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.
Even though the claims recite judicial exceptions, the core limitations of the claims involve analysis of chemical molecules using neural networks, which are too complex to be performed in the human mind. Consequently, the claims are subject matter eligible.
Election/Restrictions
Applicant’s election without traverse of Species X in the reply filed on 12 June 2026 is acknowledged.
Claims 28-31, 52, and 54 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 12 June 2026.
Claims 21-54 are pending in the application.
Claims 21-27, 32-51, and 53 are examined in the instant Office action.
Information Disclosure Statements
The IDSs filed have been considered.
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 36-40 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.
While claim 36 recites a neural network specifically for updating nodes and a different neural network for updating edges, it is unclear as to the metes and bounds of having neural networks specific to nodes or edges because coordinates and sizes of nodes and edges are linked. In other words, updating the size and/or location of an edge affects coordinates of an attached node, and updating the coordinates and/or size of a node affects an attached edge.
Claim Rejections - 35 USC § 112(a) - Enablement
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 36-40 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 enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
1. While claim 36 recites a neural network specifically for updating nodes and a different neural network for updating edges, it is not understood as to how to have neural networks specific to nodes or edges because coordinates and sizes of nodes and edges are linked. In other words, updating the size and/or location of an edge affects coordinates of an attached node, and updating the coordinates and/or size of a node affects an attached edge.
2. While paragraph 214 of the specification has possession of this limitation, the specification does not teach how updating nodes does not affect attached edges and updated edges does not affect attached nodes.
3. The prior art of Lim et al. [Journal of Cheminformatics, volume 10, July 2018, 9 pages] teaches that the nodes and edges of a structure interact, and that neural networks that update edges also update nodes (e.g. Figures 3-6 of Lim et al.).
4. The claims and specification do not teach how updating edges and nodes are independent. The prior art of Lim et al. teaches that neural networks that update nodes also update edges. In absence of guidance of how to update nodes and edges of a chemical structure independently, such a neural network meeting these requirements would function unpredictably. Such unpredictability yields UNDUE EXPERIMENTATION.
In view of the above, it is the Examiner’s position that with the insufficient guidance and working examples and in view of unpredictability and the state of art, one of skill in the art could not make and/or use the invention with the claimed breadth without an undue amount of experimentation.
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.
Claim(s) 21-27, 32-35, 41-51, and 53 is/are rejected under 35 U.S.C. 103 as being unpatentable over Matsumura et al. [US PGPUB 2018/0018408 A1] in view of Lim et al. [Journal of Cheminformatics, volume 10, July 2018, 9 pages] as evidenced by Tehrany et al. [Journal of Food Engineering, volume 64, 2004, pages 315-320].
Claim 21 is drawn to an inferring device. The inferring device comprises storage devices and one or more processors. The processors are configured to input information of a plurality of atoms into a neural network capable of processing a graph. The processors are configured to infer a physical property of the plurality of atoms via the neural network.
Claim 43 is drawn to similar subject matter as claim 21, except claim 43 is drawn to a method.
Claim 51 is drawn to the subject matter of claim 43 with the additional limitation comprising calculating an error and backpropagating the error to update parameters of the neural network.
Claim 53 is drawn to the subject matter of claim 21 with the additional limitation comprising calculating an error and backpropagating the error to update parameters of the neural network.
The document of Matsumura et al. studies a material generation apparatus and method [title]. Figure 1 of Matsumura et al. illustrates the computer limitations of the claims. Figure 19 of Matsumura et al. teaches inputting a molecular structure comprising atoms into a neural network. Paragraphs 86 and 96 of Matsumura et al, suggest inferring physical properties from the processed data. Paragraph 112 of Matsumura et al. suggests updating the machine learning model with corrections.
However, Matsumura et al. only suggests inferring physical properties from the processed data.
The document of Lim et al. studies a molecular generative model based on conditional variational autoencoder for de novo molecular design [title]. Figure 1 on page 3 of Lim et al. teaches inputting a molecular structure into a neural network to update structure data and obtain a physical property. The paragraph bridging pages 2 and 3 of Lim et al. teaches that physical properties comprise MW, logP, and TPSA.
