DETAILED ACTION
Applicant’s response, filed 02 October 2025, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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 Status
Claims 1, 2, 4, and 21-34 are pending.
Claims 21-24 are withdrawn from consideration.
Claims 1, 2, 4, and 25-34 are examined herein.
Claims 1, 2, 4, and 25-34 are rejected.
Election/Restrictions
Claims 21-24 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected Group II, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 18 November 2022.
Priority
Claims 1, 2, 4, and 25-34 are not granted the claim to the benefit of priority to U.S. Provisional application 62/817344, 62/821230, and 62/962097 filed 12 March 2019, 20 March 2019, and 16 January 2020 respectively. Claims 1, 2, 4, and 25-34 are not granted the claim to the benefit of priority because the U.S. Provisional applications do not describe “wherein: the one or more molecular-orbital based features comprise: (i) a first correlation energy of a diagonal pair of molecular orbitals… (ii) a second correlation energy of an off-diagonal pair of molecular orbitals…”. Thus, the effective filling date of claims 1, 2, 4, and 25-34 is 12 March 2020.
Claim Interpretation
Claim 1 recites “(i) a first correlation energy of a diagonal pair of molecular orbitals predicted by a first neural network” and “(ii) a second correlation energy of an off-diagonal pair of molecular orbitals predicted by a second neural network” which are interpreted as product by process limitations defining the process in which a first correlation energy and second correlation energy (the products) are predicted but does not require predicting these correlation energies with a first and second neural network.
Claim 4 recites “wherein the machine learning model is trained to learn relationships between sets of molecular-orbital-based features and molecular system properties using a training dataset describing a plurality of molecular systems and their molecular system properties” which are interpreted as product by process limitations defining the process in which a the machine learning model (product) is trained but does not require an active step of training.
Claim Rejections - 35 USC § 112
The rejection on the ground of 112/b of claims 1, 3, and 17-19 for reciting “satisfies at least one criterion” in Office action mailed 02 June 2025 is withdrawn in view of the amendment received 02 October 2025.
The rejection on the ground of 112/b of claims 1-20 pertaining to the MOB-ML model predictions in Office action mailed 02 June 2025 is withdrawn in view of the amendment received 02 October 2025.
The rejection on the ground of 112/a scope of enablement of claim 16 in Office action mailed 02 June 2025 is withdrawn in view of the amendment which cancels claim 16 received 02 October 2025.
The rejection on the ground of 112/a written description of claims 1-20 for an inadequate written description a machine learning model that determines binding affinity based on predicted correlation energies in Office action mailed 02 June 2025 is withdrawn in view of the amendment of “using a machine learning process to map molecular-orbital-based features of the quantum chemical representations to molecular systems using a feature-to-structure map” in claim 1 received 02 October 2025.
The rejection on the ground of 112/a written description of claims 1-20 for reciting “wherein the molecular system comprises the molecule and a protein” in Office action mailed 02 June 2025 is withdrawn in view of the amendment to claim 1 received 02 October 2025 and in view of further consideration of the instant disclosure which inherently discloses a molecular system comprising a molecule and a protein (instant disclosure [0023]).
35 U.S.C. 112(a) New Matter
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1, 2, 4, and 25-34 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
This rejection is newly recited and necessitated by claim amendment.
Claim 1 recites “wherein: the one or more molecular-orbital based features comprise: (i) a first correlation energy of a diagonal pair of molecular orbitals… (ii) a second correlation energy of an off-diagonal pair of molecular orbitals…”. There is not an adequate written description of utilizing a first correlation energy (or a second correlation energy) as molecular-orbital based features. The instant disclosure only shows correlation energies in the context of a property of a molecular system which is predicted/outputted by a machine learning model utilizing molecular-orbital based features (instant disclosure [0079] and [0092]), but does not disclose these correlation energies are used as molecular-orbital features themselves (which are used as inputs to machine learning models). Thus, the limitation of “wherein: the one or more molecular-orbital based features comprise: (i) a first correlation energy of a diagonal pair of molecular orbitals… (ii) a second correlation energy of an off-diagonal pair of molecular orbitals…” constitutes as new matter because there is no disclosure of utilizing a first correlation energy (or second correlation energy) as input (i.e., molecular-orbital-based features) in a machine learning process. Dependent claims 2, 4, and 25-34 are rejected by virtue of their dependency on a rejected claim without alleviating the issue.
35 U.S.C. 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1, 2, 4, and 25-34 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
The rejections below are newly recited and necessitated by claim amendment.
