DETAILED ACTION
The Applicant’s response, received 02 January 2026, has been fully considered. 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 .
Status of the Claims
Claims 1-9, 11-13, and 16-24 are pending.
Claims 1-9, 11-13, and 16-24 are rejected.
Claims 1, 16, and 19 are objected to.
Priority
This application claims benefit of 63/051,698, filed 14 July 2020.
Claims 1-9, 11-13, and 16-24 claim benefit of 63/051,698, filed 14 July 2020.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 05 January 2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
Claim Interpretation
Claims 1 and 16 recite the term “hyperdimensional computing.” This term is interpreted to mean a data classification technique using patterns of numbers rather than the numbers themselves, by representing the data in the form of hypervectors (e.g., see Specification at para. [00522]; and see Ge et al. “Classification using hyperdimensional computing: A review.” IEEE Circuits and Systems Magazine, 2020 (03 June), Vol. 20, No. 2, pp. 30-47, as cited in the Office action mailed 01 October 2025).
Claims 1, 2, 4, 6, 7, 9, 16, 17, 18, 20, and 22 recite the term “hypervector.” This term is interpreted to mean raw data encoded to patterns in a high-dimensional space, i.e., high-dimensional vectors (Specification, ¶ [00347]) and also, see Ge et al., as cited above.
Claim Objections
The objection to claim 16 in the Office action mailed 01 October 2025 is withdrawn in view of the amendment received 02 January 2026.
The amendment received 02 January 2026 has been fully considered, however after further consideration, new grounds of objection are raised in view of the amendment.
Claims 1 and 16 are objected to because of the following informalities: The claims do not comply with 37 C.F.R. 1.121(c)(2), because:
all claims shall be submitted with markings to indicate the changes that have been made relative to the immediate prior version of the claims, as described at MPEP 714 & 37 C.F.R. 1.121(c)(2). Claims 1 and 16 in the immediate prior version (received 21 April 2025) recite “a processor configured to execute HD vector operations,” however claims 1 and 16 in the amendment received 02 January 2026 do not recite this limitation, and the claims do not provide any markings to indicate the change relative to the immediate prior version of the claims.
Claim 19 is objected to because of the following informalities: The word “a” should be inserted between the word “comparing” and the word “predefined” in lines two and three.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The rejection of claims 1-9, 11-13, and 16-23 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, in the Office action mailed 01 October 2025 is withdrawn in view of the amendment received 02 January 2026.
The rejection of claims 1-9, 11-13, and 16-23 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, in the Office action mailed 01 October 2025 is maintained in part and withdrawn in part in view of the amendment received 02 January 2026, as noted below.
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-9, 11-13, and 16-24 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
The following rejections in the Office action mailed 01 October 2025 are maintained in view of the amendment received 02 January 2026.
Claims 1 and 16 are indefinite for reciting “computing of the similarity measure leverages hyperdimensional computing principles to mitigate…” at the computing step, because it is not clear as to what the metes and bounds are regarding the term “principles” with respect to mitigating impact of sequencing errors, nucleotide mutations, and noise present in the reference sequence.
Claims 2-9, 11-13, and 17-24 are indefinite for depending from either of claims 1 or 16 and for failing to remedy the indefiniteness of claims 1 and/or 16.
Claims 1 and 16 are indefinite for reciting “wherein the predefined decision threshold is dynamically adjusted based on…” at the “comparing” step because it is not clear as to whether this is an intended use of the predetermined threshold, or if the claims require a step of dynamically adjusting the predefined decision threshold. This limitation is interpreted to recite an intended use of the threshold.
Claims 2-9, 11-13, and 17-24 are indefinite for depending from either of claims 1 or 16 and for failing to remedy the indefiniteness of claims 1 and/or 16.
The amendment received 02 January 2026 has been fully considered, however after further consideration, new grounds of rejection are raised under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, in view of the amendment.
Claims 12 and 24 are indefinite for reciting “the reference sequence comprises that of a chromosome or a genome,” because it is not clear as to what the metes and bounds are with regard to the limitation “comprises that of a chromosome or a genome” (emphasis added), i.e., does the reference sequence comprise the entire sequence of nucleotide characters of a whole chromosome or a genome, or does the reference sequence comprise a number of nucleotide characters that is less than and/or only representative of a particular portion of a chromosome or a genome.
