DETAILED ACTION
Applicant' s response, filed 02 July 2026, 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, 3-8, 10, 11, 13, 16-19, and 21-26 are pending and examined herein.
Claims 18, 19, and 21-26 are rejected.
Claims 1, 3-8, 10, 11, 13, 16, and 17 are allowed.
Priority
Claims 1, 3-8, 10, 11, 13, 16-19, and 21-26 are granted the claim to the benefit of priority to U.S. Provisional application 63/803471 filed 09 May 2025, PCT/US2025/031891 filed 02 June 2025 which claims benefit of 63/655575 filed 03 June 2024. Thus, the effective filling date of claims 1, 3-8, 10, 11, 13, 16-19, and 21-26 is 03 June 2024.
Drawings
The replacement drawings received 02 July 2026 are accepted. The objection to the drawings received 29 December 2025 in Office action mailed 07 April 2026 is withdrawn in view of the replacement drawings received 02 July 2026.
Claim Objections
The objection of claims 4 in Office action mailed 07 April 2026 is withdrawn in view of the amendment of “at least one neural network” received 02 July 2026.
Claim Interpretation
Claim 13 recites “wherein the machine learning model is trained using a two-step process including: pre-training the machine learning model using training data, and fine-tuning the machine learning model using additional strain-specific-specific data, wherein the training data is a larger data set compared to the strain specific data” which is a product by process limitation (see MPEP 2113(I)) which does not require an active step of the method of training the machine learning model in this manner.
Claim Rejections - 35 USC § 112
The rejection on the ground of 112/b of claims 3-8 for claim 3 reciting “the generating comprises…” in Office action mailed 07 April 2026 is withdrawn in view of the amendment of “wherein generating the set of embeddings based on the information identifying the set of genetic edits comprises…” received 02 July 2026.
The rejection on the ground of 112/b of claim 5 for reciting “wherein the one or more embedding models include two or more of, a GenePT model, a Proteinfer model, a pFBA-PCA model, or a GO-PCA model” in Office action mailed 07 April 2026 is withdrawn in view of the amendment of “wherein the one or more embedding models include a plurality of embedding models” received 02 July 2026.
The rejection on the ground of 112/b of claim 6 for reciting “wherein each token of the set of embeddings…” in Office action mailed 07 April 2026 is withdrawn in view of the amendment of “wherein each embedding of the set of embeddings corresponds to an edit from the set of genetic edits” received 02 July 2026.
The rejection on the ground of 112/b of claim 7 for reciting “wherein generating the set of embeddings occurs at prediction time” in Office action mailed 07 April 2026 is withdrawn in view of the amendment of “wherein generating the set of embeddings occurs after training of the machine learning model” received 02 July 2026.
The rejection on the ground of 112/b of claim 8 for reciting “wherein generating the set of embeddings occur prior to training, the method further comprising caching the generated embeddings for later use at prediction time” in Office action mailed 07 April 2026 is withdrawn in view of the amendment of “wherein generating the set of embeddings occurs prior to training the machine learning model, and the method further comprises…” received 02 July 2026.
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 18, 19, and 21-26 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.
Claims 18 recites “A system comprising: one or more computers; and one or more storage devices communicatively coupled to the one or more computers, wherein the one or more storage devices store instructions that, when executed by the one or more computers, cause the one or more computers to perform operations comprising… automatically adjusting one or more operational parameters of a bioreactor to establish the second fermentation environment for fermenting the edited biological strain” and claim 19 recites “One or more non-transitory computer storage media storing instructions that when executed by one or more computers cause the one or more computers to perform operations comprising… automatically adjusting one or more operational parameters of a bioreactor to establish the second fermentation environment for fermenting the edited biologic strain” which renders the metes and bounds of the claims indefinite. The indefiniteness in claim 18 arises because it is unclear if “automatically adjusting one or more operational parameters of a bioreactor to establish the second fermentation environment for fermenting the edited biological strain” is meant to mean that updated operational parameters are transmitted to a bioreactor or if this limitation is meant to mean that the system itself includes a bioreactor which is automatically adjusted to establish the second fermentation environment with one or more operational parameters. Further the indefiniteness in claim 19 arises because it is unclear if “automatically adjusting one or more operational parameters of a bioreactor to establish the second fermentation environment for fermenting the edited biological strain” is meant to mean that updated operational parameters are transmitted to a bioreactor or if this limitation is meant to meant that the instructions stored on the one or more non-transitory computer storage media include instructions for controlling a bioreactor by adjusting operational parameters of the bioreactor itself. Dependent claims 21-26 are rejected by virtue of their dependency on rejected claims without alleviating the indefiniteness. For the sake of furthering examination, claim 18 will be interpreted that the system itself includes a bioreactor which is automatically adjusted to establish the second fermentation environment with one or more operational parameters and claim 19 will be interpreted as the instructions stored on the one or more non-transitory computer storage media include instructions for controlling a bioreactor by adjusting operational parameters of the bioreactor itself.
Examiners Comment
The above 112/b rejection may be overcome with an amendment to claim 18 of “A system comprising: one or more computers; a bioreactor; and one or more storage devices communicatively coupled to the one or more computers, wherein the one or more storage devices store instructions that, when executed by the one or more computers, cause the one or more computers to perform operations comprising…” and an amendment to claim 19 of “One or more non-transitory computer storage media storing instructions that when executed by a system comprising one or more computers and a bioreactor cause the system to perform operations comprising…”.
