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 .
The following is a non-final, first office action on the merits, in response to application filed 3/23/2023. Claims 1-18 have been examined and are currently pending.
Priority
Acknowledgment is made of applicant's claim for a provisional application filed on 9/30/2020. The Applicant claims benefit of continuation of PCT/US2021/052999 filed on 9/30/2021.
Receipt is acknowledged of papers submitted under 35 U.S.C. 119(a)-(d), which papers have been placed of record in the file.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 3/23/2023 follows the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Specification
Modification made to [0001] of original specification on 3/23/2023, and a clean substitute copy made to the original specification on 3/23/2023 is acknowledged.
Drawings
Amendment made to the original drawings on 3/23/2023 is acknowledged.
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 1-18 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.
Alice Corp. also establishes that the same analysis should be used for all categories of claims, regardless of a system/apparatus, a method, or a product claim.
The claimed invention (Claims 1-18) is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more. The claim(s) recite(s) abstract ideas including “Certain Methods of Organizing Human Activity”, “an idea of itself”, “mental process” which have been identified/found by the courts as abstract ideas in new 101 memos of the subject matter eligibility in here (https://www.uspto.gov/patent/laws-and-regulations/examination-policy/subject-matter-eligibility) including 2019 Revised Patent Subject Matter Eligibility Guidance. This judicial exception is not integrated into a practical application because it does not impose any meaningful limits on practicing the abstract idea. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because it/they is/are recited at a high level of generality and/or are recited as performing generic computer functions routinely used in the computer applications:
Independent claim 1 (Step 2A, Prong I): is directed to multiple abstract ideas including “Certain Methods of Organizing Human Activity”, and “Mental process”.
Claim 1, Steps of,
filtering columns of aligned coded sequences wherein evolutionary activity satisfies an evolutionary diversity threshold (d);
determining a pair-wise column P- distance matrix for remaining columns of the matrix subject to the evolutionary diversity threshold (d);
performing on the remaining columns using the P-distance matrix; and
extracting an m-ary approximation of a co-evolution data motif complex structure, the extracting or approximating including:
constructing a vertex set of the data motif complex by identifying data sites with specified high informational variation;
constructing specified high dimensional simplices which systematically represent key or critical, informational patterns within the data set; and
determining and outputting collections of sites within the coded sequences that are acted upon as blocks by selection pressure based on the key or critical, informational patterns.
fall within “Certain Methods of Organizing Human Activity”, the instant steps filtering columns, determining distance matrix, performing the remaining columns, extracting data, constructing data, determining data, outputting/displaying data,
which are human activities and/or interactions between users/people/devices and therefore, certain methods of organizing human activity which encompasses both certain activity of a single person, certain activity that involves multiple people, and certain activity between a person and a computer.
Further, the instant claim also falls within the abstract “Mental Processes” grouping of abstract ideas since these limitation covers performance of the limitations in the mind or by paper and pen. For example, a human being can observe/receive/extract/filter/display/present data, can evaluate/determine data.
Further, step of (“outputting….”) are considered as “insignificant extra-solution activity” to the judicial exception since they are merely receiving/collecting data/information.
Independent claim 1, Step 2A (Prong II): Accordingly, the claim recites an abstract idea(s) as pointed out above. This judicial exception(s) is/are not integrated into a practical application. In particular, the claim recites no additional element that are significant more than the abstract ideas. In particular, there is no machine/hardware/computer to actually perform the abstract steps mentioned above. Thus, nothing in the claim element precludes the step from practically being performed in the mind, and is simply organized information through human activity or merely mental tasks, and is part of, or a related, judicial exception and does not meaningfully limit the application of the identified judicial exception, and as such does not constitute significantly more.
There is no specificity regarding any technology, just broadly, execute the programming instructions to manage data, including collect data, extract data, filter data, determine data, display data. There are no additional elements, for example, hardware processor of a machine to actually perform all of the steps at all. The steps are mainly collecting data, managing data, processing data. The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. Accordingly, there is neither improvement to another technology or technical field nor an improvement to the functioning of the computer itself, and does not integrate the abstract idea into a practical application because it does not impose any meaningful limits on practicing the abstract idea.
Independent claim 1, (step 2B):
There are no additional elements in claim 1 to actually perform the steps. There is no additional element that are significant more than the abstract ideas; thus, they are not significantly more than the identified abstract idea. Thus, no additional element adds nothing of substance to the underlying abstract idea; thus, they are not significantly more than the identified abstract idea.
Dependent claims 2-9, 17-18 are merely add further details of the abstract steps/elements recited in claim 1 without including an improvement to another technology or technical field, an improvement to the functioning of the computer itself, or meaningful limitations beyond generally linking the use of an abstract idea to a particular technological environment. Therefore, dependent claims 2-9, 17-18 are also non-statutory subject matter.
Independent claim 10: Alice Corp. also establishes that the same analysis should be used for all categories of claims. Therefore, independent system claim 10 is also rejected as ineligible subject matter under 35 U.S.C. 101 for substantially the same reasons as the method claim(s) 1.
There is no additional element that is significant more than the abstract ideas; thus, they are not significantly more than the identified abstract idea. Thus, no additional element adds nothing of substance to the underlying abstract idea; thus, they are not significantly more than the identified abstract idea.
Further, the component (i.e., a system) described in independent claims 10, add nothing of substance to the underlying abstract idea. Similarly, as it relates to the computer system claims, the limitations appear to be performed by a generic processor/computing system/device. These components are merely recited at a high level of generality and/or are recited as performing generic computer functions routinely used in the computer applications; thus, they are not significantly more than the identified abstract idea. Generic computer components recited as performing generic sensing/computer functions that are well-understood, routine and convention activities amount to no more than implementing the abstract idea with a computerized system. The use of generic encoder/decoder/computer components to receive/analyze/generate/transmit/send/display information over communication network/internet does not impose any meaningful limit on the computer implementation of the abstract idea. At best, the claim(s) are merely providing an environment to implement the abstract idea. (see analysis in claim 1).