With regard to claim 22-27, 32-35, and 44-48, Figure 2 of Matsumura et al. teaches a three dimensional representation of atomic positions, angles formed between atoms, kinds of atoms, boundary conditions (i.e. the dimensions of the lattice box), a focused atom (i.e. atom1), and a preliminary graph of the atomic structure of the molecule (i.e. atoms are nodes and bonds are edges). Figure 19 of Matsumura et al. teaches inputting these features into a neural network. The abstract of Lim et al. teaches analysis of the vectors of Figure 2 of Matsumura et al. in latent space. Figure 2 of Matsumura et al. is interpreted to correspond to a coordinate system using an invariant representation
With regard to claims 41-42 and 49-50, the paragraph bridging pages 2 and 3 of Lim et al. teaches that physical properties comprise MW, logP, and TPSA. It is evident from the first equation on page 315 of Tehrany et al. that the partition coefficient of a compound (i.e. logP) is a measure of a change in Gibbs free energy of the compound between two phases of liquid. Paragraph 84-90 of Matsumura et al. teach differentiating magnetic forces on the compounds on an atomic basis.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the analysis of the atomic structure of a molecule in a neural network of Matsumura et al. to product a physical property as in Lim et al. wherein the motivation would have been that producing the physical property alongside an updated molecular structure gives a biophysical application to the understanding of the compound [Figures 1-6 of Lim et al.]. There would have been a reasonable expectation of success in combining Matsumura et al. and Lim et al. because both studies are analogously appliable to analysis of data resulting from inputting molecular structures into neural networks.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Double Patent Rejection #1:
Claims 21, 41, 43, and 49 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 8, 13, and 18, respectively, of copending Application No. 18/533,469 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously applicable to inputting a molecular structure into a neural network and analysis of the resultant data for property or force deduction. While the claims of ‘469 recite more limitations than the instantly rejected claims, the claims of ‘469 anticipate the instantly rejected claims.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Double Patent Rejection #2:
Claims [22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 42, or 53], and [44, 45, 46, 47, 48, 50, or 51] are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 13, respectively, of copending Application No. 18/533,469 (reference application) in view of Matsumura et al. in view of Lim et al. Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously applicable to inputting a molecular structure into a neural network and analysis of the resultant data for property or force deduction. The claims of ‘469 do not teach all of the limitations of the instantly rejected claims.
With regard to claim 22-27, 32-35, and 44-48, Figure 2 of Matsumura et al. teaches a three dimensional representation of atomic positions, angles formed between atoms, kinds of atoms, boundary conditions (i.e. the dimensions of the lattice box), a focused atom (i.e. atom1), and a preliminary graph of the atomic structure of the molecule (i.e. atoms are nodes and bonds are edges). Figure 19 of Matsumura et al. teaches inputting these features into a neural network. The abstract of Lim et al. teaches analysis of the vectors of Figure 2 of Matsumura et al. in latent space. Figure 2 of Matsumura et al. is interpreted to correspond to a coordinate system using an invariant representation
With regard to claims 41-42 and 49-50, the paragraph bridging pages 2 and 3 of Lim et al. teaches that physical properties comprise MW, logP, and TPSA. It is evident from the first equation on page 315 of Tehrany et al. that the partition coefficient of a compound (i.e. logP) is a measure of a change in Gibbs free energy of the compound between two phases of liquid. Paragraph 84-90 of Matsumura et al. teach differentiating magnetic forces on the compounds on an atomic basis.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the analysis of the atomic structure of a molecule in a neural network of the claims of ‘469 by use of the structural analysis of Matsumura et al. wherein the motivation would have been that Matsumura et al. adds additional structural data to facilitate the machine learning analysis [Figure 2 of Matsumura et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the analysis of the atomic structure of a molecule in a neural network of the claims of ‘469 and Matsumura et al. to product a physical property as in Lim et al. wherein the motivation would have been that producing the physical property alongside an updated molecular structure gives a biophysical application to the understanding of the compound [Figures 1-6 of Lim et al.]. There would have been a reasonable expectation of success in combining the claims of ‘469, Matsumura et al., and Lim et al. because all three studies are analogously appliable to analysis of data resulting from inputting molecular structures into neural networks.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
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.
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 24 September 2026
Prosecution Insights