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
Applicants’ amendment filed 9/16/2025 has been received and entered. The claims do not appear to provide any amendments consistent with the original status identifiers indicated.
Claims 1-25 are pending.
Priority
This application filed 11/24/2021 is a CIP of PCT/US2020/037441 filed 6/12/2020 which claims benefit to US Provisional applications 63/009563 filed 4/14/2020 and 62/861821 filed 6/14/2019.
Applicants do not comment on the summary of priority in the present response.
With respect to priority of limitations recited in the present claims it was noted that support for the term ‘scenario’ in claim 2 is not identified in the specification of the parent PCT and considered an embodiment added as part of the CIP; for claim 3 and the term ‘randomly’ fails to find support and is only present in conjunction with support for ‘random forest’ model and not for randomly generating values (see specification [0213]). Therefore, while independent claims 1, 13 and 25 appear to be broadly supported by the PCT for using machine learning in protein synthesis, dependent claim embodiments appear to provide new limitations and embodiments not specifically contemplated in the PCT specification and are only be supported by the present disclosure and are accorded the priority date of 11/24/2021.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 9/16/2025 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Newly provided WO 2019/023616 A1 does not provide for the application of machine learning in protein synthesis.
Claim Rejections - 35 USC § 112
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 1-25 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 is withdrawn.
Upon review of Applicants arguments and consideration of the claims, it is agreed that the claims are clear with what is required and encompassed by the limitations for the method. The preamble of the claim sets forth automating the process of peptide synthesis using machine learning engine, specifically the operating condition of the flow rate profile and can comprise any general use of machine learning engine and any application for automating the process by indicating the flow rate profile as the operating condition in the solid phase slug flow used to synthesize peptides.
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 1-25 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.
Claim analysis
Claim 1 is generally directed to automating peptide synthesis. More specifically, the claims are directed to indicating a process to synthesize a peptide then selecting values of operating conditions based on flow rate of the process. In view of the guidance of the specification, it appears that machine learning is generally taught and indicated that application can be used to optimize a process, and appears that it is a computer implemented method for analyzing and optimizing peptide synthesis conditions. Claim 1 claim sets forth automating the process of peptide synthesis using machine learning engine, specifically the operating condition of the flow rate profile and can comprise any general use of machine learning engine and any application for automating the process by indicating the flow rate profile as the operating condition in the solid phase slug flow used to synthesize peptides. In practicing the method, no particular outcome is required, no specific means of automating any of the steps, no particular or specific application of machine learning is set forth, providing broadly simply using machine learning to provide a flow condition which could be set such that the process is automated. Dependent claims further provide for more than one value for various scenarios, but in limiting claim 1 provides for different inputs but one operating condition of flow rate profile; and while the prediction of quality is provided relative to yield, purity or production time relative to flow rate profile, the claim fail to provide any detail or requirement of any specific necessary outcome or accuracy of the prediction.
Response to Applicants arguments
Applicants provide an overview of the rejection and note MPEP 2106 analyzing each of the steps. For step 1 Applicants argue that the claims are directed to a statutory category.
In response, the action and analysis support this same conclusion.
Applicants indicate the basis of the rejection and analysis asserts that the claims are directed to an abstract idea and argue the judicial exception is integrated into a practical application. Applicants provide an overview of MPEP 2106.04d and argue that automating the process using machine learning is an improvement.
In response, the claims broadly provide for using machine learning to provide a flow rate profile. Given this breadth, a plain reading indicates that machine learning is generically applied to some conditions to arrive at a flow rate. The claims fail to provide for how this value is integrated and simply appears that ML provides a value of flow to be used in the production process. There is no particularity to what ML is used, how it is used, what values are assessed or how they are assessed to provide a flow rate, nor once a rate it obtained how it is integrated to be an automated process. In review of the breadth of the claims and evidence of record, there does not appear to be any evidence that the use of machine learning is integrated into any process or that it provides for any improvement given the limitations and requirements of the claims.
Therefore, for the reasons above and of record, the rejection is maintained. The basis of the 101 analysis is provided below for completeness of the record.
For step 1 of the 101 analysis, the claims are found to be directed to a statutory category of a method and process.
For step 2A of the 101 analysis, the judicial exception of the claims are the steps of accessing peptide synthesis conditions and choosing processing conditions for peptide synthesis. The judicial exception is a set of instructions for applying machine learning to automate and optimize peptide synthesis and appears to fall into the category of Mental Processes, that is concepts performed in the human mind (including an observation, evaluation, judgment, opinion). Here, the claims encompass any peptide chemistry for any type of pepetide as a possible process and machine learning appears to be generically indicated for use of automating the process without any specific outcome.
