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 .
Claim Status
Claims 1-11 are pending and are examined on the merits.
Priority
As recorded on the 05/23/2025 filing receipt, the instant application claims the benefit of priority to provisional application 63/198,849, filed 11/17/2020. Accordingly, the effective filing date of the claimed invention is 11/17/2020. At this point in examination, all claims have been interpreted as being accorded on this priority date. In future actions, the effective filing date of one or more claims may change, due to amendments to the claims, or further analysis of the disclosure(s) of the priority application(s).
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 05/11/2023 follows the provisions of 37 CFR 1.97. Accordingly, the list of cited references was considered in full by the examiner. A signed copy of the corresponding 1449 form has been included with this Office action.
Drawings
The drawings filed 05/11/2023 are accepted.
Specification
The amendments to the specification filed 10/27/2023 is accepted.
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 1-11 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355). Applicant is also directed to MPEP 2106.
Step 1: The instantly claimed invention (claims 1-10 being representative) is directed to a method and (claim 11 being representative) is directed to a system. Therefore, the instantly claimed invention falls into one of the four statutory categories. [Step 1: YES]
Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in in Prong Two if the recited judicial exception is integrated into a practical application of that exception.
Step 2A, Prong 1: Under the MPEP § 2106.04, the Step 2A (Prong 1) analysis requires determining whether a claim recites an abstract idea, law of nature, or natural phenomenon.
Claims 1-11 recite the following steps which fall under the mathematical concepts, mental processes, and/or certain methods of organizing human activity groupings of abstract ideas:
Claims 1 and 11 recite calculating a Qnet for each genomic sequence of the first plurality of aligned genomic sequences by: calculating a conditional inference tree for each index of the aligned genomic sequences using other indices in the aligned genomic sequences as predictive features; the limitation calculating a Qnet by calculating a conditional inference tree is considered a mathematical calculation, and as such, falls into mathematical concepts groupings of abstract ideas.
Claims 1 and 11 further recite calculating predictors for indices that were used as predictive features when calculating the conditional inference tree for each index; the limitation calculating predictors is considered a mathematical calculation (see specification [0075]: for the formula to calculate predictors), and as such, falls into mathematical concepts groupings of abstract ideas.
Claim 4 recites calculating distances between pairs of sequences of the first plurality of aligned genomic sequences based on the Qnet; the limitation calculating a distance is considered a mathematical calculation, and as such, falls into mathematical concepts groupings of abstract ideas.
Claim 5 recites calculating q-distances as the square root of the Jensen-Shannon divergence of conditional nucleotide distributions from the Qnet for a sequence to conditional nucleotide distributions from the Qnet for a different sequence; the limitation calculating distances is considered a mathematical calculation, and as such, falls into mathematical concepts groupings of abstract ideas.
Claim 6 recites predicting a future dominant strain of the virus based on the calculated q-distances; the limitation predicting based on a calculated distance, given the plain meaning of “predicting”, encompasses observation, evaluation, judgment, and opinion (See MPEP 2106.04(a)(2), subsection III.) performable by human mind (mental process), since human mind is capable of predicting based on known information/calculated distances.
Claim 7 recites determining which sequence of the plurality of aligned genomic sequences has a smallest q-distance from a current dominant strain that is a member of the plurality of aligned genomic sequences; the limitation determining a sequence, given the plain meaning of “determining”, encompasses observation, evaluation, judgment, and opinion (See MPEP 2106.04(a)(2), subsection III.) performable by human mind (mental process), since human mind is capable of determining based on the result of an analysis.
Claim 8 recites calculating Qnets for a second plurality of aligned genomic sequences of the virus, the second plurality of aligned genomic sequences having a second common background different than the first common background of the first plurality of aligned genomic sequences; the limitation calculating Qnets is considered a mathematical calculation, and as such, falls into mathematical concepts groupings of abstract ideas.
Claim 9 recites calculating q-distances from genomic sequences of the first plurality of aligned genomic sequences to genomic sequences of the second plurality of aligned genomic sequences (mathematical calculation of a distance/ mathematical concepts).
Claim 10 recites calculating a probability of the virus jumping from the first species to the second species based on the calculated q-distances from genomic sequences (mathematical calculation of a probability/ mathematical concepts).
Additionally, claims 1-11 recite a correlation between genomic sequence of a virus and a mutation prediction, and as such, falls into judicial exception of Laws of nature and natural phenomena. See MPEP 2106(b) I.