Response to Arguments
The Applicant’s arguments/remarks received 02 January 2026 have been fully considered, and are both persuasive in part and not persuasive in part to the extent that some rejections have been withdrawn and some rejections have been maintained, as noted in the above rejection.
The Applicant states on page 14/19 (as originally labeled) of the Remarks that the instant claims satisfy the requirements of 35 U.S.C. 112(b), however the Applicant does not provide an argument against the indefiniteness rejections as maintained above. Therefore, the Applicant’s arguments/remarks are not persuasive in part to the extent of the rejections above that are maintained from the previous Office action.
Claim Rejections - 35 USC § 101
The amendment received 02 January 2026 has been fully considered, however after further consideration, the rejection of claims 1-9, 11-13, and 16-23 under 35 U.S.C. 101 in the Office action mailed 01 October 2025 is maintained with modification in view of the amendment.
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 1-9, 11-13, and 16-24 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite: (a) mathematical concepts, (e.g., mathematical relationships, formulas or equations, mathematical calculations); and (b) mental processes, i.e., concepts performed in the human mind, (e.g., observation, evaluation, judgement, opinion).
Subject matter eligibility evaluation in accordance with MPEP 2106.
Eligibility Step 1: Step 1 of the eligibility analysis asks: Is the claim to a process, machine, manufacture or composition of matter?
Claims 1-9, 11-13, and 16-24 are directed to a method (i.e., a process).
Therefore, the claims are encompassed by the categories of statutory subject matter, and thus, satisfy the subject matter eligibility requirements under step 1.
[Step 1: YES]
Eligibility Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in Prong Two whether the recited judicial exception is integrated into a practical application of that exception.
Eligibility Step 2A Prong One: In determining whether a claim is directed to a judicial exception, examination is performed that analyzes whether the claim recites a judicial exception, i.e., whether a law of nature, natural phenomenon, or abstract idea is set forth or described in the claim.
Independent claim 1 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
encoding the reference sequence by mapping each nucleotide character in the reference sequence to a corresponding base hypervector, wherein the encoding maintains positional relationships of nucleotide characters within the reference sequence and facilitates parallel computational processing of sequence data (i.e., mental processes and mathematical concepts);
generating a reference hypervector by aggregating the base hypervectors corresponding to nucleotide characters appearing in all sub-strings of the reference sequence, the sub-strings having a length between a specified lower length and a specified upper length (i.e., mental processes and mathematical concepts);
constructing a query hypervector by combining respective near orthogonal base hypervectors for each nucleotide character included in the query sequence, wherein the query hypervector preserves nucleotide ordering and sequence-dependent information (i.e., mental processes and mathematical concepts);
computing a similarity measure between the query hypervector and the reference hypervector by performing a dot product operation, wherein the similarity measure is indicative of a likelihood that the query sequence is present in the reference sequence, and wherein computing of the similarity measure leverages hyperdimensional computing principles to mitigate impact of sequencing errors, nucleotide mutations, and noise present in the reference sequence (i.e., mental processes and mathematical concepts);
comparing a predefined decision threshold to the similarity measure to determine whether the query sequence is present within the reference sequence, wherein the predefined decision threshold is dynamically adjusted based on computational evaluation of sequence variations, mismatches, or probabilistic confidence metrics (i.e., mental processes and mathematical concepts); and
generating an output indicative of whether the query sequence matches or is included in the reference sequence, wherein the output is formatted for further computational processing or display within a genome pattern matching system (i.e., mental processes and mathematical concepts).
