DETAILED ACTION
Applicant's response, filed 5/07/2026, has been fully considered.
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 .
Priority
This application filed 07/28/2022 claims priority from Provisional Application 63229897 , filed 08/05/2021. The claims are therefore examined as filed on 08/05/2021, the effective filing date. In future actions, the effective filing date of one or more claims may change, due to amendments to the claims, or further review of the priority application(s).
Election/Restrictions
Claims 4-15 and 17-21 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected species, there being no allowable generic or linking claim.
Claims 25-30, drawn to a nonelected invention, have been cancelled by the Applicant.
Elections were made without traverse in the reply filed on 5/07/2026.
Applicant’s election without traverse of claims 1-3, 16, and 22-24 in the reply filed on 5/07/2026 is acknowledged.
Claim Status
Claims 1-24 are pending.
Claims 4-15 and 17-21 are withdrawn.
Claims 1-3, 16, and 22-24 are directed to the elected invention.
Claims 25-30 are cancelled.
Claims 1-3, 16, and 22-24 are examined.
Claims 1-3, 16, and 22-24 are rejected.
Information Disclosure Statement
The Information Disclosure Statements are in compliance with the provisions of 37 CFR 1.97. Accordingly, all references have been considered.
Claim Interpretation
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 following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
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.
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) are the variant encoding subnetwork (claims 1-3), the protein contact map generation sub-network (claims 1, 16, and 22-24 ), and the pathogenicity scoring sub-network (claim 1).
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. Sections [76-78] describe the sub-networks as being implemented in computer software or hardware, or a combination.
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
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.
Claim 16 is 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 16 recites " The variant pathogenicity prediction network of claim 12...” There is insufficient antecedent basis for this limitation in the claim, as claim 12 is currently withdrawn. Therefore, the claim is considered indefinite. Claim 16 should be amended to depend from an elected claim.
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 1-3, 16, and 22-24 are rejected under 35 U.S.C. 101 because the claimed invention is not directed to one of the four categories of Statutory Subject Matter.
The MPEP at MPEP 2106 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of matter?
(2A)(1) Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea?
(2A)(2) Do the claims recite additional elements that integrate the judicial exception into a practical application?
(2B) If the claims recite a judicial exception and do not integrate the judicial exception, do the claims recite additional elements that provide an inventive concept and amount to significantly more than the judicial exception?
With regard to step (1) (Are the claims directed to a process, machine, manufacture or composition of matter?): No. The claims are not directed to one of the statutory classes. Claims 1-22 are directed to a “variant pathogenicity prediction network” comprising memory and sub-networks. A network, without reciting a physical, non-transitory embodiment on which the network is implemented or stored, is not considered statutory subject matter, as it is not a process, machine, manufacture or composition of matter. Further, while the claimed network comprises memory, the broadest reasonable interpretation of “memory” can encompass non-statutory transitory forms of signal transmission, such as a propagating electrical or electromagnetic signal per se. See In re Nuijten, 500 F.3d 1346, 84 USPQ2d 1495 (Fed. Cir. 2007). When the broadest reasonable interpretation encompasses transitory forms of signal transmission, a rejection under 35 U.S.C. 101 as failing to claim statutory subject matter would be appropriate (see MPEP 2106.03 section II).
As such, the claims are not eligible subject matter under 35 U.S.C. 101, and additional analysis cannot proceed.
Claim Rejections - 35 USC § 103
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 (i.e., changing from AIA to pre-AIA ) 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.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim Rejection
Claims 1-3, 16, and 22-24 are rejected under 35 U.S.C. 103 as being unpatentable over SUNDARAM 2019 “Semi-Supervised Learning For Training An Ensemble Of Deep Convolutional Neural Networks” (US 20190114544 A1) in view of WANG 2017 “Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model” (as cited on the IDS filed 11/16/2022).
Claim Interpretation and Scope and Contents of Prior Art
Claim 1 recites a variant pathogenicity prediction network, comprising memory storing a reference amino acid sequence of a protein, and an alternative amino acid sequence of the protein that contains a variant amino acid caused by a variant nucleotide, and a variant encoding sub-network, having access to the memory, configured to process the alternative amino acid sequence, and generate a processed representation of the alternative amino acid sequence.
With respect to this limitation, SUNDARAM teaches a deep learning network ensemble for variant pathogenicity classification [0195, 280], comprising memory [0352-353, 445] that stores a reference amino acid sequence and an alternative amino acid sequence comprising a variant amino acid caused by a variant nucleotide ([076, 0227, 303-304], Fig 23), and further processes the alternative amino acid sequence to generate a representation [0240-241, 305-306].
Claim 1 further recites that the prediction network comprises a protein contact map generation sub-network, in communication with the variant encoding sub-network, configured to process the reference amino acid sequence and the processed representation of the alternative amino acid sequence, and generate a protein contact map of the protein.
With respect to these limitations, SUNDARAM teaches a secondary structure network and solvent accessibility prediction network as part of the network ensemble that processes the reference amino acid sequence and alternative amino acid sequences as multiple sequence alignments to predict the secondary structure [0190, 0205, 0207, 0280-281]. SUNDARAM does not teach that this is the same as a protein contact map generation sub-network, however WANG teaches a protein contact map produced using the same data processed and/or output by the secondary structure and solvent accessibility prediction network of SUNDARAM, such as sequence profile, predicted secondary structure and solvent accessibility (pg 4, Fig 1). It would be obvious to one of ordinary skill that a protein contact map could be used in place of or in conjunction with a secondary structure and solvent accessibility prediction network to produce the outputs needed for input to the variant pathogenicity prediction network, as they individually and/or combined can provide the network with the required information about protein structure.