Claim 1 recites “outputting… the specified property” and claim 33 recites “the specified property” which renders the metes and bounds of the claim indefinite. The indefiniteness arises because it is unclear which specified property of the “at least one specified molecular property” “the specified property” is referring to or if these limitations are meant to output the at least one property. Dependent claims 2, 4, 25-32, and 34 are rejected by virtue of their dependency on a rejected claim without alleviating the indefiniteness. For the sake of furthering examination, these limitations will be interpreted as “the at least one specified molecule property”.
Claims 32 and 34 recite “the molecular system” which renders the metes and bounds of the claims indefinite. The indefiniteness arises because it is unclear if “the molecular system” is referring to a molecular system of the online databases or the molecular system comprising the specified property. For the sake of furthering examination, these limitations will be interpreted as referring to the molecular system comprising the specified property.
Claim 34 recites the limitation “the protein” in lines 1-2 of the claim. There is insufficient antecedent basis for this limitation in the claim. The indefiniteness arises because the claim does not make clear what “the protein” is. It is further unclear if “the molecule” is referring to the molecule of “an inverse molecule design process” or one of the molecules of the “two molecules”. This rejection could be overcome by amendment of “the protein” to and “a protein”. For the sake of furthering examination “the protein” will be interpreted as “a protein” and that this protein and this molecule further limits one of the molecules of the molecular system property which comprises a binding affinity between two molecules.
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, 2, 4, and 25-34 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
Any newly recited portions of the rejection below are necessitated by claim amendment.
(Step 1)
Claims 1, 2, 4, and 25-34 fall under the statutory category of a process.
(Step 2A Prong 1)
Under the BRI, the instant claims recite judicial exceptions that are an abstract idea of the type that is in the grouping of a “mental process”, such as procedures for evaluating, analyzing or organizing information, and forming judgement or an opinion. Along with abstract ideas of the type that is in the grouping of a “mathematical concept”, such as mathematical relationships and mathematical equations.
Independent claim 1 recites a mathematical concept of “using a machine learning process to map molecular-orbital-based features of the quantum chemical representations to molecular systems using a feature-to-structure map”.
Independent claim 1 recites a mental process of “searching the mapped feature space for one or more molecular-orbital-based features comprising at least one specified molecular system property to identify a molecular system comprising the at least one specified property wherein the one or more molecular-orbital-based features comprise… and the at least one molecular system property comprises…”.
The claims recite steps of evaluating/analyzing data and making observations from data as searching the mapped feature space for one or more molecular-orbital-based features. The human mind is capable of evaluating/analyzing data and making observations from data. The claims recite steps that fall under mathematical calculations as “using a machine learning process to map molecular-orbital-based features of the quantum chemical representations to molecular systems using a feature-to-structure map”. Dependent claims 2, 4, 25-29, and 34 further limit the mental process/mathematical concept recited in the claims but do not change their nature as a mental process/mathematical concept.
(Step 2A Prong 2)
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). Integration into a practical application is evaluated by identifying whether there are any additional elements recited in the claim and evaluating those additional elements to determine whether they integrate the exception into a practical application.
The additional element in claims 1 of using a generic computer to perform judicial exceptions to perform judicial exceptions does not integrate the judicial exception into a practical application because this is simply applying the judicial exception to a generic computer without an improvement to computer technology (see MPEP 2106.04(1)). This additional element only interacts with the judicial exceptions by utilizing a computer as a tool to perform the judicial exceptions.
The additional element in claim 1 of outputting a representation of the molecular system comprising the specified property and the additional element in claims 33 of wherein outputting the representation of the molecular system comprising the specified property comprises outputting a plurality of representations of a plurality of molecular systems comprising the specified property do not integrate the judicial exceptions into a practical application because this step is insignificant extra solution activity of outputting data in a computer environment. It is noted that the content of the data being outputted does not change the active step of outputting data in a computer environment and the content of the data is part of the abstract idea.
The additional element in claim 1 of obtaining, using a processor, one or more online databases comprising quantum chemical representations of molecular systems (i.e., receiving data), the additional element in claim 30 wherein the one or more online databases comprise SQL databases, and the additional element in claim 31 wherein the one or more online databases comprise no-SQL databases does not integrate the judicial exception into a practical application because this is adding insignificant extra solution activity of data gathering. This additional element only interacts with the judicial exceptions in a manner that provides data to be processed/analyzed by the judicial exception. It is noted that the content of the data being received does not change the active step of receiving data in a computer environment and the content of the data is part of the abstract idea.
