Patents by Inventor Peter Skopp
Peter Skopp has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Publication number: 20260268048Abstract: A predictive system may access a set of physical structures corresponding to a molecule. Each physical structure is representative of a configuration. The predictive system may encode the accessed physical structures to produce a set of encoded physical structures by encoding, for each accessed physical structure, a position of each constituent unit of the molecule within the accessed physical structure. The predictive system may train a machine-learned model using the encoded physical structures. The predictive system may retrain the machine-learned model by iteratively: accessing a set of two or more candidate physical structures, determining a force associated with a constituent unit in the molecule based on a relative energy associated with a plurality of neighboring positions for the constituent unit, obtaining ground truth force data, and comparing the force associated with the constituent unit determined by the machine-learned model to the ground truth force data.Type: ApplicationFiled: April 24, 2026Publication date: September 10, 2026Inventors: Paul Maragakis, Andreas Kraemer, James P. Roney, Peter Skopp
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Publication number: 20260260045Abstract: A predictive system may access a set of physical structures corresponding to a molecule. Each physical structure is representative of a configuration. The predictive system may encode the accessed physical structures to produce a set of encoded physical structures by encoding, for each accessed physical structure, a position of each constituent unit of the molecule within the accessed physical structure. The predictive system may train a machine-learned model using the encoded physical structures. The predictive system may retrain the machine-learned model by iteratively: accessing a set of two or more candidate physical structures, determining a first energy difference among the set of candidate physical structures, obtaining a second energy difference between a set of physical structures corresponding to the set of candidate physical structures using a method to calculate reference energy values.Type: ApplicationFiled: April 24, 2026Publication date: September 3, 2026Inventors: Paul Maragakis, Andreas Kraemer, James P. Roney, Peter Skopp
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Patent number: 12632623Abstract: A predictive system may access a set of physical structures corresponding to a physical system. Each physical structure representative of a configuration. The predictive system may encode the accessed physical structures to produce a set of encoded physical structures by encoding, for each accessed physical structure, a position of each constituent unit of the physical system within the accessed physical structure. The predictive system may train a machine-learned model using the encoded physical structures. The predictive system may retrain the machine-learned model by iteratively: accessing a set of two or more candidate physical structures, determining a first energy difference among the set of candidate physical structures, obtaining a second energy difference between a set of physical structures corresponding to the set of candidate physical structures using a method to calculate reference energy values.Type: GrantFiled: August 23, 2024Date of Patent: May 19, 2026Assignee: D. E. Shaw Research, LLCInventors: Paul Maragakis, Andreas Kraemer, James P. Roney, Peter Skopp
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Publication number: 20260073143Abstract: A system is disclosed for encoding a data string of a first modality into a hierarchical tokenized representation for processing by a text-based deep neural network (DNN) trained on a second modality. The data string comprises multiple units, each having one or more attributes. Each attribute is represented in the tokenized string as a sequence of hierarchical tokens, with a first hierarchical token encoding one or more most significant bits and a subsequent hierarchical token encoding one or more less significant bits. The DNN processes the data string bidirectionally, across the sequence of units and within the token hierarchy, to select tokens that capture attribute information. The selected hierarchical tokens output by the DNN from a representation of the original data string that preserves attribute detail while enabling cross-modal processing using models trained on text.Type: ApplicationFiled: November 18, 2025Publication date: March 12, 2026Inventors: Paul Maragakis, Andreas Kraemer, James P. Roney, Peter Skopp
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Publication number: 20260057148Abstract: A predictive system may access a set of physical structures corresponding to a physical system. Each physical structure representative of a configuration. The predictive system may encode the accessed physical structures to produce a set of encoded physical structures by encoding, for each accessed physical structure, a position of each constituent unit of the physical system within the accessed physical structure. The predictive system may train a machine-learned model using the encoded physical structures. The predictive system may retrain the machine-learned model by iteratively: accessing a set of two or more candidate physical structures, determining a first energy difference among the set of candidate physical structures, obtaining a second energy difference between a set of physical structures corresponding to the set of candidate physical structures using a method to calculate reference energy values.Type: ApplicationFiled: August 23, 2024Publication date: February 26, 2026Inventors: Paul Maragakis, Andreas Kraemer, James P. Roney, Peter Skopp
