DETAILED ACTION
Notice of AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Status of the Claims
Claims 1-20 are pending.
Claims 1, 10 and 19 are objected to.
Claims 1-20 are rejected.
Priority
This application is a is a CON of PCT/US2021/049561 (09/09/2021), which claims priority from US Application No. 63/077,357 (09/11/2020), as reflected in the filing receipt mailed on 06/13/2023. The claims to the benefit of priority are acknowledged and the effective filing date of claims 1-20 is 09/11/2020.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 02/23/2023, 06/04/2024 and 12/17/2025 were considered by the examiner.
Nucleotide and/or Amino Acid Sequence Disclosures
Requirements for patent applications containing nucleotide and/or amino acid sequence disclosures
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825.
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a "Sequence Listing" has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the "Sequence Listing" in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings in Figs. 2 and 4-5 are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Claim objections
Claims 1, 10 and 19 are objected to because of the following informality: the recited "each of the set of sequences" should read "each of the sequences in the set of sequences" for proper claim language, otherwise the claim element would lack meaning since the preceding accessing step refers to only one set of sequences in "accessing a set of sequences." Appropriate correction is required.
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 1-20 are rejected under 35 USC § 101 because the claimed inventions are directed to one or more Judicial Exceptions (JEs) without significantly more. Regarding JEs, "Claims directed to nothing more than abstract ideas..., 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)).
101 background
MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
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)?
Analysis of instant claims
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
The instant claims are directed to a method (claims 1-9), a system (claims 10-18) and a CRM (claims 19-20); each of which falls within one of the categories of statutory subject matter. [Step 1: claims 1-20: 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))?
Background
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)).
Analysis of instant claims
With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims are found to recite abstract ideas that fall into the grouping of mathematical concepts (in particular mathematical relationships and formulas) and mental processes (in particular procedures for observing, analyzing and organizing information) are as follows.
Mathematical concepts (in particular mathematical relationships and formulas) include:
• "generating, for each reference position of the set of reference positions, a feature vector for the reference position that represents each base from the ordered sets of bases aligned to the reference position" (independent claims 1, 10 and 19) and
• "processing the feature vectors for the set of references positions using a machine learning model to generate the consensus sequence for the particular molecule" (independent claims 1, 10 and 19).
The claims identified above read on math. The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation and determined each element performed by mathematical operation. The step directed to “generating and applying feature vectors to generate the consensus sequence prediction for the particular molecule" requires mathematical techniques as the only supported embodiments because it describes the mathematical technique of adding numbers together in words (MPEP 2106.04(a)(2) pertains). Further support for the mathematical techniques used in the claims is provided in the specification at [0064], which discloses one or more look-up tables and/or algorithms to associate one or more raw-data characteristics with a confidence of a base prediction; and at [0050-0051] which discloses a clustering technique to generate a guide tree that identifies relationships between sequences and that then iteratively combines alignments in a manner that begins with a most-similar pair and progresses to repeatedly align a next-most similar sequence; wherein a feature vector may be generated for each of the positions represented in the alignment. Thus, the recited terms correspond to verbal equivalents of mathematical concepts because they constitute actions executed by a group of mathematical steps in a form of a mathematical algorithm; thus mathematical concepts (MPEP 2106.04(a)(2)). A mathematical concept need not be expressed in mathematical symbols, because "words used in a claim operating on data to solve a problem can serve the same purpose as a formula." In re Grams, 888 F.2d 835, 837 and n.1, 12 USPQ2d 1824, 1826 and n.1 (Fed. Cir. 1989). MPEP 2106.04(a)(2) pertains.
Mental processes, defined as concepts or steps practically performed in the human mind such as steps of observations, evaluations, judgments, analysis, opinions or organizing information include:
• "accessing a set of sequences of the particular molecule, each of the set of sequences having been generated independently from other sequences in the set of sequences, each of the set of sequences including an ordered set of bases" (independent claims 1, 10 and 19);
• "performing an alignment process using the set of sequences to generate an alignment result that associates, for each base of the ordered sets of bases of the sets of sequences, the base with a reference position from among a set of reference positions" (independent claims 1, 10 and 19);
• "determining that the sequence includes one or more homopolymers, each of the one or more homopolymers including multiple sequential representations of a same base in the sequence" (claims 5 and 14) and
• "generating a collapsed representation of the sequence in which each of the one or more homopolymers is collapsed to a single base, wherein the alignment process is performed using the collapsed representations of the sequence" (claims 5 and 14).
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined to each cover performance either in the mind (i.e. concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) or because the method only requires a user to manually determine action based on an added number. Under the BRI, the recited limitations are mental processes because a human mind is also sufficiently capable of performing a sequence alignment using pen and paper, determining that the sequence includes homopolymers and generating/writing a collapsed sequences based on the homopolymers identified.