Independent claim 16 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
encoding the reference sequence of nucleotide characters by mapping each nucleotide character in the reference sequence to a corresponding base hypervector, wherein the encoding maintains positional relationships of nucleotide characters within the reference sequence and facilitates parallel computational processing of sequence data (i.e., mental processes and mathematical concepts);
generating a reference hypervector by aggregating the base hypervectors corresponding to the nucleotide characters appearing in all sub-strings of the reference sequence, the sub-strings having a length between a specified lower length and a specified upper length within the reference sequence (i.e., mental processes and mathematical concepts);
constructing a query hypervector combining respective near orthogonal base hypervectors for each nucleotide character included in the query sequence, wherein the query hypervector preserves nucleotide ordering and sequence-dependent information (i.e., mental processes and mathematical concepts);
computing a similarity measure between the query hypervector and the reference hypervector by performing a dot product operation, wherein the similarity measure is indicative of a likelihood that the query sequence is present in the reference sequence, and wherein computing of the similarity measure leverages hyperdimensional computing principles to mitigate impact of sequencing errors, nucleotide mutations, and noise present in the reference sequence (i.e., mental processes and mathematical concepts);
comparing a predefined decision threshold to the similarity measure to determine whether the query sequence is present within the reference sequence, wherein the predefined decision threshold is dynamically adjusted based on computational evaluation of sequence variations, mismatches, or probabilistic confidence metrics (i.e., mental processes and mathematical concepts); and
generating an output indicative of whether the query sequence matches or is included in the reference sequence, and determining if the output satisfies requirements of the predefined decision threshold indicative that the query sequence matches or is included in the reference sequence (i.e., mental processes and mathematical concepts).
Dependent claims 2-9, 11, 12, and 17-24 recite the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas, as noted below.
Dependent claim 2 further recites:
defining a variable sliding window having a length that varies from a lower number of nucleotide characters to an upper number of nucleotide characters, the variable sliding window configured to be moved from an initial position in the reference sequence to a last position in the reference sequence (i.e., mental processes and mathematical concepts); and
multiplying a respective hypervector corresponding to each nucleotide character included in the variable sliding window at a current position in a range from the lower number for the variable sliding window to the upper number for the variable sliding window to generate an initial value for a pattern hypervector R (i.e., mental processes and mathematical concepts).
Dependent claim 3 further recites:
(a) moving the variable sliding window so that the current position becomes a previous position and a next position becomes the current position, wherein a first one of the nucleotide characters in the previous position is now outside the variable sliding window and a next one of the nucleotide characters when the variable sliding window was in the previous position is now in a last one of the nucleotide characters included in the current position of the variable sliding window (i.e., mental processes).
Dependent claim 4 further recites:
(b) multiplying a hypervector representing the first one of the nucleotide characters in the previous position that is now outside the variable sliding window by the pattern hypervector R to provide a pattern hypervector S (i.e., mental processes and mathematical concepts); and
(c) multiplying a hypervector representing the next one of the nucleotide characters to generate an updated value for the pattern hypervector R (i.e., mental processes and mathematical concepts).
Dependent claim 5 further recites:
repeating operations (a) through (c) until the variable sliding window reaches the last position in the reference sequence (i.e., mental processes and mathematical concepts).
Dependent claims 6 and 17 further recite:
performing a respective permutation operation on each of the respective near orthogonal base hypervectors representing each of the nucleotide characters included in the query sequence based on a position of a respective nucleotide character in the query sequence to a respective permuted base hypervector for each nucleotide character in the query sequence (i.e., mental processes and mathematical concepts); and
multiplying each respective permuted base hypervector together to generate the query hypervector (i.e., mental processes and mathematical concepts).
Dependent claims 7 and 18 further recite:
the output is a measure of similarity between the query hypervector and the reference hypervector, and comprises dividing the dot product by a value D indicating that the query hypervector and the reference hypervector are equal (i.e., mental processes and mathematical concepts).
Dependent claims 8 and 19 further recite:
determining whether the query sequence is present within the reference sequence comprises comparing a predefined decision threshold value T to the similarity measure, and wherein the query sequence is determined to be included in the reference sequence if the similarity measure exceeds the predefined decision threshold value T (i.e., mental processes and mathematical concepts).
Dependent claim 9 further recites:
replacing the pattern hypervector S with a refined hypervector equal to the pattern hypervector S multiplied by (1 - (dot product of the pattern hypervector S and the pattern hypervector R) divided by the output (i.e., mental processes and mathematical concepts).
