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Analysis

1 / 702
1.20220180975METHODS AND SYSTEMS FOR DETERMINING GENE EXPRESSION PROFILES AND CELL IDENTITIES FROM MULTI-OMIC IMAGING DATA
US - 09.06.2022
Int.Class G16B 40/30
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
40ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
30Unsupervised data analysis
 Appl.No 17553691 Applicant The Broad Institute, Inc. Inventor Aviv Regev

The present disclosure relates to systems and method of determining transcriptomic profile from omics imaging data. The systems and methods train machine learning methods with intrinsic and extrinsic features of a cell and/or tissue to define transcriptomic profiles of the cell and/or tissue. Applicants utilize a convolutional autoencoder to define cell subtypes from images of the cells.

2.WO/2023/059663SYSTEMS AND METHODS FOR ASSESSMENT OF BODY FAT COMPOSITION AND TYPE VIA IMAGE PROCESSING
WO - 13.04.2023
Int.Class A61B 5/00
AHUMAN NECESSITIES
61MEDICAL OR VETERINARY SCIENCE; HYGIENE
BDIAGNOSIS; SURGERY; IDENTIFICATION
5Measuring for diagnostic purposes ; Identification of persons
 Appl.No PCT/US2022/045706 Applicant THE BROAD INSTITUTE, INC. Inventor KHERA, Amit
The subject matter disclosed herein relates to utilizing the silhouette of an individual to measure body fat volume and distribution. Particular examples relates to providing a system, a computer-implemented method, and a computer program product to utilize a binary outline, or silhouette, to predict the individual's fat depot volumes with machine learning models.
3.WO/2024/097314METHODS AND SYSTEMS FOR DETERMINING DONOR CELL FEATURES AND FORMULATING CELL THERAPY PRODUCTS BASED ON CELL FEATURES
WO - 10.05.2024
Int.Class G16B 40/00
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
40ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
 Appl.No PCT/US2023/036628 Applicant SANA BIOTECHNOLOGY, INC. Inventor JOHNSON, Adam James
Methods of profiling cells for donor capability with a recipient subject are provided. In particular, methods relating to identifying cells, such as T cells, suitable for making a cell therapy product and administration to a patient (e.g., as CAR T cell therapy). Methods are also provided of profiling the donor capability of a cell or population of cells for cell therapy, such methods comprising evaluating the cell or the population of cells for predicted function. A predicted cell function may be evaluated by assaying one or more cell parameters. Further, cells and cell therapy products manufactured according to such methods are provided.
4.WO/2021/167984SYSTEMS AND METHODS FOR MACHINE LEARNING FEATURES IN BIOLOGICAL SAMPLES
WO - 26.08.2021
Int.Class G06K 9/00
GPHYSICS
06COMPUTING; CALCULATING OR COUNTING
KGRAPHICAL DATA READING; PRESENTATION OF DATA; RECORD CARRIERS; HANDLING RECORD CARRIERS
9Methods or arrangements for recognising patterns
 Appl.No PCT/US2021/018388 Applicant 10X GENOMICS, INC. Inventor WEISENFELD, Neil Ira
Systems and methods for machine learning tissue classification are provided herein. Datasets for a plurality of biological samples are first generated. The dataset of each biological sample includes image data of the biological sample and molecular measurement data of the biological sample captured at a plurality of capture areas of the biological sample. The capture areas of the biological sample are registered to corresponding locations in the image data of the biological sample. Then, a machine learning module is trained with the datasets. Another dataset for another biological sample is generated (e.g., in the same or similar manner as the other datasets). And, the other dataset of the other biological sample is processed through the trained machine learning module to predict features in the other biological sample.
5.WO/2023/141277SYSTEMS AND METHODS FOR SKIN BIOMOLECULAR PROFILE ASSESSMENT USING ARTIFICIAL INTELLIGENCE
WO - 27.07.2023
Int.Class A61B 5/00
AHUMAN NECESSITIES
61MEDICAL OR VETERINARY SCIENCE; HYGIENE
BDIAGNOSIS; SURGERY; IDENTIFICATION
5Measuring for diagnostic purposes ; Identification of persons
 Appl.No PCT/US2023/011249 Applicant VANDERBILT UNIVERSITY Inventor MARASCO, Christina, C.
Skin biomolecular profile assessment methods and systems that can analyze the molecular composition of the skin using molecular-level, user-specific data to assess an individual's skin state and/or disease state are described herein. An example method includes receiving skin data associated with a subject, where the skin data includes a biomolecular profile. The method also includes inputting the skin data into a trained artificial intelligence (AI) model and receiving, from the trained AI model, a skin care prediction.
6.20240071569APPARATUSES, SYSTEMS, AND METHODS FOR EXTRACTING MEANING FROM DNA SEQUENCE DATA USING NATURAL LANGUAGE PROCESSING (NLP)
US - 29.02.2024
Int.Class G16B 40/00
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
40ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
 Appl.No 18034417 Applicant BASF CORPORATION Inventor Erin Marie Davis

