DETAILED ACTION
Comments
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA . In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Information Disclosure Statement
The IDS of 7/14/2025 has been considered.
Election/Restrictions
Applicant's election with traverse of Species B in the reply filed on 12 January 2026 is acknowledged. The traversal is on the ground(s) that no explanation was given justifying the species election requirement. This is not found persuasive because each species of molecular graph analysis requires distinct physical and mathematical manipulations. Consequently, searching all three of the species would require an undue search burden.
The requirement is still deemed proper and is therefore made FINAL.
Claims 5-8 and 13-17 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected species, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 12 January 2026.
In view of further consideration, claim 4 is rejoined.
Claims 1-19 are pending in the application
Claims 1-4, 9-12, and 18-19 are examined in the instant Office action.
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitation(s) is/are: “first module” and “second module” in claims 2-3.
Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof.
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
Claim Rejections - 35 USC § 112(b) - Indefiniteness
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 2-3 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.
Claim limitations “first module” and “second module” invoke 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. The specification does not give structural support for the modules. Consequently, it is unclear as to the structure of the modules (e.g. hardware or software). For the purpose of examination, it is interpreted that the modules comprise hardware or software. Therefore, the claim is indefinite and is rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph.
Applicant may:
(a) Amend the claim so that the claim limitation will no longer be interpreted as a limitation under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph;
(b) Amend the written description of the specification such that it expressly recites what structure, material, or acts perform the entire claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(c) Amend the written description of the specification such that it clearly links the structure, material, or acts disclosed therein to the function recited in the claim, without introducing any new matter (35 U.S.C. 132(a)).
If applicant is of the opinion that the written description of the specification already implicitly or inherently discloses the corresponding structure, material, or acts and clearly links them to the function so that one of ordinary skill in the art would recognize what structure, material, or acts perform the claimed function, applicant should clarify the record by either:
(a) Amending the written description of the specification such that it expressly recites the corresponding structure, material, or acts for performing the claimed function and clearly links or associates the structure, material, or acts to the claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(b) Stating on the record what the corresponding structure, material, or acts, which are implicitly or inherently set forth in the written description of the specification, perform the claimed function. For more information, see 37 CFR 1.75(d) and MPEP §§ 608.01(o) and 2181.
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.
Claim(s) 1-4, 9-12, and 18-19 is/are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea/law of nature/natural phenomenon without significantly more. Claims 1-4 and 9-12 are drawn to methods, claim 18 is drawn to a system comprising a processor, and claim 19 is drawn to a non-transitory computer-readable storage medium.
In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1 : YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
The independent claims recite the mental step of specifying a plurality of molecular structures to perform chemical reaction prediction based on a user input received through a service page.
The independent claims recite the mental step of storing information on the plurality of molecular structures in a memory.
The independent claims recite the mental step of acquiring molecular graphs for the plurality of molecular structures by converting atoms into nodes and converting bonds between atoms into edges based on the plurality of molecular structures in the memory.
The independent claims recite the mental step of receiving a user query for the chemical reaction prediction related to the plurality of molecular structures through the service page.
The independent claims recite the mental step of processing the molecular graphs for the plurality of molecular structures as an input of a chemical reaction prediction model so that a chemical reaction corresponding to the user query is predicted.
The independent claims recite the mental step of performing the chemical reaction prediction on the plurality of molecular structures by the chemical reaction prediction model.
The independent claims recite the mental step of acquiring a product of the chemical reaction prediction for the plurality of molecular structures from the chemical reaction prediction model.
The independent claims recite generating an answer to the user query using the product of the chemical reaction prediction.
Claim 2 recites the mental steps of receiving molecular structures, predicting a graph-based chemical reaction, analyzing information related to the chemical reaction prediction related to the molecular structures from text data, and generating the product of the chemical reaction prediction.
Claim 3 recites the mental step of verifying the product of the chemical reaction prediction.