Dependent claims 11 and 23 further recite:
the query sequence is betweem 100-200 nucleotide characters (i.e., mental processes).
Dependent claims 12 and 24 further recite:
the reference sequence comprises that of a chromosome or a genome (i.e., mental processes).
Dependent claim 20 further recites:
defining a variable sliding window having a length that varies from a lower number of nucleotide characters to an upper number of nucleotide characters, wherein the variable sliding window is configured to be moved from an initial position in the reference sequence to a last position in the reference sequence (i.e., mental processes);
multiplying a respective hypervector corresponding to each nucleotide character included in the variable sliding window at a current position in a range from the lower number for the variable sliding window to the upper number for the variable sliding window to generate an initial value for a pattern hypervector R (i.e., mental processes and mathematical concepts); and
(a) moving the variable sliding window so that the current position becomes a previous position and a next position becomes the current position, wherein a first one of the nucleotide characters in the previous position is now outside the variable sliding window and a next one of the nucleotide characters when the variable sliding window was in the previous position is now in a last one of the nucleotide characters included in the current position of the variable sliding window (i.e., mental processes);
(b) multiplying a hypervector representing the first one of the nucleotide characters in the previous position that is now outside the variable sliding window by the pattern hypervector R to provide a pattern hypervector S (i.e., mental processes and mathematical concepts); and
(c) multiplying a hypervector representing the next one of the nucleotide characters to generate an updated value for the pattern hypervector R (i.e., mental processes and mathematical concepts).
Dependent claim 21 further recites:
repeating operations (a) through (c) until the variable sliding window reaches the last position in the reference sequence (i.e., mental processes and mathematical concepts).
Dependent claim 22 further recites:
replacing the pattern hypervector S with a refined hypervector equal to the pattern hypervector S multiplied by (1 - (dot product of the pattern hypervector S and the pattern hypervector R) divided by the output (i.e., mental processes and mathematical concepts).
The abstract ideas recited in the claims are evaluated under the broadest reasonable interpretation (BRI) of the claim limitations when read in light of and consistent with the specification. As noted in the foregoing section, the claims are determined to contain limitations that can practically be performed in the human mind with the aid of a pen and paper (e.g., encoding sequences into hypervectors; and computing similarity measures; (e.g., see Ge et al., cited above)), and therefore recite judicial exceptions from the mental process grouping of abstract ideas. Additionally, the recited limitations that are identified as judicial exceptions from the mathematical concepts grouping of abstract ideas (e.g., computing similarity measures; and generating and manipulating hypervectors, which are ordered arrays of numbers, just like a standard vector, but with a high number of dimensions (e.g., see Ge et al., cited above)) are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind.
Therefore, claims 1-9, 11-13, and 16-24 recite an abstract idea.
[Step 2A Prong One: YES]
Eligibility Step 2A Prong Two: In determining whether a claim is directed to a judicial exception, further examination is performed that analyzes if the claim recites additional elements that when examined as a whole integrates the judicial exception(s) into a practical application (MPEP 2106.04(d)). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. The claimed additional elements are analyzed to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d)(III)).
The judicial exceptions identified in Eligibility Step 2A Prong One are not integrated into a practical application because of the reasons noted below.
Dependent claims 2-9, 11, 12, and 17-24 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional elements in independent claims 1 and 16 include:
a computing system comprising a non-transitory memory (claims 1 and 16);
an acceleration architecture implemented on a platform configured for performing parallel computing operations (claim 1);
an acceleration architecture configured for performing parallel computing operations (claim 1); and
receiving a query sequence representing nucleotide characters to be searched within a reference sequence stored in the memory, wherein the query sequence and the reference sequence correspond to genomic data and are formatted for computational analysis (i.e., receiving data) (claims 1 and 16).
The additional elements in dependent claim 13 include:
a graphics processing unit (GPU) performing general purpose computing on the GPU (GPGPU), a field-programmable gate array (FPGA), or an application-specific integrated circuit (ASIC).
