DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Claim 1 is a method which recites determining a query feature vector for the first molecular representation; determining a first centroid feature vector with a similarity to the query feature vector that satisfies a first predetermined similarity condition, the first centroid feature vector associated with a centroid of a first group of chemical structures; and searching a first subset of the chemical structure database to determine whether the first molecular representation is present in the first subset of the chemical structure database, the first subset of the chemical structure database comprising chemical structures of the chemical structure database associated with the first centroid feature vector.
In the context of the claims, the limitations of determining a query feature vector, determining a first centroid feature vector, and searching a first subset of the chemical structure database to determine are limitations that encompass a user reviewing data or information, considering or analyzing it and arriving at a decision or conclusion about it. Thus, the broadest reasonable interpretation is that those steps fall within the mental process groupings of abstract ideas because they cover concepts performed in the human mind, including observation, evaluation, judgment, and opinion. See MPEP 2106.04(a)(2) III. The claim recites an abstract idea.
This judicial exception is not integrated into a practical application. The claim recites the additional claim elements of receiving a query comprising a first molecular representation. The claim element is recited at a high level of generality and without any specificity regarding the step of receiving that it amounts to no more than mere data gathering. Consequently, the claim element is insignificant extra-solution activity. See MPEP 2106.05(g). The claim is directed to an abstract idea.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because as discussed above, the additional claim element amounts to no more than insignificant extra-solution activity. Further, given the broadest reasonable interpretation in light of the specification, the additional claim element encompasses merely receiving or transmitting data over a network. As such, it is well-understood, routine, conventional activity. See MPEP 2106.05(d). The claim is not patent eligible.
Claims 2-7 depend from claim 1 and recite the same abstract idea as claim 1. The additional claim limitations recited in claims 2-7 serve merely to either add additional steps to the abstract idea (claims 2-7) or add additional extra-solution activity (claim 5). That is the additional limitations of determining, searching and clustering cover concepts performed in the human mind, including observation, evaluation, judgment, and opinion. See MPEP 2106.04(a)(2) III. The additional claim element of receiving in claim 5 is recited at a high level of generality and without any specificity regarding the step of receiving that it amounts to no more than mere data gathering. Consequently, the claim element is insignificant extra-solution activity. See MPEP 2106.05(g). Further, given the broadest reasonable interpretation in light of the specification, it encompasses merely receiving or transmitting data over a network. As such, it is well-understood, routine, conventional activity. See MPEP 2106.05(d). The limitations recited in claims 2-7 neither integrate the abstract idea into a practical application nor amount to significantly more. The claims are not patent eligible.
Claim 8 is a method which recites determine a query feature vector for the first molecular representation; determine a first centroid feature vector with a similarity to the query feature vector that satisfies a first predetermined similarity condition, the first centroid feature vector associated with a centroid of a first group of chemical structures; and search a first subset of the chemical structure database to determine whether the first molecular representation is present in the first subset of the chemical structure database, the first subset of the chemical structure database comprising chemical structures of the chemical structure database associated with the first centroid feature vector.
In the context of the claims, the limitations of determine a query feature vector, determine a first centroid feature vector, and search a first subset of the chemical structure database to determine are limitations that encompass a user reviewing data or information, considering or analyzing it and arriving at a decision or conclusion about it. Thus, the broadest reasonable interpretation is that those steps fall within the mental process groupings of abstract ideas because they cover concepts performed in the human mind, including observation, evaluation, judgment, and opinion. See MPEP 2106.04(a)(2) III. The claim recites an abstract idea.
This judicial exception is not integrated into a practical application. The claim recites the additional claim elements a processor; and a memory device that stores program code structured to cause the processor to: receive a query comprising a first molecular representation. The claim elements of a processor and a memory device are recited at a high level of generality that it amounts to mor more than merely a computer used as a tool to perform generic computer functions. See MPEP 2106.05(f). The claim element receive a query is recited at a high level of generality and without any specificity such that it amounts to no more than mere data gathering. Consequently, the claim element is insignificant extra-solution activity. See MPEP 2106.05(g). The claim is directed to an abstract idea.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because as discussed above, the additional claim element amounts to no more than a computer used as a tool to perform generic computer functions or insignificant extra-solution activity. Further, given the broadest reasonable interpretation in light of the specification, the additional claim element receive a query encompasses merely receiving or transmitting data over a network. As such, it is well-understood, routine, conventional activity. See MPEP 2106.05(d). The claim is not patent eligible.
