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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 06/30/2026 has been entered.
Applicant Response
Applicant's response, filed 06/30/2026, 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 Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn.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.
Claim Status
Claims 2 and 12 are canceled.
Claims 1, 3-11, and 13-20 are pending and under examination herein.
Claims 1, 3-10, 15 and 18 appear allowable.
Claims 11, 13-14, 16-17 and 19-20 are rejected.
Priority
The instant application does not claim priority to another application. As such, the effective filing date assigned to each of claims 1, 3-11, and 13-20 is 09/30/2021.
Drawings
The drawings filed 09/30/2021 were accepted by the examiner in the office action mailed 10/01/2025.
Claim Objections
The objections to claims 5, 10, 15 and 18 are withdrawn in view of claim amendments filed 06/01/2026.
Claim Rejections - 35 USC § 112
The rejections of claims 1-20 are rejected under 35 U.S.C. 112(b) are withdrawn in view of claim amendments filed 12/30/2025.
Claim Rejections - 35 USC § 101
The rejections of claims 1 and 3-10 under 35 U.S.C. 101 are withdrawn in view of claims amendments filed 06/01/2026, which integrate the recited judicial exceptions into practical application. Specifically, the generation of sub-alignment data using fused instructions performed by a parallel processor and/or comprising SIMD instructions provides an improvement in computer technology by allowing for few instructions and fewer cycles relative to a conventional instruction sequence, as disclosed in the instant specification para 0161-0163.
The rejections of claims 15, and 18 under 35 U.S.C. 101 are withdrawn in the office action mailed 04/01/2026 in view of claims amendments filed 12/30/2025, which integrated the recited judicial exceptions into practical application. Specifically, the generation of sub-alignment data using fused instructions performed by a parallel processor and/or comprising SIMD instructions provides an improvement in computer technology by allowing for few instructions and fewer cycles relative to a conventional instruction sequence, as disclosed in the instant specification para 0161-0163.
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 11, 13-14, 16-17 and 19-20 remain rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea/law of nature/natural phenomenon without significantly more. In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
Claims 11 and 20 recite generating first sub-alignment data included in a first cell in a first array of cells based on second sub-alignment data included in a second cell in the first array of cells and a second array of cells, wherein the generating the first sub-alignment data includes: generating a first E value included in the first sub-alignment data based on fourth sub-alignment data included in a fourth cell in the second array of cells; generating a first F value included in the first sub-alignment data based on the second sub-alignment data included in the second cell; and generating a first sub-alignment score included in the first sub-alignment data based on the first E value, the first F value, and a fifth cell in the second array of cells; and generating third sub-alignment data included in a third cell in the first array of cells based on the first sub-alignment data included in the first cell and the second array of cells.
Claims 6 and 16 recite further comprising …overwriting fourth sub-alignment data included in a fourth cell in the second array of cells with fifth sub-alignment data based on sixth sub-alignment data included in a fifth cell in the second array of cells and the first array of cells.
Claims 8 recite further comprising: determining a maximum sub-alignment score and a predicate based on a first sub-alignment score included in the third sub- alignment data and a previous maximum sub-alignment score, wherein the predicate indicates that the first sub-alignment score is a source of the maximum sub-alignment score; and based on the predicate, setting a maximum scoring column position equal to a column position associated with the first sub- alignment score.
These recitations equate to steps of collecting information, analyzing data and making observations, evaluations and judgements that can be carried out in the human mind. Specifically, executing instructions to generate or overwrite sub-alignment data included in arrays based on other sub-alignment data can be practically performing the human mind as claimed, and are similar to the concepts of collecting and comparing known information in Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1067, 100 USPQ2d 1492, 1500 (Fed. Cir. 2011) and collecting information, analyzing it, and reporting certain results of the collection and analysis in Electric Power Group v. Alstom, S.A., 830 F.3d 1350, 1353-54, 119 USPQ2d 1739, 1741-42 (Fed. Cir. 2016) that the courts have identified as concepts that can be practically performed in the human mind. Therefore, each of the above recited limitations fall under the “Mental Processes” grouping of abstract ideas. Furthermore, the steps of generating or overwriting sub-alignment data included in arrays based on other sub-alignment data when performing sub-alignment computation for a matrix-filling phase of a Smith-Waterman algorithm equate to organizing information and manipulating information through mathematical correlations and reciting a mathematical equation, similar to the concepts of taking existing information, manipulating the data using mathematical functions, and organizing this information into a new form in Digitech Image Techs., LLC v. Electronics for Imaging, Inc., 758 F.3d 1344, 1350, 111 USPQ2d 1717, 1721 (Fed. Cir. 2014). Therefore, these limitations fall under the “mathematical concepts” grouping of abstract ideas. Claims 3-5, 7, 9, 13, 17, and 19 further qualify the judicial exceptions. As such, claims 11, 13-14, 16-17 and 19-20 recite an abstract idea (Step 2A, Prong 1: YES).
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). This judicial exception is not integrated into a practical application because the claims do not recite an additional element that reflects an improvement to technology, applies or uses the recited judicial exception to affect a particular treatment for a condition, implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, effects a transformation or reduction of a particular article to a different state or thing or applies or uses 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. Rather, the instant claims recite additional elements that amount to mere data gathering and outputting and mere instructions to implement the abstract idea in a generic computing environment. Specifically, the claims recite the following additional elements:
Claim 11 recites one or more non-transitory computer readable media and one or more processors; execution of a first and second fused instruction.
Claim 14 recites wherein the first array of cells is stored contiguously in a first register file.
