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 .
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 03 December 2025 has been entered.
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The rejection under 35 USC 112(b) is withdrawn in view of removal of the “different” requirement, but see the Claim Interpretation below. The following rejections and/or objections are either maintained or newly applied. They constitute the complete set applied to the instant application.
Claim Objections
Claims 1 and 10 are objected to because of the following informalities: the wherein clause is amended to recite “a entropy encoder” and should read “an entropy encoder”.
Claim 18 is amended to recite, in its second element, “entropy, by the one or more computer processors, decoding” rather than “entropy decoding, by the one or more computer processors.”
Claim 18 appears to have unnecessary line breaks in the second and third elements. Claim 18 also lacks an “and” between the wherein clauses.
Appropriate correction is required.
Claim Interpretation based on 35 U.S.C. 112(f)
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one having ordinary skill in the art. he broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f):
(A) the claim limitation uses the term "means" or "step" or a term used as a substitute for "means" that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term "means" or "step" or the generic placeholder is modified by functional language, typically, but not always linked by the transition word "for" (e.g., "means for") or another linking word or phrase, such as "configured to" or "so that"; and
(C) the term "means" or "step" or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word "means" (or "step") in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f). The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word "means" (or "step") in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f). The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitation(s) is/are: the “genome compressor” and “reference genome differential coder” for generating a first and second descriptor of the reference genome as found in claims 1 and 10, a “entropy encoder” as found in claims 1, 5, 10, 14, 17, and 28, and a “different entropy decoder” in claims 18 and 25,
Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof. The corresponding structure in the instant specification and independent claims is "a hardware processing device," and thus the steps are interpreted as computer-implemented. The specification must disclose an algorithm for performing the claimed specific computer function, or else the claim is indefinite under 35 U.S.C. 112(b) (MPEP 2181 (II)(B)).
Regarding the recited “genome compressor,” an algorithm associated with a reference genome compressor is not disclosed. Alternative, general purpose compressors are disclosed, such as the ZIP, GZIP, LZMA (pg. 20, line 22) and LZ type algorithm (pg. 21, line 36). Their comparison to the “proposed method” in the specification (pg. 39, Table 17) implies the genome compressor algorithm comprises the recited steps, but the algorithmic steps for the “genome compressor” specifically are not clearly disclosed.
Regarding the “reference genome differential encoder,” the specification discloses “a reference genome differential coding apparatus” which “generates descriptors representing the positions and type of mismatches between the reference genome and the contigs” (pg. 41, last paragraph to pg. 42, first paragraph). These mismatch are disclosed as rftp and rftt in Table 1 of the specification (pg. 13), and the steps for their implementation are interpreted as disclosed in the steps on pg. 25 of the specification.
Regarding the “entropy encoder” and “different entropy decoder,” entropy coders do not appear to be described in the specification (pg. 23).
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
Claim Rejections - 35 USC § 112(a) based on 112(f) Interpretation
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-2, 5-11, 14-18, 21-25, and 28-30 are rejected under 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph, because the claims 1, 10, 18, and 25 recite limitations for steps implemented using a “genome compressor,” “different entropy encoder,” and “different entropy decoder” that has been interpreted to invoke 35 U.S.C. 112(f)/35 U.S.C. 112, sixth paragraph. However, as discussed in the Claim Interpretation section above, the instant specification does not describe the algorithms associated with these elements. Structure provided by the recited algorithms is required but absent. The specification does not provide a disclosure of the algorithm in sufficient detail to demonstrate to one of ordinary skill in the art that the inventor possessed the invention a rejection, and thus fails to provide adequate written description under 35 U.S.C. 112(a) (MPEP 2161.01). Therefore, the recited elements/steps do not meet the written description requirement for means-plus-function limitations.
Claim Rejections - 35 USC § 112(b) based on 112(f) Interpretation
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 1-2, 5-11, 14-18, 21-25, and 28-30 are rejected under 35 U.S.C. U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph, because the claims 1, 10, 18, and 25 recite limitations for steps implemented using a “genome compressor,” a “entropy encoder,” and a “different entropy decoder” that has been interpreted to invoke 35 U.S.C. 112(f)/35 U.S.C. 112, sixth paragraph. Claim limitations of “genome compressor,” “entropy encoder,” and “a different entropy decoder” invoke 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. The specification discloses a genome differential encoder but the steps of more than one different entropy encoder are not disclosed; it is similar with the reciprocal decoders. The steps for compressing the reference genome are unclear as they are not clearly disclosed in the specification. Therefore, the claim is indefinite and is rejected under 35 U.S.C. 112(b).
Applicant may:
(a) Amend the claim so that the claim limitation will no longer be interpreted as a limitation under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph;
(b) Amend the written description of the specification such that it expressly recites what structure, material, or acts perform the entire claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(c) Amend the written description of the specification such that it clearly links the structure, material, or acts disclosed therein to the function recited in the claim, without introducing any new matter (35 U.S.C. 132(a)).