Dependent claims 2-4, 6-9, 11-13, 15-18 and 20 recite further steps that limit the judicial exceptions in independent claims 1, 10 and 19 and, as such, also are directed to those abstract ideas. For example, claims 2, 6, 11, 15 and 20 recite further details about the sequence alignment; claims 3-4, 7-8, 12-13 and 16-17 recite further details about the processing feature vectors step; claims 9 and 18 recite further details about the accessing step.
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))?
Background
MPEP 2106.04(d).I lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application:
An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using 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, as discussed in MPEP § 2106.05(e).
Analysis of instant claims
Instant claims 10-20 recite additional elements that are not abstract ideas:
• "one or more data processors; and a non-transitory computer readable storage medium" (claims 10-18) and
• "computer-program product tangibly embodied in a non-transitory machine-readable storage medium" (claims 19-20).
Considerations under Step 2A, Prong Two
The recited limitations in claims 1-20 are interpreted as requiring the use of a computer. Hence, the claims explicitly recite steps executed by computers and therefore can be described as computer functions or instructions to implement on a generic computer.
Further steps directed to additional non-abstract elements of a computing device/computer do not describe any specific computational steps by which the "computer parts" perform or carry out the judicial exceptions, nor do they provide any details of how specific structures of the computer are used to implement these functions. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions.
The judicial exceptions in the claims are considered to perform the claimed abstract idea with a computer, which is not sufficient to integrate an abstract idea into a practical application (see MPEP 2106.05(f)); since steps that can be performed mentally and merely performing the mental process in a computer environment do not negate the fact that something that can be carried out in the human mind. See MPEP 2106.04(a)(2).III.C.
The recited claims read on data gathering activities; not amounting to a practical application. The type of data doesn’t change that it is mere data gathering or conventional computer receiving means.
Hence, these are mere instructions to apply the abstract idea using a computer and insignificant extra-solution activity and therefore the claims do not integrate that abstract idea into a practical application (see MPEP 2106.04(d) § I; 2106.05(f); and 2106.05(g)).
In Step 2A, Prong One above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs).
In this Step 2A, Prong Two immediately above claim steps and/or elements were identified as part of one or more additional elements. Additional elements are further discussed in Step 2B below.
Here in Step 2A, Prong Two, no additional step or element clearly demonstrates integration of the JE(s) into a practical application.
[Step 2A Prong Two: claims 1-20: No]
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during examination 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).
Claims 1-20 recite a computer or computer functions, interpreted as instructions to apply the abstract idea using a computer, where the computer does not impose meaningful limitations on the judicial exceptions; which can be performed without the use of a computer (MPEP 2106.04(d) § I; and MPEP 2106.05(f)).
When the claims are considered as a whole, they do not integrate the abstract idea into a practical application; they do not confine the use of the abstract idea to a particular technology; they do not solve a problem rooted in or arising from the use of a particular technology; they do not improve a technology by allowing the technology to perform a function that it previously was not capable of performing; and they do not provide any limitations beyond generally linking the use of the abstract idea to a broad technological environment. See MPEP 2106.05(a) and 2106.05(h).
The instant claims constitute insignificant extra solution activity, and when considered individually, are insufficient to constitute inventive concepts that would render the claims significantly more than an abstract idea (see MPEP 2106.05(g)). Hence, these elements, when considered individually, are insufficient to constitute inventive concepts that would render the claims significantly more than an abstract idea (see MPEP 2106.05(d)).
[Step 2B: claims 1-20: No]
Conclusion: Instant claims are directed to non-statutory subject matter
For the reasons above, the claims in this instant application, when the limitations are considered individually and as a whole, are directed to an abstract idea and lack an inventive concept not clearly anything significantly more.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless -
(a)(l) the claimed invention was patented, described in a printed publication, or in public use, on sale,
or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-4, 9-13 and 18-20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Bindewald ("RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers." RNA 12(3):342-352 (2006)) as cited on the attached Form PTO-892.
Claim 1 recites a method for generating a consensus sequence of a particular molecule, the method comprising steps. Claim 10 recites a system for generating a consensus sequence of a particular molecule, the system comprising: one or more data processors; and a non-transitory computer readable storage medium containing instructions which, when executed on the one or more data processors, cause the one or more data processors to perform a set of actions including said steps. Claim 19 recites a computer-program product tangibly embodied in a non-transitory machine-readable storage medium, including instructions configured to cause one or more data processors to perform a set of actions including said steps.