The additional element in claim 32 of synthesizing a molecular system does not integrate the judicial exception into a practical application because this step constitutes as mere instructions to apply the exception. This synthesis step constitutes as mere instructions to apply the judicial exception because it is reciting only a solution or outcome without details of how it is accomplished (see MPEP 2106.05(f)). Further this synthesis step constitutes as mere instructions to apply the judicial exceptions due to the generality of the application of the judicial exception by not providing details for synthesizing the molecule (see MPEP 2106.05(f)).
Thus, the additional elements do not integrate the judicial exceptions into a practical application and claims 1, 2, 4, and 25-34 are directed to the abstract idea.
(Step 2B)
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because:
The additional element in claims 1 of using a generic computer to perform judicial exceptions/mere instructions to apply the exception to a generic computer is conventional see MPEP 2106.05(b) and 2106.05(d)(II).
The additional element in claims 1 of obtaining, using a processor, one or more online databases comprising quantum chemical representations of molecular systems (i.e., receiving data), the additional element in claim 1 of outputting a representation of the molecular system comprising the specified property (i.e., outputting data), the additional element in claim 30 wherein the one or more online databases comprise SQL databases, and the additional element in claim 31 wherein the one or more online databases comprise no-SQL databases, and the additional element in claims 33 of wherein outputting the representation of the molecular system comprising the specified property comprises outputting a plurality of representations of a plurality of molecular systems comprising the specified property is conventional see MPEP 2106.05(b) and 2106.05(d)(II). It is noted that the type of database is recited generally and does not change the active step of receiving data in a computer environment. It is further noted that the content of the data being received (or outputted) does not change the active step of receiving data (or outputting data) in a computer environment and the content of the data is part of the abstract idea.
The additional element in claims 32 of synthesizing a molecule is conventional as shown by Zubay. (Annu Rev Genet. 1973;7:267-87; previously cited) and Wilson et al. (J Org Chem. 2006 Oct 27;71(22):8329-51; previously cited). Zubay reviews synthesizing proteins in microbial systems. Wilson reviews synthesizing small molecules that have potential pharmaceutical value.
Thus, the additional elements do not amount to significantly more than the judicial exception because they are conventional.
Response to Arguments
Applicant's arguments filed 02 October 2025 have been fully considered but they are not persuasive.
Applicant argues claim 1 does not recite a mental process because the steps of “obtaining, using a processor, one or more online databases…”, “using a machine learning process to map molecular-orbital-based features…”, “searching a mapped feature space for one or more molecular-orbital-based features…”, and “outputting a representation of the molecular system…” requires a computer system and these limitations cannot be practically be performed in the human mind or with pen and paper (Reply p. 3-4).
This argument has been fully considered but found to be not persuasive. The MPEP states at 2106.04(a)(2)(III)(C) “Claims can recite a mental process even if they are claimed as being performed on a computer”. It is noted that “searching a mapped feature space for one or more molecular-orbital-based features…” is the only limitation identified as reciting a mental process because this limitation encompasses analyzing data and making observations on data produced by using the machine learning process. Although the claims recite the use of a computer it is used as a tool to perform the mental process of searching through produced abstract data (such as numerical data) which the human mind can practically perform.
Applicant argues that none of the features of claim 1 recite a mathematical relationship or formula. While certain features may be determined or predicted using a mathematical formula, those features are “merely based on or involves a mathematical concept and do not integrate or recite any mathematical relationship or equations into the claims (Reply p. 4).
This argument has been fully considered but found to be not persuasive. The MPEP states at 2106.04(a)(2)(I)(C) “There is no particular word or set of words that indicates a claim recites a mathematical calculation. That is, a claim does not have to recite the word "calculating" in order to be considered a mathematical calculation. For example, a step of "determining" a variable or number using mathematical methods or "performing" a mathematical operation may also be considered mathematical calculations when the broadest reasonable interpretation of the claim in light of the specification encompasses a mathematical calculation”. The BRI of using a machine learning process to map molecular-orbital-based features of the quantum chemical representations to molecular systems using a feature to structure map (claim 1) in light of the specification encompasses a mathematical calculation which intakes numerical values describing molecular-orbital-based features (i.e., correlation energies) (instant disclosure [0021]) to calculate numerical values which represent a molecular system structure (such as a attributed graph with values describing nodes and edges of the graph) (instant disclosure [0116]-[0117]). Therefore, the BRI in light of the specification this limitation recites a mathematical calculation.
Conclusion
No claims are allowed.
Claims 1, 2, 4, and 21-34 are free of the prior art for the reasons discussed in the Office action mailed 15 February 2024.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/J.E.H./Examiner, Art Unit 1685
/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685