Claims 9-14 depend from claim 8 and recite the same abstract idea as claim 8. The additional claim limitations recited in claims 9-14 serve merely to either add additional steps to the abstract idea (claims 9-14) or add additional extra-solution activity (claim 12). That is the additional limitations of determine, search and cluster cover concepts performed in the human mind, including observation, evaluation, judgment, and opinion. See MPEP 2106.04(a)(2) III. The additional claim element of receive in claim 12 is recited at a high level of generality and without any specificity regarding the step of receiving that it amounts to no more than mere data gathering. Consequently, the claim element is insignificant extra-solution activity. See MPEP 2106.05(g). Further, given the broadest reasonable interpretation in light of the specification, it encompasses merely receiving or transmitting data over a network. As such, it is well-understood, routine, conventional activity. See MPEP 2106.05(d). The limitations recited in claims 9-14 neither integrate the abstract idea into a practical application nor amount to significantly more. The claims are not patent eligible.
Claim 15 is a method which recites determine a query feature vector for the first molecular representation; determine a first centroid feature vector with a similarity to the query feature vector that satisfies a first predetermined similarity condition, the first centroid feature vector associated with a centroid of a first group of chemical structures; and search a first subset of the chemical structure database to determine whether the first molecular representation is present in the first subset of the chemical structure database, the first subset of the chemical structure database comprising chemical structures of the chemical structure database associated with the first centroid feature vector.
In the context of the claims, the limitations of determine a query feature vector, determine a first centroid feature vector, and search a first subset of the chemical structure database to determine are limitations that encompass a user reviewing data or information, considering or analyzing it and arriving at a decision or conclusion about it. Thus, the broadest reasonable interpretation is that those steps fall within the mental process groupings of abstract ideas because they cover concepts performed in the human mind, including observation, evaluation, judgment, and opinion. See MPEP 2106.04(a)(2) III. The claim recites an abstract idea.
This judicial exception is not integrated into a practical application. The claim recites the additional claim elements A computer-readable storage medium comprising computer-executable instructions that, when executed by a processor, cause the processor to: receive a query comprising a first molecular representation. The claim elements of a processor and a computer-readable storage medium are recited at a high level of generality that it amounts to mor more than merely a computer used as a tool to perform generic computer functions. See MPEP 2106.05(f). The claim element receive a query is recited at a high level of generality and without any specificity such that it amounts to no more than mere data gathering. Consequently, the claim element is insignificant extra-solution activity. See MPEP 2106.05(g). The claim is directed to an abstract idea.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because as discussed above, the additional claim element amounts to no more than a computer used as a tool to perform generic computer functions or insignificant extra-solution activity. Further, given the broadest reasonable interpretation in light of the specification, the additional claim element receive a query encompasses merely receiving or transmitting data over a network. As such, it is well-understood, routine, conventional activity. See MPEP 2106.05(d). The claim is not patent eligible.
Claims 16-20 depend from claim 15 and recite the same abstract idea as claim 15. The additional claim limitations recited in claims 16-20 serve merely to either add additional steps to the abstract idea (claims 16-20) or add additional extra-solution activity (claim 19). That is the additional limitations of determine, search and cluster cover concepts performed in the human mind, including observation, evaluation, judgment, and opinion. See MPEP 2106.04(a)(2) III. The additional claim element of receive in claim 19 is recited at a high level of generality and without any specificity regarding the step of receiving that it amounts to no more than mere data gathering. Consequently, the claim element is insignificant extra-solution activity. See MPEP 2106.05(g). Further, given the broadest reasonable interpretation in light of the specification, it encompasses merely receiving or transmitting data over a network. As such, it is well-understood, routine, conventional activity. See MPEP 2106.05(d). The limitations recited in claims 16-20 neither integrate the abstract idea into a practical application nor amount to significantly more. The claims are not patent eligible.
Allowable Subject Matter
Claims 1-20 would be allowable if rewritten or amended to overcome the rejection(s) under 35 U.S.C. 101 set forth in this Office action.