The prior art to Bindewald discloses a machine learning method (i.e. reading on method and system) applying a hierarchical network of k-nearest neighbor classifiers and an RNA sequence alignment in order to predict a consensus RNA secondary structure (pg. 342 Abstract); wherein a non-transitory computer-readable medium is provided via the program KNetFold (pg. 342 Abstract).
The steps performed by the method of claim 1, an electronic device of claim 10, and a non-transitory computer-readable medium of claim 19 comprise:
accessing a set of sequences of the particular molecule, each of the set of sequences having been generated independently from other sequences in the set of sequences, each of the set of sequences including an ordered set of bases;
performing an alignment process using the set of sequences to generate an alignment result that associates, for each base of the ordered sets of bases of the sets of sequences, the base with a reference position from among a set of reference positions;
generating, for each reference position of the set of reference positions, a feature vector for the reference position that represents each base from the ordered sets of bases aligned to the reference position; and
processing the feature vectors for the set of references positions using a machine learning model to generate the consensus sequence for the particular molecule
• Bindewald teaches a machine learning method applying a hierarchical network of k-nearest neighbor classifiers and an RNA sequence alignment in order to predict a consensus RNA secondary structure (i.e. using a machine learning model to generate the consensus sequence for the particular molecule) (pg. 342 Abstract); wherein the classifier system computes a prediction as to whether any two nucleotides i and j form a base pair by using a 14-dimensional feature vector that describes the columns i and j and its four nearest neighboring diagonal and antidiagonal columns (i.e. processing the feature vectors for the set of references positions) (pg. 345 col. 1 para. 4); wherein the proposed system is trained with ‘‘full’’ alignments (i.e. ordered set of bases) and consensus secondary structures generated by RFAM, (i.e. accessing a set of sequences of the particular molecule, each of the set of sequences having been generated independently from other sequences in the set of sequences, each of the set of sequences including an ordered set of bases) (pg. 347 col. 2 para. 2); wherein for each alignment of the training set, feature vectors are computed for all possible pairs of alignment columns (i.e. generating, for each reference position of the set of reference positions, a feature vector for the reference position that represents each base from the ordered sets of bases aligned to the reference position) (pg. 347 col. 2 para. 3) to describe the columns i and j (i.e. performing an alignment process using the set of sequences to generate an alignment result that associates, for each base of the ordered sets of bases of the sets of sequences, the base with a reference position from among a set of reference positions) and its four nearest neighboring diagonal and antidiagonal columns (pg. 345 col. 1 para. 4).
Claims 2, 11 and 20 recites:
wherein performing the alignment processing includes performing multiple sequence alignment
• Bindewald teaches the proposed system being trained with ‘‘full’’ alignments and consensus secondary structures generated by RFAM, (i.e. alignment processing) (pg. 347 col. 2 para. 2); wherein the RFMA set consists of alignments with at least 30 sequences with a length not >500 nucleotides (i.e. multiple sequence alignment) (pg. 347 Table 2).
Claims 3 and 12 recites:
wherein, for each reference position of the set of reference positions, the feature vector includes, for each of the set of sequences, an indication as to which, if any, of the ordered set of bases is aligned to the reference position
• Bindewald teaches that for each alignment of the training set, feature vectors are computed for all possible pairs of alignment columns (i.e. the feature vector includes, for each of the set of sequences, an indication as to which, if any, of the ordered set of bases is aligned to the reference position) (pg. 347 col. 2 para. 3) which allows the algorithm to make a prediction whether any two nucleotides form a base pair or not (pg. 344 col. 2 para. 2).
Claims 4 and 13 recites:
wherein, for each reference position of at least one reference position of the set of reference positions, the feature vector includes an indication that each of at least one of the set of sequences does not include a base aligned to the reference position
• Bindewald teaches that training is performed on a set of ‘‘collapsed’’ alignments (pg. 346 col. 2 para. 2); wherein for each alignment of the training set, feature vectors are computed for all possible pairs of alignment columns to remove all alignment columns that correspond to a gap (pg. 347 col. 2 para. 3); wherein prediction of a collapsed alignment (a square matrix with scores) is expanded to the original alignment size by introducing rows and columns with zeros at the positions that correspond to a gap in the chosen sequence (i.e. feature vector includes an indication that each of at least one of the set of sequences does not include a base aligned to the reference position) (pg. 347 col. 1 para. 1).