Claim Rejections - 35 USC § 101
The rejection on the ground of 101 of claims 1-20 in Office action mailed 07 April 2026 is withdrawn in view of the amendment of “determining that the performance prediction for the edited biological strain in the second fermentation environment satisfies a performance threshold and automatically adjusting one or more operational parameters of a bioreactor to establish the second fermentation environment for fermenting the edited biological strain” received 02 July 2026. The amendment provides an additional element which integrates the judicial exceptions into a practical application by providing a particular machine (i.e., a bioreactor) which is integral to achieve performance of the claimed method, the claimed system is particular machines which include a bioreactor, and the claimed non-transitory medium holding instructions which when executed causes a system which is a particular machine (i.e., a system including one or more computers and a bioreactor) to perform operations. Thus, the claims are patent eligible.
Claim Rejections - 35 USC § 103
The rejection on the ground of 103 of claims 1-9, 11-13, and 16-20 as being unpatentable over Cui et al. (Nat Methods 21, 1470–1480 (2024); previously cited) in view of Zamft et al. (US 20220301658 A1; previously cited) in Office action mailed 07 April 2026 is withdrawn in view of the amendments of “receiving information identifying a set of genetic edits defining an edited biologic strain and assay data characterizing, for each of a plurality of first fermentation environments: (i) a set of fermentation conditions of the first fermentation environment, and (ii) a performance of the edited biologic strain in the first fermentation environment”, “generating, using a machine learning model, a performance prediction… by inputting to the machine learning model a model input comprising: (i) the set of embeddings characterizing the set of genetic edits, (ii) the assay data characterizing performance of the edited biologic strain in each of the plurality of first fermentation environments, and (iii) data identifying a set of fermentation conditions of the second fermentation environment”, “determining that the performance prediction for the edited biologic strain in the second fermentation environment satisfies a performance threshold”, and “automatically adjusting one or more operational parameters of a bioreactor to establish the second fermentation environment for fermenting the edited biologic strain” received 02 July 2026.
The rejection on the ground of 103 of claims 10 as being unpatentable over Cui et al. in view of Zamft et al. as applied to claim 9 above, and further in view of Rosen et al. (BioRxiv (2023): 2023-11; previously cited) in Office action mailed 07 April 2026 is withdrawn in view of the amendments identified above received 02 July 2026.
The rejection on the ground of 103 of claims 14 and 15 as being unpatentable over Cui et al. in view of Zamft et al. as applied to claim 9 above, and further in view of Zhang et al. (Nature Machine Intelligence 5.10 (2023): 1066-1075. (Year: 2023); previously cited) in Office action mailed 07 April 2026 is withdrawn in view of the amendments identified above received 02 July 2026.
Double Patenting
The provisional rejection on the ground of nonstatutory double patenting of claims 1-20 as being unpatentable over claims 1-6, 8, 10-13, 16, 19, and 20 of copending Application No. 19/338517 (reference application) (referred to as application ‘517 herein) in Office action mailed 07 April 2026 is withdrawn in view of the amendments of “receiving information identifying a set of genetic edits defining an edited biologic strain and assay data characterizing, for each of a plurality of first fermentation environments: (i) a set of fermentation conditions of the first fermentation environment, and (ii) a performance of the edited biologic strain in the first fermentation environment”, “generating, using a machine learning model, a performance prediction… by inputting to the machine learning model a model input comprising: (i) the set of embeddings characterizing the set of genetic edits, (ii) the assay data characterizing performance of the edited biologic strain in each of the plurality of first fermentation environments, and (iii) data identifying a set of fermentation conditions of the second fermentation environment”, “determining that the performance prediction for the edited biologic strain in the second fermentation environment satisfies a performance threshold”, and “automatically adjusting one or more operational parameters of a bioreactor to establish the second fermentation environment for fermenting the edited biologic strain” received 02 July 2026.
The provisional rejection on the ground of nonstatutory double patenting of claims 1-20 as being unpatentable over claims 1, 3, 12, 13, and 15-18 of copending Application No. 19/415089 (referred to as application ‘089 herein) in view of Cui et al. (Nat Methods 21, 1470–1480 (2024) in Office action mailed 07 April 2026 is withdrawn in view of the amendments identified above received 02 July 2026.
Conclusion
Claims 1, 3-8, 10, 11, 13, 16, and 17 are allowed.
Claims 18, 19, and 21-26 are rejected.
Claims 1, 3-8, 10, 11, 13, 16-19, and 21-26 are free of the prior art of record. Du, Yuan-Hang, et al. "Optimization and scale-up of fermentation processes driven by models." (Bioengineering 9.9 (2022): 473; newly cited) is made of record as being the closest prior art which shows the use of machine learning methods for the optimization of fermentation processes for microorganism products. However the prior art of record does not show or render obvious “receiving information identifying a set of genetic edits defining an edited biologic strain and assay data characterizing, for each of a plurality of first fermentation environments: (i) a set of fermentation conditions of the first fermentation environment, and (ii) a performance of the edited biologic strain in the first fermentation environment”, “generating, using a machine learning model, a performance prediction for the edited biologic strain in a second fermentation environment which is different that each of the plurality of first fermentation environments, wherein the performance prediction for the second fermentation environment is generated by inputting to the machine learning model a model input comprising: (i) the set of embeddings characterizing the set of genetic edits, (ii) the assay data characterizing performance of the edited biologic strain in each of the plurality of first fermentation environments, and (iii) data identifying a set of fermentation conditions of the second fermentation environment”, “determining that the performance prediction for the edited biologic strain in the second fermentation environment satisfies a performance threshold”, and “automatically adjusting one or more operational parameters of a bioreactor to establish the second fermentation environment for fermenting the edited biologic strain”. Thus, the claims are free of the prior art of record.
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
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