DETAILED ACTION
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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 29 June 2026 has been entered.
Introductory Remarks
In response to communications filed on 29 June 2026, claim(s) 1, 8, 15, 21, and 22 is/are amended per Applicant’s request. Therefore, claims 1-22 are presently pending in the application, of which, claim(s) 1, 8, and 15 is/are presented in independent form.
No IDS has been received since the mailing of the last Office action.
Examiner’s Note
The rejections below group claims that may not be identical, but whose language and scope are so substantively similar as to lend themselves to grouping, in the interests of clarity and conciseness. Any citation to the instant specification herein is made to the PGPub version (if applicable). The examiner notes that no statement has been entered regarding the inventorship of individual claims as required under 37 CFR 1.56, and therefore assumes that all claims have the same inventorship or are directed to inventions that were commonly owned as of the effective filing date of the invention.
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 1-22 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claim(s) recite(s) mental process steps of processing data to determine a match score and use that score for string alignment.
The additional elements in the claim are: “computer-implemented method” (claim 1), “by a sequence alignment algorithm executing within a computer system” (claims 1, 8, and 15), “similarity matrix maintained within the computer system” (claims 1, 8, and 15), “training a number of machine learning models for sequence alignment using a training dataset that comprises determined alignment between the pair of strings based on the combined score” (claims 1, 8, and 15), “determining, by the computer system, string alignment for a pair of additional strings using the number of machine learning models of the artificial intelligence system” (claims 1, 8, and 15), “retraining the number of machine learning models of the artificial intelligence system for sequence alignment using a training dataset that comprises the determined alignment between the pair of additional strings in order to improve the performance of the artificial intelligence system” (claims 1, 8, and 15), “computer system” (claim 8), “a hardware processor” (claim 8), “computer program product” (claims 15-20), and “a computer readable storage media” (claim 15). The judicial exception is not integrated into a practical application because the additional elements amount to nothing more than generic components recited at a high-level of generality such that it amounts to no more than mere instructions to apply the exception using generic computer components. See MPEP 2016.04(d)(I) and 2106.05(f).
When determining whether a claim simply recites a judicial exception with the words “apply it” (or an equivalent), such as mere instructions to implement an abstract idea on a computer, examiners may consider: (1) whether the claim recites only the idea of a solution or outcome i.e., the claim fails to recite details of how a solution to a problem is accomplished; (2) whether the claim invokes computers or other machinery merely as a tool to perform an existing process; and (3) the particularity or generality of the application of the judicial exception. See MPEP 2106.05(f). With respect to the “training a number of machine learning models of an artificial intelligence system…” additional element, there are no details about particular machine learning models or how the machine learning models operate to train for sequence alignment other than that it is being used to do so. The same holds true for the determining and retraining limitations. The machine learning models are used to generally apply the abstract idea without placing any limitation on how the models operate to determine sequence alignment as a function of the training dataset and retraining. See generally instant specification at 0057 and 0059.The independent claims omit any details as to how the models solve a technical problem, and instead the claims recite only the idea of a solution or outcome. Also, the claims invoke generic machine learning models merely as a tool for making the recited mathematical calculation rather than purporting to improve the technology or a computer. See MPEP 2106.05(f).
The independent claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above, the additional elements amount to nothing more than mere instructions to apply the exception using generic computer component(s). These cannot provide an inventive concept, and thus the claims are patent-ineligible.
Dependent claims 2, 9, and 16 merely recite further abstract idea limitations in the form of stating that matches are prevented in the middle of words, and further describing the structure of the similarity matrix. Dependent claims 3, 10, and 17 merely recite further abstract idea limitations in the form of establishing rules that prevent the middle of word matches of claims 2, 9, and 16. Dependent claims 4, 11, and 18 merely recite further abstract idea limitations in the form of stating that the match boundaries are set at space or the ends of strings, which is reiterating what is stated in claims 2, 9, and 16. Dependent claims 5, 12, and 19 merely recite further abstract idea limitations in the form of stating that match scores are normalized. Dependent claims 7 and 14 merely recite the outcome of use of the abstract idea. Dependent claim 21 adds retraining of the machine learning models, which does not amount ot anything more than the abstract idea in a generic computing environment. See Recentive Analytics v. Fox Corp., 692 F.Supp.3d 438 (D. Del. 2023). Dependent claim 22 mirrors claim 21 but adds a limitation of receiving feedback related to accuracy of the string alignment determination, which is itself an abstract idea. Summarizing, these dependent claims add no additional elements to those previously identified for the independent claims. In view of this, these claims do not integrate the abstract idea into a practical application, nor do they amount to significantly more than the abstract idea.
Dependent claims 6, 13, and 20 provide the additional element of “at least one numeric library that supports multi-dimensional arrays along with a collection of high-level mathematical functions to operate on the multi-dimensional arrays”. Put plainly, these claims state that the algorithm is configured to interoperate with a numeric library that stores various data; this mere storage of data, nor the “interoperability” of the abstract idea with stored data, fail to amount to a practical application nor are they singularly, or in combination, significantly more than the abstract idea.
Response to Arguments
Applicant's arguments filed 2 June 2026 were answered in the advisory action of 22 June 2026. No new arguments have been raised by the applicant upon filing of the RCE on 29 June 2026. Therefore, the applicant’s arguments have been fully considered but they are not persuasive. The response to the applicant’s arguments in the advisory action is fully incorporated herein.
Conclusion
All claims are identical to or patentably indistinct from, or have unity of invention with claims in the application prior to the entry of the submission under 37 CFR 1.114 (that is, restriction (including a lack of unity of invention) would not be proper) and all claims could have been finally rejected on the grounds and art of record in the next Office action if they had been entered in the application prior to entry under 37 CFR 1.114. Accordingly, THIS ACTION IS MADE FINAL even though it is a first action after the filing of a request for continued examination and the submission under 37 CFR 1.114. See MPEP § 706.07(b). 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 TYLER J TORGRIMSON whose telephone number is (571)270-5550. The examiner can normally be reached Monday - Friday 9 am - 5:30 pm.
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/TYLER J TORGRIMSON/ Primary Examiner, Art Unit 2165
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