The additional elements of a computing system comprising a non-transitory memory (claims 1 and 16); an acceleration architecture configured for performing parallel computing operations (claims 1 and 16); and a graphics processing unit (GPU) performing general purpose computing on the GPU (GPGPU), a field-programmable gate array (FPGA), or an application-specific integrated circuit (ASIC) (claim 13); invoke a computer and/or computer components merely as a tool for use in the claimed process, i.e., executing the abstract ideas, and therefore are not improvements to computer functionality itself, or an improvement to any other technology or technical field, and thus, do not integrate the judicial exceptions into a practical application (see MPEP 2106.04(d)(1)). Furthermore, the additional elements of an acceleration architecture configured for performing parallel computing operations (claims 1 and 16); and a graphics processing unit (GPU) performing general purpose computing on the GPU (GPGPU), a field-programmable gate array (FPGA), or an application-specific integrated circuit (ASIC) (claim 13); merely confine the use of the abstract idea to the particular technological environment of hardware acceleration and parallel processing (MPEP 2106.05(h)).
The additional element of receiving data is a step of gathering data for use in the claimed process – a nominal or tangential addition to the claims that does not meaningfully limit the claims, and therefore does not add more than insignificant extra-solution activity to the judicial exceptions (MPEP 2106.05(g)).
Thus, the additionally recited elements merely invoke a computer and/or computer components as a tool; and/or amount to insignificant extra-solution data gathering activity; and/or confine the use of the abstract idea to the particular technological environment; and as such, when all limitations in claims 1-9, 11-13, and 16-24 have been considered as a whole (i.e., the analysis takes into consideration all the claim limitations and how those limitations interact and impact each other when evaluating whether the exception is integrated into a practical application), the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application, and therefore claims 1-9, 11-13, and 16-24 are directed to an abstract idea (MPEP 2106.04(d)).
[Step 2A Prong Two: NO]
Eligibility Step 2B: Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims are probed for a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they amount to significantly more than the judicial exception (MPEP 2106.05A i-vi).
The claims do not include any additional elements that are sufficient to amount to significantly more than the judicial exception(s) because of the reasons noted below.
Dependent claims 2-9, 11, 12, and 17-24 do not recite any elements in addition to the judicial exception(s).
The additional elements recited in independent claims 1 and 16 and dependent claim 13 are identified above, and carried over from Step 2A: Prong Two along with their conclusions for analysis at Step 2B. Any additional element or combination of elements that was considered to be insignificant extra-solution activity at Step 2A: Prong Two was re-evaluated at Step 2B, because if such re-evaluation finds that the element is unconventional or otherwise more than what is well-understood, routine, conventional activity in the field, this finding may indicate that the additional element is no longer considered to be insignificant; and all additional elements and combination of elements were evaluated to determine whether any additional elements or combination of elements are other than what is well-understood, routine, conventional activity in the field, or simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, per MPEP 2106.05(d).
The additional elements of a computing system comprising a non-transitory memory (claims 1 and 16); and receiving data (claims 1 and 16); are conventional (see MPEP at 2106.05(b) and 2106.05(d)(II) regarding conventionality of computer components and computer processes).
The additional elements of an acceleration architecture implemented on a platform configured for performing parallel computing operations (claims 1 and 16); and a graphics processing unit (GPU) performing general purpose computing on the GPU (GPGPU), a field-programmable gate array (FPGA), or an application-specific integrated circuit (ASIC) (claim 13); are conventional. Evidence for the conventionality is shown by Chickerur et al. (Recent Patents on Computer Science, 2012, Vol. 5, pp. 226-237, as cited in the Office action mailed 01 October 2025). Chickerur et al. reviews computing systems that allow computations to be performed in hardware while retaining the flexibility of software, and provide potential to accelerate applications such as image processing, sequence searching and matching, encryption, decryption, DNA sequence matching and other compute intensive applications (Abstract). Chickerur et al. further reviews the most widely used methods for traditional execution of algorithms, i.e., ASIC (Application Specific Integrated Circuit) and microprocessors (page 226, col. 1) and further reviews reconfigurable computing devices including Field Programmable Gate arrays (FPGA; page 226, col. 2, and throughout). Chickerur et al. further discusses FPGA as an application specific process where it just performs the computations and produces the results, and further discusses the factors providing the accelerated speed gained in FPGAs (page 230, col. 2). Chickerur et al. further discusses how parallel computing can be exploited with FPGA (page 232, col. 1; and page 233, col. 2); and that reconfigurable chips may be combined with GPUs (graphics processing units) for general purpose GPU computing (GPGPU) to achieve more speedup and efficient results (page 235, col. 2).