The identified claims recite a law of nature, a natural phenomenon (product of nature) and/or fall into one of the groups of abstract ideas of mathematical concepts, mental processes, and/or certain methods of organizing human activity for the reasons set forth above. See MPEP 2106.04 (a)(2) III and MPEP 2106.04 (b) I. Therefore, claims are directed to one or more judicial exception(s) and require further analysis in Prong Two. [Step 2A, Prong 1: YES]
Step 2A: Prong 2: Under the MPEP § 2106.04, the Step 2A, Prong 2 analysis requires identifying whether there are any additional elements recited in the claim beyond the judicial exception(s) and evaluating those additional elements to determine whether they integrate the exception into a practical application of the exception. This judicial exception is not integrated into a practical application for the following reasons.
The additional elements of claims 1-11 include the following.
Claims 1 and 11 recite receiving a first plurality of aligned genomic sequences of a virus from a database.
Claim 11 recites a system comprising: a processor; and a memory, the memory storing instructions.
The additional elements of a system comprising: a processor; and a memory, the memory storing instructions are generic computer components and/or processes. There are no limitations that indicate that the processor and memory storing instruction in the system require anything other than generic computing systems. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general-purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not integrate a judicial exception into a practical application. See MPEP 2106.05(f).
Furthermore, the additional element of receiving genomic sequences amounts to necessary data gathering and outputting. The courts have found the limitations that amount to necessary data gathering and outputting are insignificant extra-solution activity that do not integrate a recited judicial exception into a practical application in Mayo, 566 U.S. at 79, 101 USPQ2d at 1968 and O/P Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015) (see MPEP 2106.05(g)).
Therefore, the additionally recited elements amount to general purpose computer and insignificant extra-solution activity and, as such, the claims, as a whole, do not integrate the abstract idea into practical application.
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 affect 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).
In Step 2A, Prong 1 above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs).
In Step 2B below, any remaining steps and/or elements are therefore in addition to the identified JE(s). Any such additional steps and additional elements are further discussed in Step 2B.
Here in Step 2A, Prong 2, no additional step or element clearly demonstrates integration of the JE(s) into a practical application.
At this point in examination, it is not yet the case that any of the Step 2A, Prong 2 considerations enumerated above clearly demonstrates integration of the identified JE(s) into a practical application. Referring to the considerations above, none of 1. an improvement, 2. treatment, 3. a particular machine or 4. a transformation is clear in the record.
In conclusion regarding Prong 2, claims 1-11 are directed to an abstract idea. [Step 2A, Prong 2: NO]
Step 2B: In the second step it is determined whether the claimed subject matter includes additional elements that amount to significantly more than the judicial exception. An inventive concept cannot be furnished by an abstract idea itself. See MPEP § 2106.05.
The additional elements of claims 1-11 include the following.
Claims 1 and 11 recite receiving a first plurality of aligned genomic sequences of a virus from a database.
Claim 11 recites a system comprising: a processor; and a memory, the memory storing instructions.
The additional elements of a system comprising: a processor; and a memory, the memory storing instructions are conventional computer components and/or processes. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general-purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not provide significantly more. See Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TU Communications LLC v. AV Auto, LLC, 823 F.3d 607,613,118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit).
Furthermore, the additional element of receiving genomic sequences amounts to necessary data gathering and outputting. The courts have found the limitations that amount to necessary data gathering and outputting are insignificant extra-solution activity that do not amount to significantly more (see MPEP 2106.05(g)).
Therefore, these additional elements are not sufficient to amount to significantly more than the judicial exception. See MPEP 2106.05(g).
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]
Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea without significantly more.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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 1-4, 6-8, and 11 are rejected under 35 U.S.C. 103 as being unpatentable over McHardy (US-20110280907-A1; as cited in the attached 892 form), in view of West (US-20050170528-A1; as cited in the attached 892 form).
Regarding claims 1 and 11, McHardy teaches a computer-implemented method and a computer system for identifying a phylogenetic tree from a plurality of biological sequences (McHardy: abstract).
The recited receiving a first plurality of aligned genomic sequences of a virus from a database, the aligned genomic sequences having a first common background, is taught as, collecting data regarding biological sequences of the biological entity of interest, such as a virus or any other entity; aligning the biological sequences derived from the data collected; an aligned set of biological sequences may be obtained from a database (McHardy: [0044], [0049]. And [0054]; FIG. 1).