Claims 9 and 18 recites:
further comprising: accessing, for each sequence of at least some of the set of sequences, a quality metric for each of one or more bases of the ordered set of bases, wherein at least one of the generated feature vectors includes one or more quality values, each of the one or more quality values including or being based on the quality metric
• Bindewald teaches a machine learning method applying a hierarchical network of k-nearest neighbor classifiers and an RNA sequence alignment in order to predict a consensus RNA secondary structure (pg. 342 Abstract); wherein classifiers form a prediction by using a vector of features where features are values derived from the alignment that describe a pair of alignment columns and its neighboring columns wherein the features are (1) the mutual information of two alignment columns; (2) the fraction of nucleotides that form complementary base pairs; and (3) a nonlinear consensus of the RNAfold prediction probability matrices (i.e. reading on generated feature vectors includes one or more quality values, each of the one or more quality values being based on the quality metric) (pg. 345 col. 1 para. 1).
Claim Rejections - 35 USC § 103
The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under pre-AIA 35 U.S.C. 103(a) are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
A. Claims 5-6 and 14-15 are rejected under 35 U.S.C. 103(a) as being unpatentable over Bindewald as applied to claims 1 and 10 above further in view of Laehnemann ("Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction." Briefings in bioinformatics 17(1):154-179 (2016)), as cited on the attached Form PTO-892.
Claims 5 and 14 recites:
further comprising, for each sequence of at least one of the set of sequences:
determining that the sequence includes one or more homopolymers, each of the one or more homopolymers including multiple sequential representations of a same base in the sequence; and
generating a collapsed representation of the sequence in which each of the one or more homopolymers is collapsed to a single base, wherein the alignment process is performed using the collapsed representations of the sequence
• Bindewald does not teach the recitation above. However, Laehnemann teaches that some properties of nucleic acid sequences are known to raise the error rates for all or most technologies, such long homopolymer stretches (pg. 155 col. 1, para. 1); wherein a tool developed for 454 pyrosequencing data clusters and aligns run-length encoded reads by collapsing all their homopolymer stretches to identify alignment columns with significant differences in homopolymer length between reads (i.e. determining that the sequence includes one or more homopolymers and generating a collapsed representation of said sequences) (pg. 174 col.1 para. 1).
Claims 6 and 15 recites:
wherein the collapsed representation includes, for each of the one or more homopolymers, an indication of a quantity of bases in the homopolymer
• Bindewald does not teach the recitation above. However, Laehnemann teaches that reads that share several of such significant homopolymer length differences across an alignment are separated into a new cluster (i.e. indication of a quantity of bases in the homopolymer) that is fed back into the original process (pg. 174 col.1 para. 1).
Rationale for combining (MPEP §2142-2143)
Regarding claims 5-6 and 14-15, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Bindewald in view of Laehnemann because all references disclose methods for generating nucleic acid sequences. The motivation would have been to incorporate modular development of error correction software for comprehensive data sets (pg. 176 col. 1para. 3 Laehnemann).
Therefore it would have been obvious to one of ordinary skill in the art to substitute generating nucleic acid sequences method of Bindewald to the methods by Laehnemann because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for generating nucleic acid sequences.
B. Claims 7-8 and 16-17 are rejected under 35 U.S.C. 103(a) as being unpatentable over Bindewald as applied to claims 1 and 10 above further in view of Im ("A generative model for constructing nucleic acid sequences binding to a protein." BMC genomics 20.Suppl 13: 967 (2019)), as cited on the attached Form PTO-892.
Claims 7 and 16 recites:
wherein the machine learning model includes a recurrent neural network
• Bindewald does not teach the recitation above. However, Im teaches a generative model for constructing single-stranded nucleic acids binding to a target protein using a long short-term memory neural network (pg. 1 Abstract); wherein the recurrent neural network is capable of learning the property of sequential data (pg. 2 col. 2 para. 2).
Claims 8 and 17 recites:
wherein the machine learning model includes one or more long short-term memory (LSTM) units
• Bindewald does not teach the recitation above. However, Im teaches a generative model for constructing single-stranded nucleic acids binding to a target protein using a long short-term memory neural network (i.e. one or more long short-term memory (LSTM) units) (pg. 1 Abstract).
Rationale for combining (MPEP §2142-2143)
Regarding claims 7-8 and 16-17, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Bindewald in view of Im because all references disclose methods for generating nucleic acid sequences. The motivation would have been to incorporate a machine learning method for constructing an efficient initial pool of nucleic acid sequences (pg. 12 col. 1 para. 1 Im).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the generating nucleic acid sequences method of Bindewald to the methods by Im because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for generating nucleic acid sequences.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FRANCINI A FONSECA LOPEZ whose telephone number is (571)270-0899. The examiner can normally be reached Monday - Friday 8AM - 5PM ET.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia Wise can be reached at (571) 272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/F.F.L./Examiner, Art Unit 1685
/JANNA NICOLE SCHULTZHAUS/Examiner, Art Unit 1685
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