According to MPEP 2106.05 (d), elements that the Courts have recognized as well-understood, routine, conventional activity in particular fields are e.g., "Receiving or transmitting data over a network, e.g., using the Internet to gather data, Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward
information); Storing and retrieving information in memory, Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93” (evidence required by Berkeimer memo). Further, according to Berkheimer memo 04/19/2018, section III.A.1, “A specification demonstrates the well-understood, routine, conventional nature of additional elements when it describes the additional elements as well-understood or routine or conventional (or an equivalent term), as a commercially available product, or in a manner that indicates that the additional elements are sufficiently well-known that the specification does not need to describe the particulars of such additional elements to satisfy 35 U.S.C. § 112(a)”.
Applicant’s Specification, [0122] indicate a general-purpose computer perform the instant steps and demonstrates the well-understood, routine, conventional nature of the information processing device (a processor/a memory/a computer) in any computing implementation. Thus, evidence has been provided to show these additional elements are well-understood, routine, conventional activity according to Berkheimer memo. Therefore, for the above-mentioned reasons, viewed as a whole, even in combination, the above steps do not amount to significantly more/do not provide an inventive concept.
Dependent claims 11-16, are merely add further details of the abstract steps/elements recited in claim 10, without including an improvement to another technology or technical field, an improvement to the functioning of the computer itself, or meaningful limitations beyond generally linking the use of an abstract idea to a particular technological environment. Therefore, dependent claims 11-16, are also non-statutory subject matter.
Viewed as a whole, the claims (1-18) do not provide meaningful limitation(s) to transform the abstract idea into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself.
Thus, the claims do NOT recite limitations that are “significantly more” than the abstract idea because the claims do not recite an improvement to another technology or technical field, an improvement to the functioning of the computer itself, or meaningful limitations beyond generally linking the use of an abstract idea to a particular technological environment.
Thus, the claimed invention, as a whole, does not provide 'significantly more' than the abstract idea, and is non-statutory subject matter.
Claim 10-16 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Independent Claim 10 is directed to a platform/system/apparatus as described in the preamble. There’s nothing in the body of the claim that’s structural. Examiner notes that claim 10 recites a system but the claims do not positively recite any elements that necessarily constitute a system, such as computer hardware. There is no structure or hardware cited in the system. Examiner further notes that claim 10 recites a system comprising processing data, outputting to display information, which reasonably can consist of purely software components described in the specification. Software per se, is not considered one of the four statutory categories. Using this interpretation, Examiner finds claim 10 void of system/apparatus structure and fails to belong to an appropriate statutory subject class.
Claims 11-16, depend from claim 10 do not cure the deficiencies set forth above.
Therefore, claims 10-16 are rejected under non-statutory subject matter. See MPEP 2105 and 2106.
Prior Art Rejection
Independent claims 1, 10, as a whole recite a combination of limitations that has Not been found and fail to teach all the claimed feature as define over prior art of record, (the combination of Dudley et al. (US 2013/0090909), Venn et al. (US 2018/0203974), Mortimer et al. (US Patent 11,788,153), Torkamani et al. (US 2019/0311785), Torkamani et al. (US Patent 10,235,496), Venn et al. (US 2022/0333212), were directed towards the entirety of the claimed subject matter and was the best reference known to one of ordinary skill in the art to address the instant claims as well as
NPL1--Kim J, He X, Sinha S. Evolution of regulatory sequences in 12 Drosophila species. PLoS Genet. 2009 Jan;5(1):e1000330. doi: 10.1371/journal.pgen.1000330. Epub 2009 Jan 9. PMID: 19132088; PMCID: PMC2607023.
NPL2--Cocco S, Monasson R, Weigt M. From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction. PLoS Comput Biol. 2013;9(8):e1003176. doi: 10.1371/journal.pcbi.1003176. Epub 2013 Aug 22. PMID: 23990764; PMCID: PMC3749948.
NPL3--Tubiana J, Cocco S, Monasson R. Learning protein constitutive motifs from sequence data. Elife. 2019 Mar 12;8:e39397. doi: 10.7554/eLife.39397. PMID: 30857591; PMCID: PMC6436896.
NPL4--T. -M. Chan, K. -S. Leung and K. -H. Lee, "Memetic Algorithms for De Novo Motif Discovery," in IEEE Transactions on Evolutionary Computation, vol. 16, no. 5, pp. 730-748, Oct. 2012, doi: 10.1109/TEVC.2011.2171972, and
NPL from IDS,
but they fail to teach all the claimed features.
Allowable Subject Matter
Claims 1-18 are deemed to be allowed in light of the specification, amendments filed on 3/23/2023. As to the prior art rejections, upon further search and consideration, it is found that claims 1-18 are allowable subject to outstanding 101 rejections.
As allowable subject matter has been indicated, applicant's reply must either comply with all formal requirements or specifically traverse each requirement not complied with, and pending remedy to outstanding issues cited above. See 37 CFR 1.111(b) and MPEP § 707.07(a).
The prior art made of record and not relied upon is considered pertinent to applicant’s disclosure.
Ranganathan et al. (US 2007/0212700), teaches using biological sequence data to identify the defining biological characteristics of the sequences--the three-dimensional structure and biochemical function.
Selifonov et al. (US Patent 7620502), teaches genetic algorithms and the application of genetic algorithms to nucleic acid shuffling method.
Conclusion
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/SUN M LI/Primary Examiner, Art Unit 3685
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