McHardy further teaches computing a distance matrix for the aligned biological sequences; McHardy further teaches that any other technique for computing a distance matrix may be used; reconstructing a phylogenetic tree from a set of biological sequences, where the input of the algorithm of this embodiment is an initial set of DNA sequences and the output of the algorithm is an unrooted, multifurcating phylogenetic tree (McHardy: [0051], [0080] and [0147-0151]).
Further regarding claims 1 and 11, McHardy does not teach calculating a conditional inference tree for each index of the aligned genomic sequences using other indices in the aligned genomic sequences as predictive features; and calculating predictors for indices that were used as predictive features when calculating the conditional inference tree for each index. West teaches these limitations.
West teaches a predictive statistical tree model that can be used for a variety of applications including the prediction of disease states, susceptibility of disease states or any other biological state of interest (West: abstract).
Regarding the limitations of calculating a conditional inference tree, West teaches inference and prediction with a single tree using statistical tests to split data and find branch probabilities (West: [0061-0066]).
Regarding the limitations of calculating predictors for indices that were used as predictive features, West teaches predicting the response Z* of a new case based on the observed set of predictor values x* (West: [0066-0067]).
Regarding limitations of a system comprising: a processor; and a memory, the memory storing instructions (claim 11), McHardy teaches a computer system having a memory storing instructions (McHardy: [0091-0094])
Regarding claim 2, the recited first common background of the first plurality of aligned genomic sequences comprises a common year of collection, is taught as, collecting dated sequence data, i.e. each biological sequence is associated with a sampling date or a time stamp; directed graph representation of the subset of biological sequences is generated based on the associated sampling dates (McHardy: [0036], and [0044]).
Regarding claim 3, the recited first common background of the first plurality of aligned genomic sequences comprises a common species from which the aligned genomic sequences were collected, is taught as, sample sequences having low genetic and accordingly, evolutionary divergence, for example, sampled from a single species (McHardy: [0033-0034]).
Regarding claims 4, the recited calculating distances between pairs of sequences of the first plurality of aligned genomic sequences based on the Qnet, is taught as, computing a distance matrix for the biological sequences based on a measure of the distance between biological sequences (McHardy: [0051-0055]). Pairwise alignment of to find best-matching alignments of two biological sequences (McHardy: [0049]). West teaches building a decision tree model starting with a root mode, and training data partitioned to what are essentially the “children” modes using a splitting rule (West: [0004]).
Regarding claim 6, the recited predicting a future dominant strain of the virus based on the calculated q-distances, is taught as, identifying the expected viral strain for a forthcoming virus outbreak, which in turn forms the basis for the vaccine preparation (McHardy: [0015]).
Regarding claim 7, the recited determining which sequence of the plurality of aligned genomic sequences has a smallest q-distance from a current dominant strain that is a member of the plurality of aligned genomic sequences; is taught as, the phylogeny identifies (i) repeated amino acid mutations significantly associated with antigenic drift which allow the recommendation of suitable vaccine strains matching the predominant viral phenotype of the upcoming influenza season (ii) the sites most relevant for antigenic drift and (iii) clades corresponding to the dominating antigenic types of the virus during the analyzed time span (McHardy: [00139]).
Regarding claims 8, the recited calculating Qnets for a second plurality of aligned genomic sequences of the virus, the second plurality of aligned genomic sequences having a second common background different than the first common background of the first plurality of aligned genomic sequences, is taught as, selecting a second node is selected from the group of undone nodes, wherein the group of undone nodes does not include the first node such that the second node is different from the first node (McHardy: [0084-0086]).
Rationale for combining McHardy and West:
In KSR Int 'l v. Teleflex, the Supreme Court, in rejecting the rigid application of the teaching, suggestion, and motivation test by the Federal Circuit, indicated that “The principles underlying [earlier] cases are instructive when the question is whether a patent claiming the combination of elements of prior art is obvious. When a work is available in one field of endeavor, design incentives and other market forces can prompt variations of it, either in the same field or a different one. If a person of ordinary skill can implement a predictable variation, § 103 likely bars its patentability.” KSR Int'l v. Teleflex lnc., 127 S. Ct. 1727, 1740 (2007).
