DETAILED ACTION
Notice of 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 .
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 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.
Withdrawal of Objections and Rejections
Applicant's response, filed 03/05/2026, has been fully considered.
In view of the amendment and remarks from 03/05/2026, the rejection of the following claims are withdrawn:
claims 1-20 under 35 USC § 112(a); and
claims 1-20 under 35 U.S.C. § 112(b).
The following rejections and/or objections are either maintained or newly applied for claims 3-7 and 18-32. They constitute the complete set applied to the instant application. Herein, "the previous Office action" refers to the Non-Final Rejection of 12/17/2025.
Status of the Claims
Claims 1-2 and 8-17 are canceled.
Claims 3-7 and 18-32 are pending.
Claims 29-32 are objected to.
Claims 3-7 and 18-32 are rejected.
Priority
This US Application 19/340,736 (09/25/2025) is a CON of PCT/US2025/031891 (06/02/2025) which claims priority from US Application 63/655,575 (06/03/2024) and from US Application 63/803,471 (05/09/2025); as reflected in the filing receipt mailed on 10/20/2025. The claims to the benefit of priority are acknowledged, and the effective filing date of claims 3-7 and 18-32 is 06/03/2024
Claim objections
Claims 29-32 are objected to because of the following informality: the recited "the non-transitory computer storage media" should read "the one or more non-transitory computer storage media". Appropriate correction is required.
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 3-7 and 18-32 are rejected under 35 USC § 101 because the claimed inventions are directed to one or more Judicial Exceptions (JEs) without significantly more. Regarding JEs, "Claims directed to nothing more than abstract ideas..., natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 §I). Abstract ideas include mathematical concepts and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2)). Any newly recited portions are necessitated by claim amendment.
101 background
MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter (MPEP 2106.03)?
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Analysis of instant claims
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
The instant claims are directed to a system (claims 3-7 and 18-22); a method (claims 23-27) a and CRM (claims 28-32); each of which falls within one of the categories of statutory subject matter.
[Step 1: claims 3-7 and 18-32: Yes]
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Background
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. MPEP § 2106.04(a)(2) further explains that abstract ideas are defined as:
• mathematical concepts (mathematical formulas or equations, mathematical relationships
and mathematical calculations) (MPEP 2106.04(a)(2)(I));
• certain methods of organizing human activity (fundamental economic principles or practices, managing personal behavior or relationships or interactions between people) (MPEP 2106.04(a)(2)(II)); and/or
• mental processes (concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) (MPEP 2106.04(a)(2)(III)).
Analysis of instant claims
With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims are found to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) and mathematical concepts (in particular mathematical relationships and formulas) are as follows:
• "operations to implement a multi-objective optimization of the biologic synthesis processes, wherein the multi-objective optimization evaluates multiple objectives of the biologic synthesis processes based on simulation of the biologic synthesis processes to … design a mutant protein that maintains at least a first feature of a first protein while also capturing a second feature of a second protein" (independent claims 3, 23 and 28);
• "identifying a set of differing residue positions between a first protein and a second protein" (independent claims 3, 23 and 28);
• "generating a set of mutant proteins based on the set of differing residue positions" (independent claims 3, 23 and 28);
• "processing each of the first protein, the second protein, and each mutant protein in the set of mutant proteins using a protein language model to generate a respective embedding of each of the first protein, the second protein, and each mutant protein in the set of mutant proteins in an embedding space" (independent claims 3, 23 and 28);
• "determining, by the protein language model, a respective viability score for each mutant protein representing a biological likelihood of mutations reflected in the mutant protein" (independent claims 3, 23 and 28);
• "generating a ranking of the set of mutant proteins using Pareto front optimization based on, for each mutant protein:(i) a classification of whether the embedding of the mutant protein is within a threshold conservation distance of the embedding of the first protein in the embedding space to maintain the first feature of the first protein,(ii) a distance between the embedding of the mutant protein and the embedding of the second protein to design towards the second feature of the second protein, and (iii) the viability score" (independent claims 3, 23 and 28);
• "selecting one or more of the mutant proteins based on the ranking of the mutant proteins" (independent claims 3, 23 and 28);
• "…simultaneously optimize a microbe, a bioreactor process, and a downstream purification process" (claim 5);
• "maximize production without minimizing growth" (claim 6); and
• "increase expression without loss of activity" (claim 7).
