公开(公告)号：US20230260593A1

公开(公告)日：2023-08-17

申请号：US17768332

申请日：2020-05-22

Applicant: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

Inventor： Xin GAO ,  Yu LI ,  Wenkai HAN

IPC: G16B20/00 ,  G16B40/20 ,  G06N3/08

CPC classification number: G16B20/00 ,  G16B40/20 ,  G06N3/08

Abstract: A method for annotating antibiotic resistance genes includes receiving a raw sequence encoding of a bacterium, determining first, in a level 0 module, whether the raw sequence encoding includes an antibiotic resistance gene (ARG), determining second, in a level 1 module, a resistant drug type, a resistance mechanism, and a gene mobility for the ARG, determining third, in a level 2 module, if the ARG is a beta-lactam, a sub-type of the beta-lactam, and outputting the ARG, the resistant drug type, the resistance mechanism, the gene mobility, and the sub-type of the beta-lactam. The level 0 module, the level 1 module and the level 2 module each includes a deep convolutional neural network (CNN) model.

公开(公告)号：US20230154006A1

公开(公告)日：2023-05-18

申请号：US17917036

申请日：2021-04-12

Applicant: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

Inventor： Xin GAO ,  Longxi ZHOU ,  Zhongxiao LI

IPC: G06T7/11 ,  G06T7/00

CPC classification number: G06T7/11 ,  G06T7/0012

Abstract: A machine-agnostic segmentation and quantification method for coronavirus diagnostic includes receiving computer tomograph, CT, raw scans; normalizing the CT raw scans to obtain normalized data, wherein the normalized data is normalized in terms of dimension, resolution, and signal intensity; generating augmented data based on (1) the CT raw scans and (2) a simulation model; segmenting three different 2-dimensional, 2D, images from the normalized data, which correspond to a same voxel, , using three functions , and , respectively; and quantizing (508) each voxel to have a value of 0 or 1, based on the three functions , and and an aggregation function g. The value 0 indicates that the voxel is not infected with the coronavirus, and the value 1 indicates that the voxel is infected with the coronavirus, and the three functions , and are trained based on the augmented data.

公开(公告)号：US20210350876A1

公开(公告)日：2021-11-11

申请号：US17285255

申请日：2019-10-16

Applicant: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

Inventor： Xin GAO ,  Sheng WANG ,  Renmin HAN

IPC: G16B40/10 ,  G16B30/10 ,  G06K9/62 ,  G01N33/487

Abstract: A method for similarity searching directly on nanopore raw current signals, the method including receiving a reference genome sequence; receiving a query genome sequence; transforming the reference genome sequence, with a nanopore sequencing device, into a raw current signal X; transforming the query genome sequence, based on a pore model, into a query current signal Y; and mapping the query current signal Y to the raw current signal X based on a subsequence extension of dynamic time warping distance Dist, which calculates a distance between the raw current signal X and a padded signal query Y′. The padded signal query Y′ is the query current signal Y to which an element y0 has been added, the raw current signal X and the query current signal Y are electrical currents, and the raw current signal X corresponds to a genome of an organism.

公开(公告)号：US20210398605A1

公开(公告)日：2021-12-23

申请号：US17297233

申请日：2019-10-24

Applicant: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

Inventor： Xin GAO ,  Ramzan UMAROV

IPC: G16B5/20 ,  G16B40/00 ,  G06N3/08 ,  G06N3/04

Abstract: A method for training a deep neural network model based on a known genome sequence includes receiving the known genome sequence; training the deep neural network model with a current negative set obtained from the known genome sequence; applying the deep neural network model to the known genome sequence and recording false positive sets; selecting a subset of the new false positive sets; updating the current negative set with the new false positive sets; and repeating the steps of training, applying, selecting and updating until a number of the new false positive sets is smaller than a given threshold.

公开(公告)号：US20210317523A1

公开(公告)日：2021-10-14

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: 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.

公开(公告)号：US20210090689A1

公开(公告)日：2021-03-25

申请号：US16967498

申请日：2019-01-08

Applicant: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

Inventor： Xin GAO ,  Meshari Saud ALAZMI ,  Hiroyuki KUWAHARA

IPC: G16C20/30 ,  G16C20/10 ,  G16C20/70 ,  G06F17/18 ,  G16B40/20

Abstract: Embodiments of the present disclosure describe a fingerprint contribution method for predicting a Gibbs free energy of biochemical reactions, methods of training a fingerprint contribution model for predicting a Gibbs free energy of biochemical reactions, methods of predicting a Gibbs free energy of biochemical reactions, a non-transitory computer readable medium comprising instructions which, when read by a computing device, cause a processor to execute a method for predicting a Gibbs free energy of biochemical reactions, and the like.

公开(公告)号：US20200370110A1

公开(公告)日：2020-11-26

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: C12Q1/6869 ,  G16B40/10 ,  G16B30/20 ,  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：US20200349725A1

公开(公告)日：2020-11-05

申请号：US16642590

申请日：2018-10-18

Applicant: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

Inventor： Xin GAO ,  Renmin HAN

IPC: G06T7/33 ,  G06T3/00 ,  G06T7/00

Abstract: Provided is an apparatus and method for aligning fiducial markers. The apparatus may align positions of the fiducial markers on the two or more micrographs forming a two or more point sets corresponding to the two or more micrographs; create a first set of matched fiducial markers and unmatched fiducial markers; transform unmatched fiducial markers into transformed point sets and match the unmatched fiducial markers resulting in a second set of matched fiducial markers. The matching of the second set of matched fiducial markers results in improved alignment of a large number of fiducial markers. The aligned positions of fiducial markers may be constrained by an upper bound of transformation deviation of aligning positions of fiducial markers on two or more micrographs.

公开(公告)号：US20200286585A1

公开(公告)日：2020-09-10

申请号：US16803122

申请日：2020-02-27

Applicant: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

Inventor： Xin GAO ,  Hiroyuki KUWAHARA

IPC: G16B20/20 ,  G06F17/18 ,  G16B50/30

Abstract: A method for analysis of transcriptional aberrations and molecular diagnostic of genetic diseases includes receiving ribonucleic acid, RNA, related data; calculating a probability λt of an error-free splicing for a coding transcript t based on the RNA data; calculating the count-per-million (CPM) normalized xt for the coding transcript t based on the RNA data; calculating an omega index based on a product of the probability λt and the CPM normalized xt for a gene g of the human genome; and determining that the gene g is a candidate for a genetic disorder.

公开(公告)号：US20200035325A1

公开(公告)日：2020-01-30

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

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.