Claim 4 recites the mental steps of converting the Lewis molecular structure into a graph structure wherein nodes represent atoms and edges represent bonds.
Claim 9 recites the mental steps of acquiring an embedding vector corresponding to the molecular graphs, performing an attention operation related to an interaction related to the interactions between atoms, performing bond prediction and atom prediction predicted as a chemical reaction of the molecular structures using the updated embedding vector, and acquiring the product of the chemical reaction prediction predicted from the molecular structure.
Claim 10 recites the mental step of updating the embedding vector by adding different biases according to a bond type between the nodes included in the first molecular graph and the second molecular graph.
Claim 11 recites the mathematical limitations of performing a dot-product using the updated embedding vector and predicting atom properties of the atoms corresponding to the updated embedding vector using an atom property probability distribution.
Claim 11 recites the mental step of constraining the atom properties to include the charge state of atoms.
Claim 12 recites the mental step of corresponding the product of the reaction prediction to a final product stabilized through a diffusion feedback process.
These recitations are similar to the concepts of collecting information, analyzing it and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014)) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind or mathematical relationships. Therefore, these limitations fall under the “Mental process” and “Mathematical concepts” groupings of abstract ideas. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then if falls within the “Mental processes” grouping of abstract ideas. As such, claim(s) 1-4, 9-12, and 18-19 recite(s) an abstract idea/law of nature/natural phenomenon (Step 2A, Prong 1 : YES).
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). This judicial exception is not integrated into a practical application because the claims do not recite an additional element that reflects an improvement to technology or applies or uses the recited judicial exception to affect a particular treatment for a condition. Rather, the instant claims recite additional elements that amount to mere instructions to implement the abstract idea in a generic computing environment or mere instructions to apply the recited judicial exception via a generic treatment.
There are no limitations that indicate that the claimed analysis engine or the formats of the provided data require anything other than generic computing systems. As such, these limitations equate to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. As such, claims 1-4, 9-12, and 18-19 is/are directed to an abstract idea/law of nature/natural phenomenon (Step 2A, Prong 2 : NO).
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 claims recite additional elements that equate to mere instructions to apply the recited exception in a generic way or in a generic computing environment.
As discussed above, there are no additional limitations to indicate that the claimed analysis engine requires anything other than generic computer components in order to carry out the recited abstract idea in the claims. Claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. MPEP 2106.05(f) discloses that mere instructions to apply the judicial exception cannot provide an inventive concept to the claims. The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B : No). As such, claims 1-4, 9-12, and 18-19 is/are not patent eligible.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
35 U.S.C. 103 Rejection #1:
Claim(s) 1-4 and 18-19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Madrid et al. [WO 2019/156872 A1; on IDS] in view of Zhou et al. [Journal of Chemical Information and Modeling, 2021, pages 3668-3880; on IDS].
Claim 1 is drawn to a computerized method. The method comprises specifying a plurality of molecular structures to perform chemical reaction prediction based on a user input received through a service page. The method comprises storing information on the plurality of molecular structures in a memory. The method comprises acquiring molecular graphs for the plurality of molecular structures by converting atoms into nodes and converting bonds between the atoms into edges based on the plurality of molecular structures stored in the memory. The method comprises receiving a user query for the chemical reaction prediction related to the plurality of molecular structures through the service page. The method comprises processing the molecular graphs for the plurality of molecular structures as an input of a chemical reaction prediction model so that a chemical reaction corresponding to the user query is predicted. The method comprises performing the chemical reaction prediction on the plurality of molecular structures by the chemical reaction prediction model.
Claim 18 recites the algorithm of claim 1, but claim 18 is drawn to a system with processor.
Claim 19 recites the algorithm of claim 1, but claim 19 is drawn to a computer-readable storage medium.