Claim 1 further recites that the prediction network comprises a pathogenicity scoring sub-network, in communication with the protein contact map generation sub-network, configured to process the protein contact map, and generate a pathogenicity indication of the variant amino acid.
With respect to these limitations, SUNDARAM teaches a pathogenicity prediction network in communication with the secondary structure and solvent accessibility networks that processes the outputs of the secondary structure and solvent accessibility networks to predict pathogenicity of the variant [0204-207].
Claim 2 recites the limitation wherein the memory further stores an amino acid-wise primate conservation profile of the protein, and wherein the processed representation of the alternative amino acid sequence is generated by the variant encoding sub-network in response to processing the alternative amino acid sequence and the amino acid-wise primate conservation profile.
With respect to this limitation, SUNDARAM teaches an amino acid-wise primate conservation profile stored and used as input [0207-208, 309], and that the representation of the amino acid sequence is generated by the variant encoding subnetwork processing the alternative amino acid sequence and the primate conservation profiles [0207, 240-242, 283, 289, 291, 312].
Claim 3 recites the limitation wherein the memory further stores an amino acid-wise mammal conservation profile of the protein, and wherein the processed representation of the alternative amino acid sequence is generated by the variant encoding sub-network in response to processing the alternative amino acid sequence and the amino acid-wise mammal conservation profile.
With respect to this limitation, SUNDARAM teaches an amino acid-wise mammal conservation profile stored and used as input [0207-208, 309], and that the representation of the amino acid sequence is generated by the variant encoding subnetwork processing the alternative amino acid sequence and the primate conservation profiles [0207, 240-242, 283, 289, 291, 312].
Claim 16 recites the limitation wherein the memory further stores an amino acid-wise position-specific scoring matrix of the protein, and wherein the protein contact map of the protein is generated by the protein contact map generation sub-network in response to processing the reference amino acid sequence and the amino acid-wise position-specific scoring matrix.
With respect to this limitation, SUNDARAM teaches storing amino acid-wise position specific scoring matrices, and that the matrices and amino acid sequences are processed to produce the secondary structure and solvent accessibility network models used for pathogenicity prediction [0289, 0307], and WANG teaches using position specific scoring matrices and sequences as well to produce the protein contact map (pg 30 par 2).
Claim 22 recites the limitation wherein the processed representation of the alternative amino acid sequence is provided as input to a first layer of the protein contact map generation sub-network. With respect to this limitation, SUNDARAM teaches providing the processed representation of the alternative amino acid sequence as input to the secondary structure and solvent accessibility networks [0205, 240-243], and WANG teaches inputting a processed representation of an amino acid sequence to a first layer of protein contact map generation network (Fig 1).
Claim 23 recites the limitation wherein the processed representation of the alternative amino acid sequence is provided as input to one or more intermediate layers of the protein contact map generation sub-network. With respect to this limitation, SUNDARAM teaches that the processed representation of the alternative amino acid sequence can be provided as input to multiple layers [0053, 237], and WANG also teaches inputting a processed representation of an amino acid sequence to intermediate layers of the protein contact map generation network (Fig 1).
Claim 24 recites the limitation wherein the processed representation of the alternative amino acid sequence is provided as input to a final layer of the protein contact map generation sub-network. With respect to this limitation, SUNDARAM teaches that the processed representation of the alternative amino acid sequence can be provided as input to a final layer (or any layer) [0053, 237] and WANG also teaches inputting a processed representation of an amino acid sequence to a final layer of the protein contact map generation network (Fig 1).
Resolving Ordinary Skill in the Art and Obviousness Rationale
A teaching, suggestion, or motivation in the prior art would have led one of ordinary skill in the art to modify or combine the prior art to arrive at the claimed invention. Specifically, a person of ordinary skill in protein analysis neural networks would have been motivated to combine the teachings of SUNDARAM with the teachings of WANG, in order to achieve the claimed invention, because the protein contact map of WANG is produced using the same data processed and/or output by the secondary structure and solvent accessibility prediction network of SUNDARAM, such as sequence profile, predicted secondary structure and solvent accessibility (pg 4, Fig 1), and a protein contact map could be used in place of or in conjunction with a secondary structure and solvent accessibility prediction network to produce the outputs needed for input to the variant pathogenicity prediction network. A person of ordinary skill would reasonably expect success from combining these teachings, as both SUNDARAM and WANG teach the use of neural networks for amino acid sequence and protein analysis, and the contact map network of WANG can be used in the network ensemble of SUNDARAM in place of or in conjunction with the secondary structure and solvent accessibility networks. Therefore, the claims at issue would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention as there is both a reason to modify or combine the prior art, and a reasonable expectation of success (see MPEP 2143.02 (I)).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARY C LEVERETT whose telephone number is (571)272-5494. The examiner can normally be reached 8:00am - 5:00pm M-Th.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz R. Skowronek can be reached at (571) 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/MARY C LEVERETT/Examiner, Art Unit 1687
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