Applying the KSR standard to McHardy and West, Examiner concludes that this combination represents the use of known techniques to improve similar methods. Both McHardy and West are directed to predicting using tree modeling.
McHardy disclosed receiving aligned genomic sequence of a virus from a database and calculating a distance matrix from aligned biological sequence to reconstruct phylogenetic tree. McHardy further teaches that any other methods can be used to calculate the distance metric. In the same field of research, West teaches a conditional inference tree calculation to be used for prediction of any biological state of interest where predictors were calculated when calculating the conditional inference tree.
Combining the phylogenetic identification method of McHardy with the known conditional inference tree calculation of West, as a downstream or standalone analysis, would have allowed evaluating statistical dependencies and conditional properties of data given the tree. One ordinary skilled in the art before he effective filing data of the claimed invention would have had a reasonable expectation of success at integrating the known conditional inference tree method of West to the method of McHardy to analyze which factors significantly drive different states. This combination would have been expected to have provided an improved prediction. Therefore, the invention would have been prima facie obvious to one of skill in the art before the effective filing date of the claimed invention, absent evidence to the contrary.
Claims 5 and 9-10 are rejected under 35 U.S.C. 103 as being unpatentable over McHardy (US-20110280907-A1; as cited in the attached 892 form), in view of West (US-20050170528-A1; as cited in the attached 892 form), as applied to claims 1-4, 6-8, and 11 above, and further in view of Nielsen (On the Jensen–Shannon Symmetrization of Distances Relying on Abstract Means, Entropy 2019, 21(5), 485, pages 1-23; as cited in the attached 892 form).
Claims 5 and 9-10 depend on claim 4 and 1. Limitations of claims 1 and 4 are taught in the above rejections.
Regarding claims 5 and 9, McHardy teaches that the distance matrix may be obtained from a number of different sources, including measured distance (for example from immunological studies) or morphometric analysis, various pairwise distance formulae (such as Euclidean distance) applied to discrete morphological characters, or genetic distance from sequence, restriction fragment, or allozyme data; The decision to split on such a variable is then based on calculating the Bayes' factor values for all pairwise comparisons among variable levels: a split is made on all levels if the Bayes' factor in one of these comparisons is among the highest across all variables, and exceeds the specified Bayes' factor threshold. A split will result in children nodes which will subsequently define further nodes. (McHardy: [0055] and [0090]). West teaches building a decision tree model starting with a root mode, and training data partitioned to what are essentially the “children” modes using a splitting rule (West: [0004]).
McHardy and West do not teach calculating q-distances as the square root of the Jensen-Shannon divergence of conditional nucleotide distributions from the Qnet for a sequence to conditional nucleotide distributions from the Qnet for a different sequence. Nielsen teaches a method of defining the Jensen–Shannon divergence of any distance using parameter mixtures derived from abstract means (Nielsen: abstract), where the square root of JSD is calculated to yield a metric distance satisfying the triangular inequality, where the shortest path between two probability distributions is a direct line transforming the divergence into a true distance metric (Nielsen: pg. 3, para. 5).
Regarding claim 10, the recited first common background comprises a first species, the second common background comprises a second species, is taught as, phylogenetic trees computed with the described method with thirteen sequence sets of different proteins of influenza, subtype H3N2 were compared to maximum parsimony trees (McHardy: [0123]). Further regarding limitations of calculating a probability of the virus jumping from the first species to the second species based on the calculated q-distances from genomic sequences, West teaches a weighted prediction of a tree by determining its implied posterior probability by a score (West: claim 7).
Rationale for combining McHardy, West, and Neilsen:
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of McHardy and West to have used the known technique of using square root of Jensen-Shannon Divergence to calculate the distances, since the square root of JSD mathematically transforms it into a tree metric space, making it usable in evaluating split-node distributions of conditional inference tree. One of ordinary skill in the art would have been motivated to combine these methods based on a finding that Neilson contained a known technique that is applicable to the base method of McHardy and West. One ordinary skilled in the art would have recognize that applying the known technique of Neilsen would have yielded predicable results and resulted in an improved prediction method.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to GHAZAL SABOUR whose telephone number is (703)756-1289. The examiner can normally be reached M-F 7:30-5:00.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Larry D. Riggs can be reached at (571) 270-3062. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/G.S./Examiner, Art Unit 1686
/LARRY D RIGGS II/Supervisory Patent Examiner, Art Unit 1686
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