Claim 20 recites one or more memories storing instructions and one or more processors; .
The execution of fused instructions is recited generically, and amounts to generally linking the use of a judicial exception to a particular technological environment or field of use (see MPEP 2106.05(h)). The claims merely recites using a generic computing systems and computer program products to carry out instructions to implement an abstract idea on a computer. The computer system and computer program product as claimed fails to recite details of how a solution to a problem is accomplished and only recites the idea of a solution or outcome. There are no limitations that indicate that the claimed steps require anything other than generic computing systems. As such, these limitations equate to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. Furthermore, 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 Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit). Therefore, there is no indication that any of these additional elements provide a practical application of the recited judicial exception outside of the judicial exception itself. As such, claims 11, 13-14, 16-17 and 19-20 are directed to an abstract idea (Step 2A, Prong 2: NO).
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). Further analyzing the additional elements under step 2B, the additional elements as described above do not rise to the level of significantly more than the judicial exception. As directed in the Berkheimer memorandum of 19 April 2018 and set forth in the MPEP, determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either 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 under the 2B analysis, 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); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit). As such, claims 11, 13-14, 16-17 and 19-20 are not patent eligible under 35 U.S.C. 101.
Response to Applicant’s Arguments
Applicant states the independent claims have been amended to recite the previously recited limitations of claim 2, which recited patentable subject matter, and request withdrawal of the rejection (Applicant’s Arguments, p 7, para 5).
It is respectfully submitted that this is not persuasive, are the arguments are not commensurate with the scope of the claims. The rejection of claim 2 under 35 U.S.C. 101 was withdrawn in the office action mailed 04/01/2026 because the generation of sub-alignment data using fused instructions performed by a parallel processor was found to provide an improvement in computer technology by allowing for few instructions and fewer cycles relative to a conventional instruction sequence, as disclosed in the instant specification para 0161-0163, and therefore integrated the recited judicial exceptions into practical application. While the amendments filed 06/01/2026 canceled claim 2 and amended claim 1 to recite some of the limitations from claim 2, claims 11 and 20 do not appear to recite the patentable subject matter, as the fused instructions are not performed by a parallel processor, and therefore, the proposed amendments do not appear to be sufficient to overcoming the current rejection. Therefore, the rejections of claims 11, 13-14, 16-17 and 19-20 are maintained. Amending the claims to include the patentable subject matter would likely be sufficient to overcoming the rejection.
Prior Art
Claims 1, 3-11, and 13-20 appear to be free of prior art as the closest prior art to Koliogeorgi et al. (2019 29th International Conference on Field Programmable Logic and Applications (FPL) 2019, pp. 74-80. IEEE; previously cited; hereafter referred to as Koliogeorgi), Fei et al. (Interdiscip Sci Comput Life Sci 2018, 10, 176–188; previously cited; hereafter referred to as Fei), and Zhao et al. (PLoS ONE 2013, 8(12), e82138, pp 1-7; previously cited; hereafter referred to as Zhao) does not appear to teach or disclose executing a first instruction to generate first sub-alignment data included in a first cell in a first array of cells based on second sub-alignment data included in a second cell in the first array of cells and a second array of cells; and executing a second instruction to generate third sub-alignment data included in a third cell in the first array of cells based on the first sub-alignment data included in the first cell and the second array of cells.
Koliogeorgi teaches dataflow acceleration of Smith-waterman and discloses optimizing the architecture using an interleaving data schemes which would operate in a round robin manner to compute the latency anti-diagonals of which corresponds to ta similarity matrix of a difference read-reference pair and affects the layout of the skewed matrix while preserving the skewed layout (title; abstract; p 3, col 1, para 3-p 4, col 1, para 1; fig 5).
Fei discloses fine-grained parallelized SW algorithms using affine gap penalty and implement a parallel computing structures to accelerating the SW with backtracking on FPGA platform and using a wavefront approach with a linear systolic computing array in which each anti-diagonal is computed in parallel with a linear PE array (abstract; p 179, col 2, para 3-p 180, col 2, para 1).
Zhao discloses a new method to generate the full optimal alignment results and a suboptimal score in linear space at little cost of efficiency and a C/C++ library, which extends Farrar’s Striped Smith-Waterman (SSW) to return alignment information in addition to the optimal Smith-Waterman score, and further discloses that they “record the optimal alignment ending positions during the SIMD SW calculation and generate the detailed alignment by a reversed SIMD SW and a banded SW. When the score matrix is filled by the SIMD SW calculation, we store the maximal score of each column in a “max” array and record the complete column that has the maximal score of the whole matrix. Next, we locate the optimal alignment ending position on the reference and the query by seeking the maximal score in the array and the recorded column respectively. The reversed SIMD SW locates the best alignment beginning position from the ending position by calculating a much smaller scoring matrix. Then, the banded SW (whose band is defined by the beginning and ending positions) generates the detailed alignment” (abstract; p 5, col 1, para 2-col 2, para 1).
However, Koliogeorgi, Fei, and Zhao appear to be silent on the execution of the first and second instructions to generate the first and third sub-alignment data as recited in the instant claims.
Conclusion
Claims 1, 3-10, 15 and 18 appear allowable. Claims 11, 13-14, 16-17 and 19-20 are rejected.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to NIDHI DHARITHREESAN whose telephone number is (571)272-5486. The examiner can normally be reached Monday - Friday 9:00 - 5:00.
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/N.D./ Examiner, Art Unit 1686
/Karlheinz R. Skowronek/ Supervisory Patent Examiner, Art Unit 1687
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