DETAILED ACTION
Applicant’s response, filed 08/26/2025, 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 Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn.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 37-54 are pending.
Claims 1-36 are canceled.
Claims 37-54 are rejected.
Priority
This application is a continuation of a US application 15/841106, now US PAT 11183271, filed on 12/13/2017 which is a continuation of PCT/CA2016/050689 filed on 06/15/2016, which is a continuation in part of US application 14/739432, now US PAT 10185803, filed on 06/15/2015.
Accordingly, each of claims 37-54 are afforded the effective filing date of 06/15/2015.
Information Disclosure Statement
The information disclosure statements (IDS) filed on 07/30/2021 and 09/24/2021 are in compliance with the provisions of 37 CFR 1.97 and have therefore been considered. Signed copies of the IDS documents are included with this Office Action.
Drawings
The amendments to specification submitted 08/26/2025 are accepted and the outstanding objections from the previous Office Action are withdrawn.
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The outstanding rejections to the claims are withdrawn in view of the amendments submitted herein.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 37-54 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 maintatined.
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 non-transitory computer-readable medium, 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).
The claims also recite a law of nature or a natural phenomenon. The MPEP at 2106.04(b) further explains that laws of nature and natural phenomena include naturally occurring principles/relations and nature-based products that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature.
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) as well as a law of nature or a natural phenomenon are as follows:
Independent claim 37:
to generate a set of input values digitally representing a variant of the two or more biologically related variants, wherein each of the two or more biologically related variants is derived from a biological sequence through a combination of substitutions, insertions, or deletions to the biological sequence
to generate a set of numerical output values representing a molecular phenotype for the variant, wherein the trained MPNN comprises one or more feature detectors, each feature detector of the one or more feature detectors obtaining input values from (i) one or more of the input values in the input layer, or (ii) an output value of another feature detector of the one or more feature detectors, and wherein the molecular phenotype comprises numerical elements which quantify biological molecules of cells
determining, a numerical link distance for pairs of variants of the two or more biologically related variants at least in part by comparing the numerical elements of the molecular phenotypes for the pairs of variants.
Dependent claim 41:
to determine the numerical link distance for a pair of variants at least in part by applying a function to a difference between the numerical elements of the molecular phenotypes for the pair of variants.
Dependent claim 46:
associating each of the unlabeled variants with the associated label of the labeled variant of the labeled variants having a smallest numerical link distance to the unlabeled variant.
Dependent claim 48:
determining a numerical weight for the unlabeled variant and the labeled variant by applying a weighting module to the numerical link distance between the unlabeled variant and the labeled variant; and
determining an associated label for the unlabeled variant by summing terms corresponding to the labeled variants, wherein each of the terms is obtained by multiplying the numerical weight for the unlabeled variant and the corresponding labeled variant into the associated label for the corresponding labeled variant.
Dependent claim 49:
dividing the numerical weight for the unlabeled variant and the labeled variant by a sum of the weights for the unlabeled variant and the labeled variant
Dependent claim 50:
to determine, for each of one or more pairs of variants in the two or more biologically related variants, a measure of proximity of the pair of variants within the biological sequence, wherein the numerical link distance is determined at least in part by processing the measure of proximity of the pair of variants with the numerical elements of the molecular phenotypes for the pair of variants.
Dependent claim 51:
determines weights differently for different values of the labels.
Dependent claim 52:
determine the numerical link distance for the pair of variants.
Dependent claim 54:
applying a training procedure to a dataset of examples, wherein each of the examples comprises a pair of variants and a target value for a link distance of the pair of variants
Dependent claims 38-39, 42-45, and 47 recite further steps that limit the judicial exceptions in independent claim 37 and, as such, also are directed to those abstract ideas. For example, claim 38 further limits the biological sequence of claim 37, claim 39 further limits the set of input values of claim 37, claim 44 further limits the molecular phenotype of claim 37, claim 45 further limits the one or more variants of claim 37, and claim 47 further limits the unlabeled variants of claim 37.
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 associating. Without further detail as to the methodology involved in “associating each of the unlabeled variants“, under the BRI, one may simply, for example, use pen and paper to associate each of the unlabeled variants with the associated label of the labeled variant of the labeled variants having a smallest numerical link distance to the unlabeled variant.
The steps of “generate a set of numerical output values”, “generate a set of numerical output values”, “determining, a numerical link distance”, “determine the numerical link distance for a pair of variants”, “determining a numerical weight for the unlabeled variant”, “determining an associated label for the unlabeled variant by summing terms”, “dividing the numerical weight for the unlabeled variant”, “to determine, … a measure of proximity:, and “applying a training procedure “ those recited in the dependent claims require mathematical techniques as the only supported embodiments, as is disclosed in the specification at: [0012, 0060, 0072, and 0075]
Therefore, claim 37 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 claim 37:
encoder
input layer
molecular phenotype neural network (MPNN)
comparator
Dependent claim 40:
input layer
to obtain an additional a set of values digitally representing a set of contexts, wherein the molecular phenotype further comprises numerical elements for at least one of the set of context
Dependent claim 41:
comparator
Dependent claim 45:
labeling unit
to obtain the numerical link distances for the pairs of variants of the two or more biologically related variants from the comparator, and associate labels with unlabeled variants of the two or more biologically related variants based at least in part on the numerical link distances
Dependent claim 50:
comparator
Dependent claim 52:
comparator
trained link neural network
Dependent claim 53:
trained link neural network
The claims also include non-abstract computing elements. For example, independent claim 37 and those dependent therefrom include a non-transitory computer-readable medium
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 “obtain”, 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 “non-transitory computer-readable medium” 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)).