Dependent claims 4, 18-22, 24-27 and 29-32 recite further steps that limit the judicial exceptions in independent claims 3, 23 and 28 and, as such, also are directed to those abstract ideas. For example, claims 4, 18-20, 26-27 and 31-31 recite further details about the biological synthesis and dependent claims 21-22, 24-25 and 29-30 recite further details about the operations to implement a multi-objective optimization.
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined to each cover performance either in the mind and/or by mathematical operation. Without further detail as to the methodology involved in "generating a respective embedding of each of the first protein, the second protein, and each mutant protein in the set of mutant proteins in an embedding space" to generate a classification and viability scoring based on the first and second proteins, under the BRI, one may simply, for example, use pen and paper to perform mathematical steps to arrive at the recited classification and viability scoring. Further support for the mathematical techniques used in the claims is provided in the specification at [0494] which describes the claimed system using processing cores to perform data transformation or integration operations; which constitutes math. Thus, the recited terms correspond to verbal equivalents of mathematical concepts because they constitute actions executed by a group of mathematical steps in a form of a mathematical algorithm; thus mathematical concepts (MPEP 2106.04(a)(2)). A mathematical concept need not be expressed in mathematical symbols, because "words used in a claim operating on data to solve a problem can serve the same purpose as a formula." In re Grams, 888 F.2d 835, 837 and n.1, 12 USPQ2d 1824, 1826 and n.1 (Fed. Cir. 1989). MPEP 2106.04(a)(2) pertains. The human mind is also sufficiently capable of determining a protein language model, identifying a set of differing residue positions and selecting mutant proteins.
[Step 2A Prong One: claims 3-7 and 18-32: Yes ]
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Background
MPEP 2106.04(d).I lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application:
An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
Analysis of instant claims
Instant claims 3-7 and 18-32 recite additional elements that are not abstract ideas:
• "computationally" (independent claims 3, 23 and 28);
• "a set of machine learning systems, a set of artificial intelligence systems, and/or a set of neural networks" (claims 5-7);
• "distributed computing architecture" (claims 21, 24 and 29);
• "one or more processors" (independent claim 3);
• "one or more computers" (independent claims 23 and 28);
• "non-transitory computer storage media" (claims 28-32)
Considerations under Step 2A, Prong Two
The recited limitations in claims 3-7 and 18-32 are interpreted as requiring the use of a computer. Hence, the claims explicitly recite steps executed by computers and therefore can be described as computer functions or instructions to implement on a generic computer. Further steps directed to additional non-abstract elements of a computing device/computer do not describe any specific computational steps by which the "computer parts" perform or carry out the judicial exceptions, nor do they provide any details of how specific structures of the computer are used to implement these functions. The claims state nothing more than a generic computer (i.e. including the recited "distributed computing architecture") which performs the functions that constitute the judicial exceptions. The instant claims state nothing more than that a generic computer performs the functions that constitute the abstract idea (MPEP 2106.05(f)).
Limitations of claims 3-7 and 18-32 are considered to perform the claimed abstract idea with a computer, which is not sufficient to integrate an abstract idea into a practical application (see MPEP 2106.05(f)); since steps that can be performed mentally and merely performing the mental process in a computer environment do not negate the fact that something that can be carried out in the human mind. See MPEP 2106.04(a)(2).III.C.
With respect to claims 5-7, the computer-related elements or the general purpose computer and the recited "a set of machine learning systems, a set of artificial intelligence systems, and/or a set of neural networks" do not rise to the level of significantly more than the judicial exception. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, which the courts have found to not provide significantly more when recited in a claim with a judicial exception (Alice Corp., 573 U.S. at225-26, 110 USPQ2d at 1984; see MPEP 2106.05(A)). The additional elements are set forth at such a high level of generality that they can be met by a general purpose computer. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the judicial exceptions (see MPEP 2106.05(b)I-III).
