DETAILED ACTION
Applicant’s response, filed 05/22/2026, 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 Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn.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
Applicant's claim for the benefit of a prior-filed application, PCT/IB2020/053867, filed 04/23/2020 and claims domestic benefit to US provisional application 62/851898, filed 05/23/2019, which Accordingly, each of claims 1-20 are afforded the effective filing date of the 05/23/2019.
Drawings
The amended specification submitted 03/03/2026 are accepted and the outstanding objections from the previous Office Action are withdrawn.
Claim Rejections - 35 USC § 101
The previous 101 rejection is maintained.
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.
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, device, and system, 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, 12 and 17:
calculating usage of all alternative polyadenylation sites (PAS) in a genomic sequence to identify genomic regulatory patterns,
processing each genomic sub-sequence of the plural genomic sub-sequences, with a corresponding base neural network of plural base neural networks to extract feature vectors representing cis-regulatory elements specific to that PAS
supplying plural feature vector outputs from the plural base neural networks to a specialized interaction layer that includes a sequence of forward Bidirectional Long Short Term Memory Network (Bi-LSTM) cells and a sequence of backward Bi-LSTM cells, wherein each specific pair of a forward Bi-LSTM cell and a backward Bi-LSTM cell uniquely receives a corresponding feature vector output corresponding to a single PAS to model a non-linear, mutually exclusive site competition between that PAS and all other PAS in the gene locus simultaneously.
generating, with a linear transformation layer a scalar value for each PAS, based on a concatenated output from the corresponding specific pair of the forward Bi-LSTM cell and the backward Bi-LSTM cell, wherein the scalar value quantifies a physical recognition efficiency of the PAS by a 3'end processing machinery.
Dependent claims 2, 13, and 18:
simultaneously considering the plural feature vector outputs from the plural base neural networks to jointly calculate the scalar values for all the PAS.
Dependent claim 8:
generating within the specialized interaction layer a scalar value, which represents a log probability for each corresponding PAS.
Dependent claim 9:
applying a soft-max layer to the scalar values of the PAS to generate a usage percentage value of each PAS, where a sum of all the percentage values is 100%.
Dependent claim 11:
wherein the recurrent neural network layer has hidden memory cells configured to remember a state for an arbitrary number of time steps, and each time step corresponds to a single PAS.
Dependent claims 4-7 recite further steps that limit the judicial exceptions in independent claims 1-4 and, as such, also are directed to those abstract ideas. For example, claim 4 further limits the neural network of claim 1, claim 5 further limits the convolutional neural network of claim 4, claim 6 further limits the neural network of claim 4, and claim 7 further limits the outputs of claim 1.
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. Without further detail as to the methodology involved in “processing each genomic sub-sequence”, “extract feature vectors representing cis-regulatory elements specific to that PAS“, “generating a scalar value“, “calculate the scalar values “, “generating within the specialized interaction layer a scalar value “, and “applying a soft-max layer to the scalar values of the PAS to generate a usage percentage “; under the BRI, recited require mathematical techniques.
Therefore, claims 1, 12, and 17 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, 12, and 17:
receiving an arbitrary number of plural genomic sub-sequences, each centered on a corresponding different PAS of a plurality of competing PAS within a same gene locus;
Dependent claims 3, 14, and 19 recite steps that further limit the recited additional elements in the claims. For example, claim 3, 14, and 19 further limits the plural forward Bi-LSTM cells of claim 1;
The claims also include non-abstract computing elements. For example, independent claims 12 and 17 includes a computing device, a processor, and a neural network system.
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 “supply” 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 computing device, a processor, and a neural network system” 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 12 and 17 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 [0081-0084]. 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 relevant technical field here is not generalized "machine learning." The relevant technical field is genomic data processing, specifically, the computational modeling of alternative polyadenylation sites (PAS) [p. 10, par. 2].
It is respectfully found not persuasive. Genomic data processing, specifically, the computational modeling of alternative polyadenylation sites (PAS) is a mathematical algorithm performed on a generic computer and therefore is not a technology or technical field. The additional elements found in the independent claims are a receiving step and general computer elements which do not integrate into a practical application. 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.
Applicant submits the genomic bottleneck recognized by the examiner is the inability of prior art systems to simultaneously resolve high-dimensional, non-linear biochemical interdependencies of hundreds of genomic features across an arbitrary, variable number of competing physical sites [p. 10, par. 4].
It is respectfully found not persuasive. The described process is a mathematical algorithm which is not an additional element. The additional elements found in the independent claims are a receiving step and general computer elements which do not integrate into a practical application.
Applicant submits Examiner dismissed Applicants' Rule 132 Declaration, asserting that an improvement of less than 2% is "not considered a significant [p. 11, par. 5].
It is respectfully found not persuasive. The 2% improvement was to the algorithm, which is math, not to the computer, therefore there is not improvement to technology just an improvement to data processing procedure.
Applicant submits applicants strongly object to the Examiner's assertion under Step 2A, Prong One, that the claimed mathematical operations and data routing can be performed using "pen and paper" [p. 13, par. 2].
As stated in the response to arguments in the Office action: It is respectfully found persuasive. Although these steps have been determined not to be performed in the mind they are mathematical concepts and therefore are still a judicial exception.
Applicant submits this specific architectural arrangement was not routine or conventional in the field of genomic data processing, and it amounts to significantly more than any alleged abstract idea [p. 14, par. 3].
It is respectfully found not persuasive. The claim as a whole integrates the judicial exception into a practical application or amounts to significantly more than the judicial exception when the additional elements are considered both individually and in combination. When an additional element is considered individually by the examiner, the additional element may be enough to integrate the judicial exception into a practical application or to qualify as "significantly more" if it meaningfully limits the judicial exception, e.g., it improves another technology or technical field, improves the functioning of a computer itself MPEP 2106.07(b). The described process is a mathematical algorithm which is not an additional element. The additional elements found in the independent claims are receiving steps and general computer elements which do not qualify as significantly more.
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.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Dawn Bickham whose telephone number (703)756-1817. The examiner can normally be reached on Monday - Friday 8-4.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia Wise can be reached on (571)272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see https://ppair-my.uspto.gov/pair/PrivatePair. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/D.M.B./ Examiner, Art Unit 1685
/Soren Harward/Primary Examiner, TC 1600
Prosecution Insights