Apparatuses, systems, and methods are provided that may analyze deoxyribonucleic add (DNA) sequence data using a natural language processing (NLP) model to, for example, identify genetic elements such as known and/or novel cis-regulatory elements {e.g., known and/or putative novel drought-responsive cis-regulatory elements (DREs)). Apparatuses, systems, and methods are also provided that may identify transcriptional regulators {e.g., upstream transcriptional regulators of a novel putative DRE) based on natural language processing (NLP) model data and expression genome-wide association study (eGWAS) data. Apparatuses, systems, and methods are also provided that may verify putative novel cis-regulatory elements based on a comparison of natural language processing (NLP) model output data and other model output data.

7.WO/2022/098588APPARATUSES, SYSTEMS, AND METHODS FOR EXTRACTING MEANING FROM DNA SEQUENCE DATA USING NATURAL LANGUAGE PROCESSING (NLP)
WO - 12.05.2022
Int.Class C12Q 1/68
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
1Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
68involving nucleic acids
 Appl.No PCT/US2021/057491 Applicant BASF CORPORATION Inventor DAVIS, Erin, Marie
Apparatuses, systems, and methods are provided that may analyze deoxyribonucleic add (DNA) sequence data using a natural language processing (NLP) model to, for example, identify genetic elements such as known and/or novel cis-regulatory elements {e.g., known and/or putative novel drought-responsive cis-regulatory elements (DREs)). Apparatuses, systems, and methods are also provided that may identify transcriptional regulators {e.g., upstream transcriptional regulators of a novel putative DRE) based on natural language processing (NLP) model data and expression genome-wide association study (eGWAS) data. Apparatuses, systems, and methods are also provided that may verify putative novel cis-regulatory elements based on a comparison of natural language processing (NLP) model output data and other model output data.
8.20200395099TECHNIQUES FOR PROTEIN IDENTIFICATION USING MACHINE LEARNING AND RELATED SYSTEMS AND METHODS
US - 17.12.2020
Int.Class G16B 40/30
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
40ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
30Unsupervised data analysis
 Appl.No 16900582 Applicant Quantum-Si Incorporated Inventor Michael Meyer

Described herein are systems and techniques for identifying polypeptides using data collected by a protein sequencing device. The protein sequencing device may collect data obtained from detected light emissions by luminescent labels during binding interactions of reagents with amino acids of the polypeptide. The light emissions may result from application of excitation energy to the luminescent labels. The device may provide the data as input to a trained machine learning model to obtain output that may be used to identify the polypeptide. The output may indicate, for each of a plurality of locations in the polypeptide, one or more likelihoods that one or more respective amino acids is present at the location. The output may be matched to an amino acid sequence that specifies a protein.

9.WO/2021/211787SYSTEMS AND METHODS FOR QUANTIFICATION OF LIVER FIBROSIS WITH MRI AND DEEP LEARNING
WO - 21.10.2021
Int.Class G16H 50/20
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
HHEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
50ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
20for computer-aided diagnosis, e.g. based on medical expert systems
 Appl.No PCT/US2021/027398 Applicant CHILDREN'S HOSPITAL MEDICAL CENTER Inventor DILLMAN, Jonathan
Embodiments provide a deep learning framework to accurately segment liver and spleen using a convolutional neural network with both short and long residual connections to extract their radiomic and deep features from multiparametric MRI. Embodiments will provide an "ensemble" deep learning model to quantify biopsy derived liver fibrosis stage and percentage using the integration of multiparametric MRI radiomic and deep features, MRE data, as well as routinely available clinical data. Embodiments will provide a deep learning model to quantify MRE-derived liver stiffness using multiparametric MRI, radiomic and deep features and routinely-available clinical data.
10.20210256394METHODS AND SYSTEMS FOR THE OPTIMIZATION OF A BIOSYNTHETIC PATHWAY
US - 19.08.2021
Int.Class G06N 3/12
GPHYSICS
06COMPUTING; CALCULATING OR COUNTING
NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
3Computing arrangements based on biological models
12using genetic models
 Appl.No 17175120 Applicant Zymergen Inc. Inventor Stepan TYMOSHENKO

The present disclosure provides methods and systems for identifying variants of a given target protein or target gene that perform the same function and/or improve the phenotypic performance of a host cell transformed with such a variant. To enhance the diversity of identified candidate sequences, the methods may implement the use of a metagenomic database and/or machine learning methods. The methods and systems may be implemented in optimizing a biosynthetic pathway, e.g., to improve the production of a target molecule of interest.

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