DETAILED ACTIONS
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 1-2, 5-11, 14-18, 21-25, and 28-30 are pending and examined herein.
Claims 3-4, 12-13, 19-20, and 26-27 are canceled.
Priority
As detailed on the 30 April 2022 filing receipt, the application claims priority as early as 04 February 2017. At this point in examination, all claims have been interpreted as being accorded this priority date as the effective filing date.
Withdrawal / Revision of Objections and/or Rejections
The claim objections based on “a” versus “an”, comma placement, and line breaks are withdrawn in view of amendment correcting typographical issues.
The claim rejections based on 35 USC 112(f) interpretation are withdrawn in view of explanation of the compressor as generating syntax elements (descriptors) and the encoder as encoding the descriptors using arithmetic entropy coding.
The rejection under 35 USC 112(b) not following from 35 USC 112(f) interpretation is withdrawn based on persuasive argument that the different entropy decoders may be the same entropy decoder applied to different descriptors and thus interpreted as separate decoders.
The following rejections and/or objections are either maintained or newly applied. They constitute the complete set applied to the instant application.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-2, 5-11, 14-18, 21-25, and 28-30 are rejected under 35 USC § 101 because the claimed inventions are directed to non-statutory subject matter. "Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 § I). Abstract ideas include mathematical concepts, and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2)). The claims as a whole, considering all claim elements individually and in combination, are directed to a judicial exception at Step 2A, Prong 2, and the additional elements of the claims, considered individually and in combination, do not provide significantly more at Step 2B than the abstract idea of "encoding" or "decoding… genome sequence data."
MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter (MPEP 2106.03)?
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 (MPEP 2106.04(a-c))?
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
The claims are directed to methods (claims 1-2, 5-9, 18, and 21-24) and computer systems (claims 10-11, 14-17, 25, and 28-30), each of which falls within one of the categories of statutory subject matter. [Step 1: Yes]
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 (MPEP 2106.04(a-c))?
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. MPEP § 2106.04(a)(2) further explains that abstract ideas are defined as:
• mathematical concepts (mathematical formulas or equations, mathematical relationships
and mathematical calculations) (MPEP 2106.04(a)(2)(I));
• certain methods of organizing human activity (fundamental economic principles or practices, managing personal behavior or relationships or interactions between people) (MPEP 2106.04(a)(2)(II)); and/or
• mental processes (concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) (MPEP 2106.04(a)(2)(III)).
Mental processes, defined as concepts practically performed in the human mind such as steps of observing, evaluating, or judging information, recited in the independent claims 1, 10, 18, and 25 are: "aligning… reads to one or more reference sequences" (claims 1 and 10), where the human mind is practically equipped to match patterns in nucleotides required for alignment; "assembling… aligned reads" (claims 1 and 10), where the human mind is practically equipped to make an assembly based on matching patterns similar to alignment; "comparing… reference sequence and… contig" to obtain information (claims 1 and 10), where the human mind is practically equipped to make a comparison between strings of nucleotides; "modifying the contig" which comprises "entropy decoding" (claims 18 and 25), "entropy coding" (claims 1, 10), "parsing an encoded input file" (claims 18 and 25), "creating a contig" (claim 10) and "entropy decoding" (claim 18 and 25). The human mind is practically equipped to perform these tasks because the human mind can match the patterns required to align, map, and assemble reads into contigs, compare two sequences, receiving information, and perform modifications of the sequence data to match sequence nucleotide frequencies. Claims 1 and 10 recite a “genome compressor” and “reference genome differential coder,” which are interpreted as abstract, algorithmic steps carried out on a computer system. A similar interpretation is applied to the decoder in claims 18 and 25.
Alternatively, the encoding could be construed as a mathematical concept in which the values are numerically converted and concatenated into vectors. A mathematical formula as such is not accorded the protection of our patent laws (Diehr, 450 U.S. at 191, 209 USPQ at 15 (citing Benson, 409 U.S. 63, 175 USPQ 673)), and thus the discovery of [a mathematical formula] cannot support a patent unless there is some other inventive concept in its application (Flook, 437 U.S. at 594, 198 USPQ at 199) (MPEP 2106.04(a)(2)). Interpretation of encoding in such a way is supported by the 12 May 2026 application remarks as “a class of formal compression algorithms” and “rigorously defined mathematical procedure” (pg. 15, second paragraph), and thus mathematical concepts.
Claims 2 and 11 recite further information about the alignment, which is a mental step.
Claims 5 and 14 recite further information about the contig length selection, which is a mental step.
Claims 6-7, 15-16, 22-23, and 29-30 recite further information about the binarization step, which may be interpreted as a mathematical concept or a mentally performable step.
Claims 8-9, 17, 19, 24, and 28 recite details of the information content of the contigs and thus are part of the mental process.
Hence, the claims explicitly recite numerous elements that, individually and in combination,
constitute abstract ideas. The claims must therefore be examined further to determine whether they
integrate that abstract idea into a practical application (MPEP 2106.04(d)). [Step 2A, Prong One: Yes]
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
The claims recite "mapping… data… on a reference genome" (claims 1 and 10), "a hardware processing device" (claims 1, 10, and 25), and digital encoding or decoding by “one or more computer processors” (claims 1, 10, 18, and 25). The analysis at Step 2A Prong 2 considers the claims as a whole, i.e., the additional elements in combination with the judicial exceptions (see MPEP 2106.05(a)), although the integration or improvement provided in the claim must flow from the additional elements and not the judicial exceptions to be considered persuasive.
Regarding the mapping step, this step is a required data gathering step for creating the contigs, which are then used in the abstract step of entropy coding, and thus it is interpreted as insignificant extra-solution activity (MPEP 2106.05(g)).
