DETAILED ACTION
Applicant’s response, filed 08/19/2025, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn. 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 .
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.
Claim Status
Claims 1-20 are pending.
Claims 1-20 are rejected.
Priority
Each of claims 1-20 are afforded the effective filing date of 09/23/2021.
Drawings
The Drawings submitted 09/23/2021 are accepted.
Claim Rejections- 35 USC § 112
The outstanding rejections to the claims are withdrawn in view of the amendments submitted herein.
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.
For the following rejections, underlined text indicates newly recited portions necessitated by claim amendment.
Claims 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more. Any newly recited portions are necessitated by claim amendment. The previous rejection is maintained.
MPEP 2106 organizes judicial exception analysis into Steps 1, 2A (Prongs One and Two) and 2B as follows 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.
Framework with which to Evaluate Subject Matter Eligibility:
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter;
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;
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1
With respect to Step 1: yes, the claims are directed to method, system, and computer program product, i.e., a process, machine, or manufacture within the above 101 categories [Step 1: YES; See MPEP § 2106.03].
Step 2A, Prong One
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
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:
Independent claims 1, 8, and 14:
determining whether a human interactome is detected in the DNA data; in responsive to having determined that the human interactome does exist from the DNA data,
training a first graph deep learning algorithm by utilizing a combination of features of a human interactome, features of DNA sequences associated with genes identified as exhibiting circadian behavior, and features of DNA sequences associated with genes identified as not exhibiting circadian behavior further comprising
identifying the DNA sequences wherein the genes either exhibit or does not exhibit circadian behavior is based on a full gene list, P values of one or more organ under a P value threshold, value of FDR (false discovery rate) under an FDR threshold, value of rAMP (minimum relative amplitude) above a rAMP threshold and value of R2 above a R2 threshold; in responsive to having determined that the human interactome does not exist,
generating a mapping of the DNA sequences associated with the genes exhibiting circadian behavior to the human interactome as a mapped human protein interactome;
converting the mapped human protein interactome into a connected graph and translated to an adjacency matrix representation; in responsive to having determined that the human interactome is not detected in the DNA data,
training a second graph deep learning algorithm by utilizing features of animal or plant interactomes
classifying the DNA sequence as exhibiting circadian behavior utilizing the first or second graph deep learning algorithm
Dependent claims 2, 9, and 15:
a graph convolutional network
Independent claims 3, 10, and 16:
training the graph convolutional network utilizing k-mer spectra representing the DNA sequences associated with genes identified as exhibiting circadian behavior and k-mer spectra representing the DNA sequences associated with genes identified as not exhibiting circadian behavior.
Independent claim 5, 12, and 18:
identifying the genes exhibiting circadian behavior
translating the DNA sequences associated with the genes exhibiting circadian behavior to a representation suitable for machine learning
identifying the genes not exhibiting circadian behavior
translating the DNA sequences associated with the genes not exhibiting circadian behavior to a representation suitable for machine learning
Independent claim 6, 13, and 19:
generating a mapping of the DNA associated with the genes not exhibiting circadian behavior to the human interactome
translating the generated mapping to a representation suitable for machine learning
Independent claim 8:
determining whether a human interactome is detected in the DNA data; in responsive to having determined that the human interactome does exist from the DNA data,
training a first graph deep learning algorithm by utilizing a combination of features of a human interactome, features of DNA sequences associated with genes identified as exhibiting circadian behavior, and features of DNA sequences associated with genes identified as not exhibiting circadian behavior further comprising:
identifying the DNA sequences wherein the genes either exhibit or does not exhibit circadian behavior is based on a full gene list, P values of one or more organ under a P value threshold, value of FDR (false discovery rate) under an FDR threshold, value of rAMP (minimum relative amplitude) above a rAMP threshold and value of R2 above a R2 threshold;
generating a mapping of the DNA sequences associated with the genes exhibiting circadian behavior to the human interactome as a mapped human protein interactome;
converting the mapped human protein interactome into a connected graph and translated to an adjacency matrix representation; in responsive to having determined that the human interactome is not detected in the DNA data,
training a second graph deep learning algorithm by utilizing features of animal or plant interactomes;
classifying the DNA sequence as exhibiting circadian behavior utilizing the first or second graph deep learning algorithm.