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Patent number: 12511482Abstract: A system is disclosed for encoding a data string of a first modality into a hierarchical tokenized representation for processing by a text-based deep neural network (DNN) trained on a second modality. The data string comprises multiple units, each having one or more attributes. Each attribute is represented in the tokenized string as a sequence of hierarchical tokens, with a first hierarchical token encoding one or more most significant bits and a subsequent hierarchical token encoding one or more less significant bits. The DNN processes the data string bidirectionally, across the sequence of units and within the token hierarchy, to select tokens that capture attribute information. The selected hierarchical tokens output by the DNN from a representation of the original data string that preserves attribute detail while enabling cross-modal processing using models trained on text.Type: GrantFiled: August 22, 2025Date of Patent: December 30, 2025Assignee: D. E. Shaw Research, LLCInventors: Paul Maragakis, Andreas Kraemer, James P. Roney, Peter Skopp
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Patent number: 12217834Abstract: Discovering molecules (which may be known or may never have been cataloged or ever synthesized) that have desired characteristics is addressed using a machine learning approach. As compared to a brute-force search of a database of known molecules, which may not be computationally feasible, the present machine learning approach renders identification of both known and unknown molecules computationally tractable. Furthermore, the computational effort is largely shifted to training of the machine learning system using a database of known molecules, and the generation of molecules to match any particular characteristics requires relatively little computation. The molecules using the present approach may be further studied, for example, with computer-based simulation or after physical synthesis using biological experimentation to ultimately yield useful chemical compounds.Type: GrantFiled: May 29, 2020Date of Patent: February 4, 2025Assignee: D. E. Shaw Research, LLCInventors: Paul Maragakis, Hunter Nisonoff, Peter Skopp, John Salmon
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Publication number: 20240296918Abstract: A machine-learning approach jointly generates molecular graphs and corresponding three-dimensional geometries, for example, for searching a chemical space of potential molecules with desired chemical properties. In some examples, molecules are generated incrementally by repeatedly adding atoms to a molecular graph as well as determining geometric (e.g., location) information for the added atoms until a complete molecule is generated. This incremental process can be stochastic enabling random sampling from a chemical space.Type: ApplicationFiled: September 28, 2022Publication date: September 5, 2024Inventors: James Peter Roney, Pavlos Maragkakis, Peter Skopp
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Publication number: 20220230713Abstract: Discovering molecules (which may be known or may never have been cataloged or ever synthesized) that have desired characteristics is addressed using a machine learning approach. As compared to a brute-force search of a database of known molecules, which may not be computationally feasible, the present machine learning approach renders identification of both known and unknown molecules computationally tractable. Furthermore, the computational effort is largely shifted to training of the machine learning system using a database of known molecules, and the generation of molecules to match any particular characteristics requires relatively little computation. The molecules using the present approach may be further studied, for example, with computer-based simulation or after physical synthesis using biological experimentation to ultimately yield useful chemical compounds.Type: ApplicationFiled: May 29, 2020Publication date: July 21, 2022Inventors: Paul Maragakis, Hunter Nisonoff, Peter Skopp, John Salmon
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Patent number: 6256739Abstract: A method and apparatus to determine user identity and limit access to a communications network. A first message containing user identity information is received from a client computer in accordance with a first protocol. A first network address is determined from the first message. A second message containing an information request is also received from the client in accordance with a second protocol, and a second network address is determined from the second message. The requesting user identity is then determined based on the first network address, the user identity information and the second network address. Based on the requesting user identity, it can be decided whether to grant the information request. If access is granted, the requested information is retrieved using the communications network.Type: GrantFiled: November 26, 1997Date of Patent: July 3, 2001Assignee: Juno Online Services, Inc.Inventors: Peter Skopp, Benjamin F. Vitale, Vinod R. Marur, Clifford S.C. Tse, Dharmender S. Dulai