Regarding the hardware processing device and processors, these steps are interpreted as a general purpose computer. Using a general purpose computer to implement the abstract ideas does not integrate the abstract ideas into a practical application (MPEP 2106.04(d) § I; and MPEP 2106.05(f)).
None of the dependent claims recite any additional non-abstract elements; they are all directed
to further aspects of the information being analyzed, the manner in which that analysis is performed, or
the mathematical operations performed on the information. [Step 2A Prong Two: No]
Step 2B: Whether the Claims Contain Additional Elements that Amount to an Inventive Concept (MPEP 2106.05)
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 of 101 analysis determines whether the claims contain additional elements that amount to an inventive concept, and an inventive concept cannot be furnished by an abstract idea itself (MPEP 2106.05).
Instructions to implement the abstract idea using a computer are insufficient to constitute an inventive concept that would render the claims significantly more than an abstract idea (see MPEP 2106.05(f)). Receiving and transmitting data (Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information); TLI Communications LLC v. AV Auto. LLC, 823 F.3d 607, 610, 118 USPQ2d 1744, 1745 (Fed. Cir. 2016)) and storing and retrieving information in memory (Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93) are conventional computer functions (MPEP 2106.05(g)). The step of mapping the reads to a reference is a conventional step in creating a contig, as taught by the sequence compression review by Zhu (Briefings in Bioinformatics 16(1): 1-15, 2013; newly cited), as “typical” (pg. 6, col. 1, paragraph 1). Therefore, the additional elements are interpreted as conventional. [Step 2B: No]
Conclusion: Claims are Directed to Non-statutory Subject Matter
For these reasons, the claims, when the limitations are considered individually and as a whole,
are directed to an abstract idea and lack an inventive concept. Hence, the claimed invention does not
constitute significantly more than the abstract idea, so the claims are rejected under 35 USC § 101 as
being directed to non-statutory subject matter.
Response to the 12 May 2026 Applicant Remarks Regarding 35 USC 101
Regarding Step 2A Prong One, applicant remarks state the Patent Office must determine whether the claim is "directed to" a judicial exception such as an abstract idea (pg. 11, last paragraph). This is not consistent with the MPEP, which states, at Prong One, it is determined whether the claims recite a judicial exception (MPEP 2106.04(II)(A)). Whether a claim is directed to an abstract idea is the aim of Step 2A overall.
Further regarding Step 2A Prong One, applicant remarks state the Patent Office must find that the claims as a whole are directed to an abstract idea and it is not enough to find that a claim involves an abstract idea, rather, the claim as a whole must directed to an abstract idea (pg. 12, Section A). This is not consistent with the MPEP, which does not state, in the excerpted portion of MPEP 2106.04(II)(A)(1), that the claim as a whole must be directed to an abstract idea. This is supported by later quoted MPEP 2106.04(a)(2)(III)(A), which is specifically about limitations of the claims being abstract: “Claims do not recite a mental process when they do not contain limitations that can practically be performed in the human mind.” Therefore, at Step 2 Prong One, the limitations are analyzed individually for the presence of abstract ideas, then, if any are found, elements in addition to the abstract ideas are subsequently analyzed to determine if they integrate the abstract ideas into a practical application.
Applicant remarks state the entropy coding steps are not mental steps because they are not the same as human cognition (pg. 15, second and third paragraphs). While it is not clear that a 1:1 correspondence between these steps and human brain function is required as asserted, where entropy coding is disclosed as relating mismatches and their position to a reference and readily understandable by the human mind (Fig. 5), the remarks support the entropy coding steps as a mathematical process: “a class of formal compression algorithms” and “rigorously defined mathematical procedure” (pg. 15, second paragraph). Therefore, these elements are still interpreted as abstract ideas.
Further regarding abstract ideas, applicant remarks state no mathematical formula or calculation explicitly recited and thus the independent claims do not recite mathematical calculation at all (pg. 19, second paragraph). Applicant remarks assert the entropy coding steps are algorithmic, mathematical elements. A mathematical relationship may be expressed in words and there is no particular word or set of words that indicates a claim recites a mathematical calculation. That is, a claim does not have to recite the word "calculating" in order to be considered a mathematical calculation. For example, a step of "determining" a variable or number using mathematical methods or "performing" a mathematical operation may also be considered mathematical calculations when the broadest reasonable interpretation of the claim in light of the specification encompasses a mathematical calculation (MPEP 2106.04(a)(2)).
At Step 2A Prong Two, applicant remarks state steps such as mapping data to a reference are not extra-solution activity because the method cannot be performed without this step (pg. 16, fourth paragraph). Insignificant extra-solution activity in the form data gathering is well-known, imposes tangentially related limitation, and is necessary to perform the steps (MPEP 2106.05(g)). Here, mapping to a reference genome is well-known, does not provide meaningful limitation because the claim is related to compression and not sequence alignment and mapping, and is required for the compression steps.
Further regarding 2A Prong Two, applicant remarks state an improvement provided is enhanced compression using different encoders (pg. 23, first paragraph), including selecting a different entropy decoder to decode each of the first descriptor and the second descriptor based on a binary representation of each of the first descriptor and the second descriptor (pg. 23, second paragraph). However, this indicates the improvement is based on abstract ideas: the entropy encoders (and respective decoders), which were previously asserted in the remarks to be mathematical concepts, and selecting said encoders (and decoders) based on the descriptors, where making a selection is a mental process. Therefore, an additional element does not integrate the judicial exception(s) into a practical application (MPEP 2106.04(d)).
Thus the rejection is maintained.
Conclusion
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Robert J Kallal whose telephone number is (571)272-6252. The examiner can normally be reached Monday through Friday 8 AM - 4 PM EST.
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/R.J.K./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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