying the first and second encoded sequence to a first level of a model comprising a plurality of levels; and generating a second predicted characteristic of the enzyme by applying the first and the second encoded sequences to a second level of the model comprising a plurality of levels.

公开(公告)号：US11836895B2

公开(公告)日：2023-12-05

申请号：US17848780

申请日：2022-06-24

Applicant: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

Inventor： Xin Gao ,  Yu Li ,  Renmin Han

IPC: G06T3/40 ,  G01N21/64 ,  G06N3/08 ,  G06T5/00 ,  G06T5/20 ,  G06T5/50

CPC classification number: G06T3/4076 ,  G01N21/6458 ,  G06N3/08 ,  G06T3/4046 ,  G06T5/002 ,  G06T5/20 ,  G06T5/50 ,  G06T2207/10056 ,  G06T2207/10064 ,  G06T2207/20084

Abstract: A method for structure simulation for super-resolution fluorescence microscopy, the method including receiving a first image having a first resolution, which is indicative of a distribution of fluorophores; applying a Markov model to the fluorophores to indicate an emission state of the fluorophores; generating a plurality of second images, having the first resolution, based on the first image and the Markov model; adding DC background to the plurality of second images to generate a plurality of third images, having the first resolution; downsampling the plurality of third images to obtain a plurality of fourth images, which have a second resolution, lower than the first resolution; and generating a time-series, low-resolution images by adding noise to the plurality of fourth images. The time-series, low-resolution images have the second resolution.

公开(公告)号：US11646101B2

公开(公告)日：2023-05-09

申请号：US16432123

申请日：2019-06-05

Applicant: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

Inventor： Xin Gao ,  Renmin Han ,  Sheng Wang ,  Yu Li

IPC: G16B30/00

CPC classification number: G16B30/00

Abstract: A method for global mapping between a first sequence Xp and a second sequence Xg. The method includes receiving the first sequence Xp and the second sequence Xg at a computing device, wherein the first sequence Xp is related to measured raw electrical current signals and the second sequence Xg is related to calculated electrical current signals; applying a continuous wavelet transform (CWT) algorithm to each of the first and second sequences Xp and Xg to obtain raw CWT signals and expected CWT signals, respectively; extracting raw features and expected features from the raw CWT signals and the expected CWT signals, respectively; generating a context-dependent boundary BI around a previous warping path WI, wherein the previous warping path WI is calculated using a dynamic time warping (DTW) algorithm that relates the raw features to the expected features and I is an index associated with an element of the previous warping path; calculating a new warping path WI−1 based on the context-dependent boundary BI; and identifying a nucleotide sequence associated with the first sequence Xp and the second sequence Xg, based on the new warping path WI−1.

公开(公告)号：US11851704B2

公开(公告)日：2023-12-26

申请号：US17355823

申请日：2021-06-23

Applicant: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

Inventor： Xin Gao ,  Yu Li ,  Sheng Wang ,  Renmin Han

IPC: G01N33/48 ,  G01N33/50 ,  C12Q1/6869 ,  G16B40/30 ,  G16B40/10 ,  G16B30/20 ,  G06N3/088

CPC classification number: C12Q1/6869 ,  G06N3/088 ,  G16B30/20 ,  G16B40/10 ,  G16B40/30

Abstract: A method for sequencing biopolymers. The method includes selecting with a sequence generator module an input nucleotide sequence having plural k-mers; simulating with a deep learning simulator, actual electrical current signals corresponding to the input nucleotide sequence; identifying reads that correspond to the actual electrical current signals; and displaying the reads. The deep learning simulator includes a context-dependent deep learning model that takes into consideration a position of a k-mer of the plural k-mers on the input nucleotide sequence when calculating a corresponding actual electrical current.

公开(公告)号：US11078531B2

公开(公告)日：2021-08-03

申请号：US16769127

申请日：2018-10-30

Applicant: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

Inventor： Xin Gao ,  Yu Li ,  Sheng Wang ,  Renmin Han

IPC: G01N33/48 ,  G01N33/50 ,  C12Q1/6869 ,  G16B40/30 ,  G16B40/10 ,  G16B30/20 ,  G06N3/08

Abstract: A method for sequencing biopolymers. The method includes selecting with a sequence generator module an input nucleotide sequence having plural k-mers; simulating with a deep learning simulator, actual electrical current signals corresponding to the input nucleotide sequence; identifying reads that correspond to the actual electrical current signals; and displaying the reads. The deep learning simulator includes a context-dependent deep learning model that takes into consideration a position of a k-mer of the plural k-mers on the input nucleotide sequence when calculating a corresponding actual electrical current.