Regarding the first consideration at MPEP 2106.04(d)(1), the record, including for example the specification, does not yet clearly disclose an explanation of improvement over the previous state of the technology field. The claims do not yet clearly result in such an improvement (e.g. specification: [19-20, 214, 420, 550, 561, 583, 729-905, etc.].
Hence, these are mere instructions to apply the abstract idea using a computer and insignificant extra-solution activity and therefore the claims do not integrate that abstract idea into a practical application (see MPEP 2106.04(d) § I; 2106.05(f); and 2106.05(g)).
In Step 2A, Prong One above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs).
In this Step 2A, Prong Two immediately above claim steps and/or elements were identified as part of one or more additional elements. Additional elements are further discussed in Step 2B below.
Here in Step 2A, Prong Two, no additional step or element clearly demonstrates integration of the JE(s) into a practical application.
[Step 2A Prong Two: claims 3-7 and 18-32: No]
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during examination that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
Claims 3-7 and 18-32 recite a computer or computer functions, interpreted as instructions to apply the abstract idea using a computer, where the computer does not impose meaningful limitations on the judicial exceptions; which can be performed without the use of a computer (MPEP 2106.04(d) § I; and MPEP 2106.05(f)).
The computer-related elements or the general purpose computer and the set of machine learning systems, set of artificial intelligence systems, and/or set of neural networks do not rise to the level of significantly more than the judicial exception. The claims state a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, which the courts have found to not provide significantly more when recited in a claim with a judicial exception (Alice Corp., 573 U.S. at225-26, 110 USPQ2d at 1984; see MPEP 2106.05(A)).
When the claims are considered as a whole, they do not integrate the abstract idea into a practical application; they do not confine the use of the abstract idea to a particular technology; they do not solve a problem rooted in or arising from the use of a particular technology; they do not improve a technology by allowing the technology to perform a function that it previously was not capable of performing; and they do not provide any limitations beyond generally linking the use of the abstract idea to a broad technological environment. See MPEP 2106.05(a) and 2106.05(h).
The instant claims constitute insignificant extra solution activity, and when considered individually, are insufficient to constitute inventive concepts that would render the claims significantly more than an abstract idea (see MPEP 2106.05(g)). Hence, these elements, when considered individually, are insufficient to constitute inventive concepts that would render the claims significantly more than an abstract idea (see MPEP 2106.05(d)).
[Step 2B: claims 3-7 and 18-32: No]
Conclusion: Instant claims are directed to non-statutory subject matter
For the reasons above, the claims in this instant application, when the limitations are considered individually and as a whole, are directed to an abstract idea and lack an inventive concept not clearly anything significantly more.
Response to applicant's remarks in regard to Claim Rejection 35 U.S.C. ~ 101
The Remarks of 03/05/2026 have been fully considered but are not persuasive for the reasons below:
It appears that pg. 9 para. 6 represents the only Applicant remarks specific to 101 and the instant claims:
Claims 1-20 were rejected under 35 U.S.C. § 101. The claims have been amended to clarify the claimed subject matter. Reconsideration and withdrawal of the rejection are respectfully requested
The amended claims do not solve the above described 101 issues, thus the 101 rejection is maintained. Overall, no additional step or element clearly demonstrates integration of the JE(s) into a practical application. Furthermore, the identified additional elements or the combination of elements are well understood, routine, and conventional.
No prior art has been applied to the following claims
Claims 3-7 and 18-32 are free of the analogous art at least because close art, e.g. Seow, Lui and Sinai as cited on the 12/17/2025 Form PTO-892, either individually or in obvious combination, does not teach the recited combination of "multiple objectives of the biologic synthesis processes based on simulation of the biologic synthesis processes to computationally design a mutant protein that maintains at least a first feature of a first protein while also capturing a second feature of a second protein." Additionally, Applicant's 03/05/2026 remarks at pg. 10 para. 2 support withdrawal of the rejection.
Conclusion
No claims are allowed.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FRANCINI A FONSECA LOPEZ whose telephone number is (571)270-0899. The examiner can normally be reached Monday - Friday 8AM - 5PM ET.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia Wise can be reached at (571) 272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/F.F.L./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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