With respect to claims 37, 40-41, 45 and 50-53, the limitations in reciting “trained molecular phenotype neural network (MPNN)”, “encoder”, “input layer”, “comparator”, labeling unit”, and “trained link neural network” provide nothing more than mere instructions to implement an abstract idea on a generic computer. See MPEP 2106.05(f). MPEP 2106.05(f) provides the following considerations for 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: (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.
The recitation of “a trained molecular phenotype neural network (MPNN)” also merely indicates a field of use or technological environment in which the judicial exception is performed. Although the additional element “a trained molecular phenotype neural network (MPNN)” limits the identified judicial exceptions “processing the set of input values by the trained MPNN” this type of limitation merely confines the use of the abstract idea to a particular technological environment (neural networks) and thus fails to add an inventive concept to the claims. See MPEP 2106.05(h).
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 claim 37 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 [0046]. The prior art Fernandez et al. (US 9,740,817 B1) recognizes that these computing elements comprising a system, input elements, output elements and comparators are routine, well understood and conventional in the art. Fernandez discloses systems which comprise input/output, and comparators, wherein the system also comprises a molecular phenotype neural network. At column 17-19, Fernandez discloses that neural networks can be employed to obtain the data values required (sequences and molecular phenotype values, disclosed as “labels” by Fernandez) by the claim. Comparators are also disclosed by Fernandez, for example in Fig 1C and descriptions. The specification also notes that computer systems comprising neural networks and comparators are suitable for use in the invention and are routine, well understood and conventional at [0047]. 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).
With respect to claim 37 and those claims dependent therefrom: the additional limitations listed above do not rise to the level of significantly more than the judicial exception. The prior art Bassett, Jr. (US 2014/0359422 A1, PTO-1449) recognizes that data gathering element which obtain biological sequence variants and molecular phenotype feature values is routine, well understood and conventional in the art. The disclosures of Bassett Jr. meet the broadest reasonably interpretation of the input elements, feature detectors, and the output layers, whose only claimed functions are obtaining data. The prior art Fernandez et al. (US 9,740,817 B1) recognizes that these computing elements comprising a system, input elements, output elements and comparators are routine, well understood and conventional in the art. Fernandez discloses systems which comprise input/output, and comparators, wherein the system also comprises a molecular phenotype neural network. At column 17-19, Fernandez discloses that neural networks can be employed to obtain the data values required (sequences and molecular phenotype values, disclosed as “labels” by Fernandez) by the claim. Comparators are also disclosed by Fernandez, for example in Fig 1C and descriptions. The specification also notes that computer systems comprising neural networks and comparators are suitable for use in the invention and are routine, well understood and conventional at [0047].These limitations in addition to the law of nature do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not effect a transformation of matter, nor do they provide a non-conventional or unconventional step. These additional limitations 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 (MPEP 2106.05(b)&(c).)
With respect to claim 37 and those claims dependent therefrom, the additional limitations of an encoder do not rise to the level of significantly more than the judicial exception. The discloses of Libberchet et al (Libbrecht, Maxwell W., and William Stafford Noble. "Machine learning applications in genetics and genomics." Nature Reviews Genetics 16.6 (2015), newly cited) describe data being encoded into fixed-length features [p. 327, Fig. 5]. Libberchet also discloses adjusting weights on the edges to predict the given label [p.325, Fig. 3] which corresponds to a weighting unit. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not effect a transformation of matter, nor do they provide a non-conventional or unconventional step. These additional limitations 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 (MPEP 2106.05(b)&(c).)
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 that claim 37 is directed to patent eligible subject matter for at least the reason that claim 37 integrates the alleged judicial exception into a practical application and/or imposes meaningful limit on any alleged judicial exception [p. 9, par. 4].
It is respectfully found not persuasive. It is important to keep in mind that an improvement in the abstract idea itself (e.g. a recited fundamental economic concept) is not an improvement in technology. Furthermore, it is important to note, the judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements or by the additional element(s) in combination with the recited judicial exception. See MPEP 2106.05(a). With respect to claim 37, the additional elements of the claims do not integrate the judicial exceptions into a practical application for the following reasons. The use of an encoder, comparator, and MPNN are mere “apply it” (or an equivalent) with the judicial exception, or mere instructions to implement an abstract idea on a computer, or merely uses a computer as a tool to perform an abstract idea - see MPEP 2106.05(f).
Applicant submits that claims 37-60 include additional limitations that amount to significantly more than the alleged judicial exception, and thus are subject matter eligible [p. 9, par. 4].
It is respectfully found not persuasive. For additional elements to amount to significantly more than the judicial exception itself they must fall into one if the categories noted in MPEP 2106.05(A). The applicant states the claims solve a problem rooted in computer technology, yet 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. Also, the specification also notes that computer systems comprising neural networks and comparators are suitable for use in the invention and are routine, well understood and conventional at [0047].
Double Patenting
The previous rejection has been withdrawn due to filing of a Terminal Disclaimer on 08/30/2025.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. 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.
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/D.M.B./Examiner, Art Unit 1685 /Soren Harward/Primary Examiner, TC 1600