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US 12,749,558 B2Granted
System and method for mapping molecules into interfaces
AssigneeKisoJi Biotechnology Inc.
InventorsMorteza Babaie, Benyamin Ghojogh, Richard Wargachuk, Luis Da Cruz, Gordon Ngan, David S. F. Young
Life of this patent
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Abstract
Embodiments described herein relate to systems and methods for mapping molecules into interfaces. An example interface includes a visual interface having a map visualization. Example molecules include proteins, or any protein-like molecules or fragments thereof such as antibodies, antigens, proteins, lectins, receptors. Embodiments described herein relate to systems and methods for mapping molecules into interfaces by processing data using dimensionality reduction to generation representations of molecule maps (e.g. map visualizations).
Claims25
A computer-implemented system for mapping proteins, protein-like molecules or fragments thereof into visual interfaces and generating maps for display and interaction, the system comprising:
- a processing subsystem that includes one or more processors and one or more memories coupled with the one or more processors, the processing subsystem configured to cause the system to:
- receive data for a set or multiple sets of one or more input proteins, protein-like molecules or fragments thereof, wherein the data comprises features of the one or more proteins, protein-like molecules or fragments thereof;
- generate at least one dataset by processing the data for the set or multiple sets of the one or more input proteins, protein-like molecules or fragments thereof;
- transform one or more of the data and the at least one dataset(s) to generate a map and additional features by feature extraction or feature selection to reduce higher dimensional data representations into lower dimensional data representations for visualization by the visual interface while, wherein the lower-dimensional data representations capture valuable information of the one or more of the data and the at least one dataset(s), the lower dimensional data representations comprising one or more clusters of proteins, protein-like molecules or fragments thereof, the proteins, protein-like molecules or fragments thereof comprising the one or more input proteins, protein-like molecules or fragments thereof or generated proteins, protein-like molecules or fragments thereof;
- generate a visual map interface comprising the map as a visual representation of the lower dimensional data representations of the dataset, the map having one or more dimensions corresponding to the lower dimensional data, the visual representation comprising visualizations representing the dataset as one or more layers of proteins, protein-like molecules or fragments thereof and wherein the visualizations comprise points on the visual map, with each point representing a protein, protein-like molecule or fragment thereof, and the points are spatially located within the visual map based on the lower dimensional data representations, each layer comprising one or more of the one or more clusters of proteins, protein-like molecules or fragments thereof, wherein spatial arrangement of the points reflects similarity of the represented proteins, protein-like molecules or fragments thereof;
- provide the visual map interface with tools for interaction with the map, wherein interaction with the map comprises one or more of inspection, searching, sampling, clustering, and analysis of the one or more proteins, protein-like molecules or fragments thereof or newly generated proteins, protein-like molecules or fragments thereof;
- receive commands or detect interactions with the map by the tools at the visual map interface;
- update the map based on the commands or interactions;
- and
- trigger an update to the visual map interface with the updated map.
7 more elements
A computer process for mapping proteins, protein-like molecules or fragments thereof into visual interfaces and generating digital maps for display and interaction, the method comprising:
- receiving data for a set or multiple sets of one or more input proteins, protein-like molecules or fragments thereof, wherein the data comprises features of the one or more proteins, protein-like molecules or fragments thereof;
- generating at least one dataset by processing the data for the set or multiple sets of the one or more input proteins, protein-like molecules or fragments thereof;
- transforming one or more of the data and the at least one dataset(s) to generate a map and additional features by feature extraction or feature selection to reduce higher dimensional data representations into lower dimensional data representations for visualization by the visual interface while, wherein the lower-dimensional data representations capture valuable information of the one or more of the data and the at least one dataset(s), the lower dimensional data representations comprising one or more clusters of proteins, protein-like molecules or fragments thereof, the proteins, protein-like molecules or fragments thereof comprising the one or more input proteins, protein-like molecules or fragments thereof or generated proteins, protein-like molecules or fragments thereof;
- generating a visual map interface comprising the map as a visual representation of the lower dimensional data representations of the dataset, the map having one or more dimensions corresponding to the lower dimensional data, the visual representation comprising visualizations representing the dataset as one or more layers of proteins, protein-like molecules or fragments thereof and wherein the visualizations comprise points on the visual map, with each point representing a protein, protein-like molecule or fragment thereof, and the points are spatially located within the visual map based on the lower dimensional data representations, each layer comprising one or more of the one or more clusters of proteins, protein-like molecules or fragments thereof, wherein spatial arrangement of the points reflects similarity of the represented proteins, protein-like molecules or fragments thereof;
- and
- providing the visual map interface with tools for interaction with the map, wherein interaction with the map comprises one or more of inspection, searching, sampling, clustering, and analysis of the one or more proteins, protein-like molecules or fragments thereof or newly generated proteins, protein-like molecules or fragments thereof;
- receiving commands or detect interactions with the map by the tools at the visual map interface;
- and
- triggering an update to the visual map interface and the map based on the commands or interactions.
6 more elements
A non-transitory computer-readable medium encoded with instructions, that when executed by a processor, cause the processor to map proteins, protein-like molecules or fragments thereof into visual interfaces and generate digital maps for display and interaction, the instructions comprising instructions for:
- receiving data for a set or multiple sets of one or more input proteins, protein-like molecules or fragments thereof, wherein the data comprises features of the one or more proteins, protein-like molecules or fragments thereof;
- generating at least one dataset by processing the data for the set or multiple sets of the one or more input proteins, protein-like molecules or fragments thereof;
- transforming one or more of the data and the at least one dataset(s) to generate a map and additional features by feature extraction or feature selection to reduce higher dimensional data representations into lower dimensional data representations for visualization by the visual interface while, wherein the lower-dimensional data representations capture valuable information of the one or more of the data and the at least one dataset(s), the lower dimensional data representations comprising one or more clusters of proteins, protein-like molecules or fragments thereof, the proteins, protein-like molecules or fragments thereof comprising the one or more input proteins, protein-like molecules or fragments thereof or generated proteins, protein-like molecules or fragments thereof;
- generating a visual map interface comprising the map as a visual representation of the lower dimensional data representations of the dataset, the map having one or more dimensions corresponding to the lower dimensional data, the visual representation comprising visualizations representing the dataset as one or more layers of proteins and wherein the visualizations comprise points on the visual map, with each point representing a protein, protein-like molecule or fragment thereof, and the points are spatially located within the visual map based on the lower dimensional data representations, protein-like molecules or fragments thereof, each layer comprising one or more of the one or more clusters of proteins, protein-like molecules or fragments thereof, wherein spatial arrangement of the points reflects similarity of the represented proteins, protein-like molecules or fragments thereof;
- and
- providing the visual map interface with tools for interaction with the map, wherein interaction with the map comprises one or more of inspection, searching, sampling, clustering, and analysis of the one or more proteins, protein-like molecules or fragments thereof or newly generated proteins, protein-like molecules or fragments thereof;
- receiving commands or detect interactions with the map by the tools at the visual map interface;
- and
- triggering an update to the visual map interface and the map based on the commands or interactions.
6 more elements
Dependencies are inferred from the claim text.