Recent guidance from the office requires that the judicial exception be evaluated under a second prong to determine whether the judicial exception is practically applied. In the instant case, the claims do not have an additional element and provide only autmating of conditions and not controlling the process itself. This judicial exception requires steps recited at high level of generality and are only stored on a non-transitory, and is not found to be a practical application of the judicial exception as broadly set forth.
For step 2B of the 101 analysis, each of the independent claims recites additional elements as it could encompass physical steps of peptide synthesis, but there is not direct nexus of how the process is automated and appears that choosing the conditions is the part automated. As such, the claims do not provide for any additional element to consider under step 2B. To the extent the system implements the method on a computer, it is noted that in explaining the Alice framework, the Court wrote that "[i]n cases involving software innovations, [the step one] inquiry often turns on whether the claims focus on the specific asserted improvement in computer capabilities or, instead, on a process that qualifies as an abstract idea for which computers are invoked merely as a tool." The Court further noted that "[s]ince Alice, we have found software inventions to be patent-eligible where they have made non-abstract mprovements to existing technological processes and computer technology." Moreover, these improvements must be specific -- "[a]n improved result, without more stated in the claim, is not enough to confer eligibility to an otherwise abstract idea . . . [t]o be patent-eligible, the claims must recite a specific means or method that solves a problem in an existing technological process." Here, choosing conditions for known chemistry does not appear to be automation, but to the extent many conditions for various chemistries can be stored, it appears that this is providing such details in a computer environment. As indicated in the summary of the judicial exception above and in view of the teachings of the specification, the steps are drawn to automating conditions for peptide synthesis. While the instruction are stored on a medium and could be implemented on a computer system, together the steps do not appear to result in significantly more than a means to compare sequences. The judicial exception of the method as claimed can be performed by hand and in light of the previous claims to a computer medium and in light of the teaching of the specification on a computer. In review of the instant specification the methods do not appear to require a special type of processor and can be performed on a general purpose computer.
One way to overcome a rejection for non-patent-eligible subject matter is to persuasively argue that the claimed subject matter is not directed to a judicial exception. Another way for the applicants to overcome the rejection is to persuasively argue that the claims contain elements in addition to the judicial exception that either individually or as an ordered combination are not well understood, routine, or conventional. Another way for the applicants to overcome the rejection is to persuasively argue that the claims as a whole result in an improvement to a technology. Persuasive evidence for an improvement to a technology could be a comparison of results of the claimed subject matter with results of the prior art, or arguments based on scientific reasoning that the claimed subject matter inherently results an improvement over the prior art. The applicants should show why the claims require the improvement in all embodiments.
Claim Rejections - 35 USC § 103
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.
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.
Claims 2-25 rejected under 35 U.S.C. 103 as being unpatentable over Thomas et al (US 2017/081359), Metten et al. (1997), Phynexus (US 7 612 165) and Szededi (WO 2015/128687) is withdrawn.
It is noted that claim 1 was not subject to the rejection, and upon consideration of the analysis and teaching of the citations fails to provide use of machine learning to provide a flow rate profile for automating peptide production as required of the claim limitations.
Conclusion
No claim is allowed.
Noting the closest art of record, Thomas et al and Mitten et al both provide the basis of peptide synthesis and that a continuous flow method of solid phase peptide was known, and further that continuous analysis of the process could be performed such as continuous flow peptide synthesis including in-line photometric measurement. As acknowledged, the chemistry and systems for peptide synthesis encompassed by the claims were well known, neither Thomas nor Metten et al. teach the use of slug flow and routine optimization of remaining elements claimed. Phynexus was provided to demonstrate a method of solid phase peptide synthesis in a capillary using repeating cycles of amino acids/activators and 20% piperidine in DMF for deprotection of Fmoc as a method using slug flow, and Szegedi as evidence of a method and system for continuous flow synthesis of peptides, with high yields, including the usual amino acid residues, solvents, coupling agents, deprotection agents and washing solvents, falling within the scope of claims of the present claims. However, given the success of each and no specific teaching to optimize using machine learning in art of record, there is no motivation to use ML to provide a flow rate profile as required of the instant claims.
THIS ACTION IS MADE FINAL. 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Joseph T Woitach whose telephone number is (571)272-0739. The examiner can normally be reached Mon-Fri; 8:00-4:00.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz R Skowronek can be reached at 571 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/Joseph Woitach/Primary Examiner, Art Unit 1687