Therefore, when taken alone, all additional elements in claims 1-9, 11-13, and 16-24 do not amount to significantly more than the above-identified judicial exception(s). Even when evaluated as a combination, the additional elements fail to transform the exception(s) into a patent-eligible application of that exception. Thus, claims 1-9, 11-13, and 16-24 are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exception(s) (MPEP 2106.05(II)).
[Step 2B: NO]
Response to Arguments
The Applicant’s arguments/remarks received 02 January 2026 have been fully considered, but are not persuasive.
The Applicant states on page 14/16 (as originally numbered) independent claims 1 and 16 are directed toward a method of reducing memory access on a computing system configured for searching genomic sequences using hyperdimensional (HD) computing, and that the methods of the instant claims improve the function of a computer/device by reducing memory access when performing the methods of the instant claims, e.g., as illustrated in FIG. 44A and as set forth in paragraph [00372] of the clean version of the substitute specification submitted 23 January 2024, and that moreover, and more particularly, the methods of the instant claims related to determining if a query sequence of nucleotide characters, e.g., a query sequence between 100-200 nucleotide characters as set forth in dependent claims 11 and 23 as amended, is within a reference sequence of characters, e.g., a reference sequence comprising that of a chromosome or a genome as set forth in dependent claim 12 and new claim 24. The Applicant further states on page 15 (para. 1) that obtaining a decision score that is indicative of whether a query sequence, e.g., between 100-200 nucleotide characters, is present in a reference sequence the size of a chromosome or genome that is on the order of at least millions (106) of nucleotide bases cannot conceivably be performed in the human mind under the current law as described herein. The Applicant further states on page 15 (para. 2) that the instant claims recite patent eligible subject matter as the claims, as amended, provide a technical solution to a technical problem, i.e., reduce memory access when searching genomic sequences using HD computing, and therefore integrate any putative abstract idea that may be set forth in the claims into a practical application, improving the function of a computer/device performing the method of the instant claims, and that furthermore, methods of the instant claims at least include recitations that could not conceivably be performed in the human mind.
These arguments are not persuasive, because first, with regard to the Applicant’s argument that the “methods of the instant claims improve the function of a computer/device by reducing memory access when performing the methods of the instant claims,” it is noted that a process of manipulating data (e.g., encoding a reference sequence and/or generating a reference hypervector and/or constructing a query hypervector) to perform calculations or algorithms (e.g., computing a similarity measure and/or comparing a predefined decision threshold to the similarity measure to determine whether the query sequence is present within the reference sequence) that require less memory consumption and time is not an improvement to the functionality of a computer itself, but rather a purported improvement to the abstract idea, e.g., an algorithm that requires less memory consumption because the algorithm itself requires fewer bits to be stored in a physical memory is not an improvement to the physical memory itself. Second, with regard to the Applicant’s argument that “obtaining a decision score that is indicative of whether a query sequence, e.g., between 100-200 nucleotide characters, is present in a reference sequence the size of a chromosome or genome that is on the order of at least millions (106) of nucleotide bases cannot conceivably be performed in the human mind under the current law as described herein,” it is noted that the amount of data and/or the amount of time to perform the process steps, in and of themselves is not a limitation which takes a process out of the realm of the human mind. It is the process performed on that data which is the mental step, and mental steps identified in the claims do not have to be the fastest, most efficient, or require specialized computing elements. Thus, although the amount of data may be considered to be significantly large and take considerable time and effort to process manually, the use of a computer to perform the claimed method at a rate and accuracy that can far outstrip the mental performance of a skilled artisan does not change the nature of the activity being performed (i.e., an abstract idea), and therefore does not materially alter the patent eligibility of the claimed subject matter.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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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/S.W.B./Examiner, Art Unit 1687
/Joseph Woitach/Primary Examiner, Art Unit 1687
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