Dependent claims 4, 7, 11, 17, and 20 recite further steps that limit the judicial exceptions in independent claims 1, 8, and 14 and, as such, also are directed to those abstract ideas. For example, claims 4, 11, and 17 further limit the GCN of claims 3, 10, and 16 and claims 7 and 20 further limits the DNA sequence of claims 1, 8, and 14;
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 because the method only requires a user to classify, training, identify, translating, and generating. Without further detail as to the methodology involved in “identify, translating, and generating”, under the BRI, one may simply, for example, use pen and paper to computational classification based on DNA sequence signatures. Some of these steps and those recited in the dependent claims require mathematical techniques as the only supported embodiments, as is disclosed in the specification at: [0015 and 0018- 0020].
Therefore, claims 1, 8, and 14 and those claims dependent therefrom recite an abstract idea [Step 2A, Prong 1: YES; See MPEP § 2106.04].
Step 2A, Prong Two
Because the claims do recite judicial exceptions, direction under Step 2A, Prong Two, provides that the claims must be examined further to determine whether they integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d).III).
Additional elements, Step 2A, Prong Two
With respect to the instant recitations, the claims recite the following additional elements:
Independent claims 1, 8, and 14:
receiving, by a processor, DNA data associated with a DNA sequence
Dependent claims 5, 12, and 18:
obtaining DNA sequences associated with the genes exhibiting circadian behavior
obtaining DNA sequences associated with the genes not exhibiting circadian behavior
The claims also include non-abstract computing elements. For example, independent claim 1 includes a “A computer-implemented method, the method comprising: receiving, by a processor”, claim 8 includes “A system comprising: a memory; and a processor in communication with the memory, the processor being configured to perform operations” and claim 14 includes “A computer program product comprising a computer readable storage medium having program instructions embodied therewith, the program instructions executable by a processor to cause the processor to perform operations:.
Considerations under Step 2A, Prong Two
With respect to Step 2A, Prong Two, the additional elements of the claims do not integrate the judicial exceptions into a practical application for the following reasons. Those steps directed to data gathering, such as “receiving”, “utilizing” and “obtaining”, perform functions of collecting the data needed to carry out the judicial exceptions. Data gathering and outputting do not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. Data gathering and outputting steps are not sufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(g)).
Further steps directed to additional non-abstract elements of “a processor, a system, and a computer program product” 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, such as the computer-readable recording media, are used to implement these functions. 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, and therefore the claim does not integrate that judicial exceptions into a practical application. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc.… are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (MPEP 2106.05(f)).
Thus, none of the claims recite additional elements which would integrate a judicial exception into a practical application, and the claims are directed to one or more judicial exceptions [Step 2A, Prong 2: NO; See MPEP § 2106.04(d)].
Step 2B (MPEP 2106.05.A i-vi)
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 prosecution 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).
With respect to the instant claims, the courts have found that receiving and outputting data are well-understood, routine, and conventional functions of a computer when claimed in a merely generic manner or as insignificant extra-solution activity (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network), Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015), and OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, as discussed in MPEP 2106.05(d)(II)(i)).
As such, the claims simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception (MPEP2106.05(d)). The data gathering steps as recited in the instant claims constitute a general link to a technological environment which is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)).
With respect to claims 1, 8, and 14 and those claims dependent therefrom, the computer-related elements or the general purpose computer 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 (see MPEP 2106.06(A)). The specification also notes that computer processors and systems, as example, are commercially available or widely used at [0054-0064]. 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).
Taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself [Step 2B: NO; See MPEP § 2106.05].
Therefore, the instant claims are not drawn to eligible subject matter as they are directed to one or more judicial exceptions without significantly more. For additional guidance, applicant is directed generally to the MPEP § 2106.
Response to Applicant Arguments
Applicant submits the independent claims describe an approach by a computer-implemented method, system, and computer program product, improvements in the field of gene classification, specifically for training a deep learning algorithm to identify and classify DNA data as exhibiting circadian behavior [p. 14, par. 3].