The following is a statement of reasons for the indication of allowable subject matter:
The prior art fails to anticipate or render obvious determining a first centroid feature vector with a similarity to the query feature vector that satisfies a first predetermined similarity condition, the first centroid feature vector associated with a centroid of a first group of chemical structures; and searching a first subset of the chemical structure database to determine whether the first molecular representation is present in the first subset of the chemical structure database, the first subset of the chemical structure database comprising chemical structures of the chemical structure database associated with the first centroid feature vector, in combination with all limitations as claimed by Applicant.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure:
Hull et al. in Foreign Patent Document WO 00/62251 teaches “A novel extension of the vector space model for computing chemical similarity is described. The instant method uses, for example, the singular value decomposing (SVD, S130) of a molecule/chemical descriptor matrix (S120) to create a low dimensional representation of the original descriptor space” (Abstract).
Wang et al. in Non-Patent Literature “Application of kernel functions for accurate similarity search in large chemical databases” teaches “Similarity search in chemical structure databases is an important problem with many applications in chemical genomics, drug design, and efficient chemical probe screening among others. It is widely believed that structure based methods provide an efficient way to do the query. Recently various graph kernel functions have been designed to capture the intrinsic similarity of graphs. Though successful in constructing accurate predictive and classification models, graph kernel functions can not be applied to large chemical compound database due to the high computational complexity and the difficulties in indexing similarity search for large databases” (Abstract).
Nicolaou et al. in U.S. Patent 6,904,423 teaches “A system for analyzing a vast amount of data representative of chemical structure and activity information and concisely providing conclusions about structure-to-activity relationships. A computer may adaptively learn new substructure descriptors based on its analysis of the input data. The computer may then apply each substructure descriptor as a filter to establish new groups of molecules that match the descriptor. From each new group of molecules, the computer may in turn generate one or more additional new groups of molecules. A result of the analysis in an exemplary arrangement is a tree structure that reflects pharmacophoric information and efficiently establishes through lineage what effect on activity various chemical substructures are likely to have. The tree structure can then be applied as a multi-domain classifier, to help a chemist classify test compounds into structural subclasses.” (Abstract).
Kaufman et al. in U.S. Patent Publication 2026/0112455 teaches “A method for identifying compounds with threshold activity against a target macromolecule first generates multiple poses for each compound fragment in a plurality of compound fragments against an atomic model of the target macromolecule. This creates a collection of configurations, or a “pose set,” for the compound fragments. Each pose is associated with a subset of interaction features drawn from a broader set of such features. Each feature corresponds to a subregion of the target macromolecule's atomic model. Each pose is quantified by application to a physics model. This assigns a score to the interaction features associated with the poses. A binding hypothesis is formed for the macromolecule, using the collection of interaction features and their corresponding scores. From this hypothesis, derived compounds are identified. These derived compounds are tested for their activity against the macromolecule, leading to the identification of those that exhibit the desired threshold activity” (Abstract).
Oswald et al. in U.S. Patent Publication 2025/0384966 teaches “A plurality of instances of the molecular reaction is performed using synthons and normalized conditions. For each respective instance, at least a subset of the synthons is transformed using the molecular reaction, generating compounds. For each respective instance, a respective conversion value is obtained. A subset of instances is selected based on at least a threshold conversion value for the respective conversion value of each respective instance. The subset of instances is used to adjust one or more parameters in a plurality of parameters of the model, obtaining an updated plurality of parameters for the model. Using, subsequent to obtaining the updated plurality of parameters, the model to search for and identify an updated plurality of normalized conditions for the molecular reaction that collectively have an improved conversion value for the molecular reaction relative to the original plurality of normalized conditions” (Abstract).
Garcia et al. in U.S. Patent Publication 2024/0194299 teaches “Systems and methods of associating a test compound with a reference compound are provided. A fingerprint of a chemical structure of the test compound is obtained. Abundance values for a set of cellular constituents are also obtained, from one or more reference assays, across a plurality of cells that have been exposed to a control solution free of the test compound. The fingerprint and the abundance values are inputted into a model that outputs a predicted similarity between (i) a predicted perturbational effect of the test compound across the set of cellular constituents and (ii) a measured cell-based perturbational effect of the reference compound across the set of cellular constituents. When the predicted similarity achieves a threshold similarity, the test compound is associated with the reference compound.” (Abstract).
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/MI'SCHITA' HENSON/ Primary Examiner, Art Unit 2857
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