The document of Madrid et al. studies computational generation of chemical synthesis routes and methods [title]. Figures 10-11 of Madrid et al. illustrate chemical reaction pathways with predicted products with a chemical reaction model. Figures 7-8 of Madrid et al. illustrate conversion of the chemical reactions in molecular structure form to chemical reactions models using molecular graphs with nodes and edges that result in a target predictions.
Madrid et al. does not teach that the model responds to queries.
The document of Zhou et al. studies question answering system for chemistry [title]. The abstract of Zhou et al. teaches a computer system that provides answer to questions using chemical data from knowledge graphs.
With regard to claims 2-3, paragraph 51 of Madrid et al. teaches using text to model chemical reactions. Figure 10-11 of Madrid et al. illustrate using molecular structures to model chemical reactions, thereby verifying any comparable reaction modeling using text data.
With regard to claim 4, Figures 10-11 of Madrid et al. illustrate chemical reaction pathways with predicted products with a chemical reaction model. Figures 7-8 of Madrid et al. illustrate conversion of the chemical reactions in molecular structure form to chemical reactions models using molecular graphs with nodes and edges that result in a target predictions.
It would have been obvious to someone of ordinary skill in the art at the time of the instant invention to modify the molecular modeling and prediction of chemical reactions of Madrid et al. by use of the question and answering of Zhou et al. wherein the motivation would have been that the questioning and answering of Zhou et al. provides a physical application of the molecular modeling of Madrid et al. [abstract of Zhou et al.]. There would have been a reasonable expectation of success of combining Madrid et al. and Zhou et al. because both studies analogously pertain to analysis of chemical data.
35 U.S.C. 103 Rejection #2:
Claim(s) 9 is/are rejected under 35 U.S.C. 103 as being unpatentable over Madrid et al. in view of Zhou et al. as applied to claims 1-4 and 18-19 above, in further view of Ma et al. [CN 111710375 A; on attached 892 form]. An English machine translation of Ma et al. is cited in the instant Office action.
Claim 9 recites embedding molecular graphs into vectors and then updating the vectors. The claim recites using the embedding vector as a tool to predict target structures.
The documents of Madrid et al. and Zhou et al. make obvious a query answering system using chemical reaction prediction models, as discussed above.
Madrid et al. and Zhou et al. do not teach using embedding vectors to analysis results.
The document of Ma et al. studies a molecular property prediction method [title]. Page 4 of Ma et al. teaches a preliminary prediction model updated to a final prediction model. Pages 5-6 of Ma et al. teach embedding molecules into vectors for further analysis.
It would have been obvious to someone of ordinary skill in the art at the time of the instant invention to modify the molecular modeling and prediction of chemical reactions of Madrid et al. and the question and answering of Zhou et al. by use of embedding chemical data into vectors as in Ma et al. wherein the motivation would have been using vectors mathematically facilitates the analysis of molecular data [pages 5-6 of Ma et al.]. There would have been a reasonable expectation of success of combining Madrid et al., Zhou et al., and Ma et al. because all three studies analogously pertain to analysis of chemical data.
E-mail Communications Authorization
Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting the following statement via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300):
Recognizing that Internet communications are not secure, I hereby authorize the USPTO to communicate with the undersigned and practitioners in accordance with 37 CFR 1.33 and 37 CFR 1.34 concerning any subject matter of this application by video conferencing, instant messaging, or electronic mail. I understand that a copy of these communications will be made of record in the application file.
Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03.
Conclusion
No claim is allowed.
Claim 10-12 are free of the prior art because the claims recite mathematical and structural manipulations of the molecular graphs and involving the diffusion feedback process in the data analysis that are not in the prior art.
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Russell Negin, whose telephone number is (571) 272-1083. This Examiner can normally be reached from Monday through Thursday from 8 am to 3 pm and variable hours on Fridays.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner’s Supervisor, Larry Riggs, Supervisory Patent Examiner, can be reached at (571) 270-3062.
/RUSSELL S NEGIN/
Primary Examiner, Art Unit 1686 18 February 2026