It is respectfully found not persuasive. An improvement in the abstract idea itself (e.g. a recited fundamental economic concept) is not an improvement in technology. The judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements. See the discussion of Diamond v. Diehr, 450 U.S. 175, 187 and 191-92, 209 USPQ 1, 10 (1981)). As set forth in MPEP 2106.04(a)(2).III.C, merely claiming that a concept that can be performed in the human mind is performed on a generic computer does not negate that the claim is still considered to recite a mental process. In addition, MPEP 2106.05(f) sets forth that simply adding a general purpose computer after the fact to an abstract idea does not integrate a judicial exception into a practical application or provide significantly more. Since the claims do not provide any specific computational structures, it appears that the processor equates to a generic computer component to implement the abstract idea, which does not change the fact that the claims recite a mental process or mathematical concept.
Applicant submits the approach may be used to conduct mass screening of simulated SNP (single nucleotide polymorphisms) altered profiles. It is well known that DNA databases contain large volume of information that a human thought/mind process may not be able to practically execute. Thus, the inclusion of generic computer components, machine learning algorithms, and the use of insight data transforms the claim limitations into practical applications rather than mere mental processes [p. 14, par. 4].
It is respectfully found unpersuasive. See Bancorp Serves., L.L. C. v. Sun Life Assur. Co. of Canada (U.S.), 687 F.3d 1266,1278 (Fed. Cir. 2012) (holding that “the fact that the required calculations could be performed more efficiently via a computer does not materially alter the patent eligibility of the claimed subject matter”); see also See SiRF Tech., Inc. v. Int’l Trade Comm ’n, 601 F.3d 1319,1333 (Fed. Cir. 2010) (holding that: In order for the addition of a machine to impose a meaningful limit on the scope of a claim, it must play a significant part in permitting the claimed method to be performed, rather than function solely as an obvious mechanism for permitting a solution to be achieved more quickly, i.e., through the utilization of a computer for performing calculations). Applicant is again reminded that while since identifying one or a few altered SNPs can be performed mentally, or with paper and pencil, would take considerable time and effort, the singular purpose of computers and computer networks, is to perform large numbers of calculations, via algorithms, rapidly, and without error. Simply scaling up that analysis, or repeating it for many SNPs, doesn’t take it out of the realm of mental processes. Although a general-purpose computer can perform calculations at a rate and accuracy that can far outstrip the mental performance of a skilled artisan, the nature of the activity is essentially the same, and constitutes an abstract idea.
Applicant submits the claims improve upon existing technology by providing a novel approach gene classification, specifically for training a deep learning algorithm to identify and classify DNA data as exhibiting circadian behavior [p. 15, par. 4].
It is respectfully found not persuasive. An improvement in the abstract idea itself (e.g. a recited fundamental economic concept) is not an improvement in technology. The judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements. See the discussion of Diamond v. Diehr, 450 U.S. 175, 187 and 191-92, 209 USPQ 1, 10 (1981)). As set forth in MPEP 2106.04(a)(2).III.C, merely claiming that a concept that can be performed in the human mind is performed on a generic computer does not negate that the claim is still considered to recite a mental process. In addition, MPEP 2106.05(f) sets forth that simply adding a general purpose computer after the fact to an abstract idea does not integrate a judicial exception into a practical application or provide significantly more. Since the claims do not provide any specific computational structures, it appears that the processor equates to a generic computer component to implement the abstract idea, which does not change the fact that the claims recite a mental process or mathematical concept
Claim Rejections - 35 USC § 103
The outstanding rejections from the previous Office Action are withdrawn in view of the amendments submitted herein. Gardiner in view of Xu and Bhargava do not discloses generating a mapping of the DNA sequences associated with the genes exhibiting circadian behavior to the human interactome as a mapped human protein interactome and converting the mapped human protein interactome into a connected graph and translated to an adjacency matrix representation. Therefore, neither GARDINER, XU nor BHARGA VA teaches or suggests all the limitations of amended independent claims 1, 8, and 14.
Conclusion
No claims are allowed.
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.
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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/D.M.B./Examiner, Art Unit 1685 /Soren Harward/Primary Examiner, TC 1600
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