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1.发明授权公开(公告)号：US11756649B2
公开(公告)日：2023-09-12
申请号：US16640214
申请日：2018-10-16
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.
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公开(公告)号：US11851704B2
公开(公告)日：2023-12-26
申请号：US17355823
申请日：2021-06-23
Inventor： Xin Gao , Yu Li , Sheng Wang , Renmin Han
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.
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公开(公告)号：US11078531B2
公开(公告)日：2021-08-03
申请号：US16769127
申请日：2018-10-30
Inventor： Xin Gao , Yu Li , Sheng Wang , Renmin Han
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.
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公开(公告)号：US20170316147A1
公开(公告)日：2017-11-02
申请号：US15520568
申请日：2015-10-27
Inventor： Xin Gao , Hammad Naveed
CPC classification number: G16B15/00 , C12Q2600/158 , G01N33/6845 , G16B30/00 , G16B50/00
Abstract: The invention provides a novel integrated structure and system-based approach for drug target prediction that enables the large-scale discovery of new targets for existing drugs Novel computer-readable storage media and computer systems are also provided. Methods and systems of the invention use novel sequence order-independent structure alignment, hierarchical clustering, and probabilistic sequence similarity techniques to construct a probabilistic pocket ensemble (PPE) that captures even promiscuous structural features of different binding sites for a drug on known targets. The drug's PPE is combined with an approximation of the drug delivery profile to facilitate large-scale prediction of novel drug-protein interactions with several applications to biological research and drug development.
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公开(公告)号：US11308633B2
公开(公告)日：2022-04-19
申请号：US16642590
申请日：2018-10-18
Inventor： Xin Gao , Renmin Han
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.
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Patent Agency Ranking
公开(公告)号：US11836895B2
公开(公告)日：2023-12-05
申请号：US17848780
申请日：2022-06-24
Inventor： Xin Gao , Yu Li , Renmin Han
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.
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公开(公告)号：US11646101B2
公开(公告)日：2023-05-09
申请号：US16432123
申请日：2019-06-05
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.
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公开(公告)号：US11557068B2
公开(公告)日：2023-01-17
申请号：US16982419
申请日：2019-03-19
Inventor： Xin Gao , Renmin Han
Abstract: A method for image reconstruction from plural copies, the method including receiving a series of measured projections pi of a target object h and associated background; iteratively reconstructing images hi(k) of the target object and images gi(k) of the background of the target object for each member i of the series of the measured projections pi over plural iterations k; and generating a final image of the target object h, based on the reconstructed images hi, when a set condition is met. The index i describes how many elements are in the series of projections pi, and iteration k indicates how many times the reconstruction of the image target is performed.
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公开(公告)号：US20220136064A1
公开(公告)日：2022-05-05
申请号：US17429279
申请日：2020-02-10
Inventor： Ayman F. Abuelela , Alyaa M. Abdel-Haleem , Xin Gao , Jasmeen S. Merzaban
IPC: C12Q1/6886
Abstract: Compositions and method of cancer diagnosis and prognosis are disclosed. The methods rely on the expression profile of a 55 O-glycan forming GT (OGFGT) genes in multi-dimensional space was sufficient to classify cancer types from cancer patient samples in. These OGFGT genes ae used to distinguish between normal and cancer samples and cancer subtypes promoting the huge potential of utilizing this set of genes in diagnostic applications. The expression signature of OGFGT genes can also be used to determine survival profiles in samples from GBM patient samples.
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公开(公告)号：US20190018922A1
公开(公告)日：2019-01-17
申请号：US16067687
申请日：2017-02-02
Inventor： Xin Gao , Hiroyuki Kuwahara , Meshari Saud Alazmi , Xuefeng Cui
Abstract: The present invention relates to a method and system for dynamically analyzing, determining, predicting and displaying ranked suitable heterologous biosynthesis pathways for a specified host. The present invention addresses the problem of finding suitable pathways for the endogenous metabolism of a host organism because the efficacy of heterologous biosynthesis is affected by competing endogenous pathways. The present invention is called MRE (Metabolic Route Explorer), and it was conceived and developed to systematically and dynamically search for, determine, analyze, and display promising heterologous pathways while considering competing endogenous reactions in a given host organism.
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