If applicant is of the opinion that the written description of the specification already implicitly or inherently discloses the corresponding structure, material, or acts and clearly links them to the function so that one of ordinary skill in the art would recognize what structure, material, or acts perform the claimed function, applicant should clarify the record by either:
(a) Amending the written description of the specification such that it expressly recites the corresponding structure, material, or acts for performing the claimed function and clearly links or associates the structure, material, or acts to the claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(b) Stating on the record what the corresponding structure, material, or acts, which are implicitly or inherently set forth in the written description of the specification, perform the claimed function. For more information, see 37 CFR 1.75(d) and MPEP §§ 608.01(o) and 2181.
Response to the 03 December 2025 Applicant Remarks regarding 112(f) and Subsequent Rejections
Applicant remarks state the claims recite sufficient structure to perform the claimed function (pg. 9, paragraphs 2-4). This assertion is unpersuasive. For a computer-implemented means-plus-function limitation, the specification must disclose an algorithm for performing the claimed specific computer function or else the claim is indefinite under 35 USC 112(b) and failure to disclose sufficient structure (e.g., the computer and algorithm) will also lack written description under 35 USC 112(a) (MPEP 2181(II)(B)). As discussed in previous office actions, it is clear the steps are being conducted using a computer based on the “hardware processing device” – interpreted as a computer – found in the preambles of the independent claims 1, 10, and 25, and the presence of “computer processors” in claim 18, which was not amended similarly. However, the algorithm is also part of the structure of computer-implemented means-plus-function claims, and that is the aspect of the compressor, encoder, and decoder that are unclear and lack written description. Specifically, it is not considered clearly described what the compressor is or how it works, or what the encoder/decoders are or how they work. Alternatives to the decoders in the specification, such as ZIP, GZIP, and LZMA (pg. 20, lines 21-22) are disclosed but the steps of the instant entropy encoder and respective decoder are not interpreted as clearly disclosed and lack written description support. These rejections may be overcome by persuasive argument regarding the clarity of the compressor, encoder, and decoder and where support for these algorithms can be found in the specification
Claim Rejections - 35 USC § 112(b)
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 1-2, 5-11, and 14-17 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.
Claim 1 recites “each of the first descriptor and the second descriptor are encoded by a[n] entropy encoder” and the entropy encoder is “selected based on a statistical property of each of the first descriptor and the second descriptor.” It is unclear whether the entropy coder must differ between the two descriptors, as under a BRI the statistical property of each may indicate a selection of the same encoder. However, the matching decoder language in claim 18 specifies a “different entropy encoder,” which suggests different entropy encoders are required in claim 1. Dependent claims 2 and 5-9 depend on claim 1 and are rejected on similar grounds. Independent claim 10 and its dependent claims 11 and 14-17 are also rejected for similar reasons.
For compact examination, it is assumed that the first and second descriptors are encoded by different entropy encoders. That is, a first entropy encoder encoding the entropy code of the first descriptor, which is the position of a mismatch, and a second entropy encoder encoding the entropy code of the second descriptor, which is the type of mismatch, is considered to be recited.
To overcome this rejection, it should be clarified whether the entropy encoder for the two descriptors must differ or whether they may be the same, as the matching decoding claims require different decoders, or a similar amendment may be entered.
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), "assembling… aligned reads" (claims 1 and 10), "comparing… reference sequence and… contig" (claims 1 and 10), "obtaining information" (claims 1 and 10), "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)).
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 03 December 2025 Applicant Remarks Regarding 35 USC 101
Applicant remarks state the claims are patent eligible at Step 2A Prong Two, being an improvement to a technology or technical field (MPEP 2106.04(d)(1)) and implementing a particular manufacture (MPEP 2106.04(d)(2)). Applicant remarks point to analogy to those found in KPN Koninklijke KPN NV v. Gemalto M2M GmbH, 942 F.3d 1143 (Fed. Cir. 2019) (pg. 10). The cited case is directed to "specific implementation of varying the way check data is generated that improves the ability of prior art error detection systems to detect systematic errors" and thus the analogy lies in coding for data transmission to detect mismatches and enable lossless compression of reference genomes (pg. 10, last paragraph).
This argument is unpersuasive. The instant claims do not recite data transmission. The specification discloses reference genome availability without “off-band transmission” (pg. 23, lines 32-34) and “solutions based on including the reference genomes in the compressed representation for storage or transmission would result to be detrimental in terms of compression efficiency” (pg. 2, lines 12-14). Thus, it is unclear how the instant claims improve data transmission. Furthermore, even if data transmission was claimed, compressing the data using an algorithm and decompressing it subsequently are mental processes and mathematical concepts implemented on a computer, which does not integrate the abstract idea into a practical application (MPEP 2106.05(f)). An element in addition to the abstract ideas is neither realizing an improvement to a technology or technical field nor a particular machine or manufacture, as the claims recite a general purpose computer in the form of a hardware processing device having computer processors.
Therefore, the rejection under 35 USC 101 is maintained.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure: Paridaens (Bioinformatics 33(10): 1464-1472, 2017; newly cited) teaches “no-reference compression of genomic data with random access functionality” (abstract) using an entropy encoder (pg. 1465, col. 1, fourth paragraph).
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
/JANNA NICOLE SCHULTZHAUS/Examiner, Art Unit 1685