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 .
DETAILED ACTION
Responsive to claim set of 30NOV2022
Claims pending 1-18
Claims currently under consideration 1-18
Priority
This application was filed 11/30/2022 and does not claim priority to any earlier applications.
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)(1) 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 1,2,9,10,11,18 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Lim et al (2022 mAbs vol 14, NO. 1, e2069075 (eleven pages) -- as cited in IDS; published online 28APR2022)
Lim et al teach in the entire document and especially the abstract, figures 1,3 and pp 2-3, prediction of antibody binders and generation of synthetic antibody sequences with binding affinity for an antigen target by deep learning with a computer programmed to: receive light chain and heavy chain antibody variable domain sequences from a database; generate a plurality of optionally mutated complementarity determining regions (CDRs) necessarily connected to received framework regions (FRs), with CDRs being determined with a pretrained model; combine the received FRs with generated CDRs to produce synthetic light chain and heavy chain antibody variable domains; and concatenate the synthetic antibody variable domains as single-chain variable fragment (scFvs) antibodies with greater affinity against said target. The foregoing reads on claims 1,2,9,10,11,18.
Claim Rejections - 35 USC § 103
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.
Claims 1,2,9,10,11,18 and 4,6,13,15 are rejected under 35 U.S.C. 103 as being unpatentable over Lim et al (2022 mAbs vol 14, NO. 1, e2069075 (eleven pages) -- as cited in IDS; published online 28APR2022) in view of Saka et al (2021 Nature Scientific Reports 11:5852 thirteen pages).
Lim et al is relied upon as above
Lim et al do not teach: a Long Short-Term Memory (LSTM) network to learn CDR “vocabulary” as recited in claims 4,6,13,15.
In an effort to guide mutagenesis, Saka et al teaches throughout the document and especially the title and p 10 a LSTM network to learn CDR “vocabulary” as recited in claims 4,6,13,15.
It would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to have used the LSTM network for guiding mutagenesis by learning CDR vocabulary as in Saka et al for generating antibodies by machine learning according to Lim et al.
One of ordinary skill in the art would have been motivated to have used the LSTM network for guiding mutagenesis by learning CDR vocabulary as in Saka et al for generating antibodies by machine learning according to Lim et al and had a reasonable expectation of success in doing so, since Saka et al enhanced dissociation constants by 1800 fold as noted in the abstract and report impressive actual physical results in table 3.
Claims 1,2,9,10,11,18 and 4,6,13,15 and 7,8,16,17 are rejected under 35 U.S.C. 103 as being unpatentable over Lim et al (2022 mAbs vol 14, NO. 1, e2069075 (eleven pages) -- as cited in IDS; published online 28APR2022) in view of Saka et al (2021 Nature Scientific Reports 11:5852 thirteen pages) and further in view of Neumann (US AppPub 20240078451)
Lim et al in view of Saka et al is relied on as above.
Lim et al in view of Saka et al do not teach GPT-2 nor Markov models of claims 7,8,16,17.
Neumann suggests throughout the document and especially figures 1,5 and paragraphs 0021, 0035 and 0121, an apparatus for physiologically informed gestational inquiries including a computing device with natural language processing modules for pattern recognition with hidden Markov models (that inherently extract frequency and other parameters per claims 7 & 16) or GPT-2 (that inherently implements one or more techniques per claims 8 & 17). Said passages further read on claims 4 and 13 as well.
It would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to have utilized the Markov models or GPT-2 for pattern recognition like Neumann in order to better characterize the antibody repertoire of Lim et al in view of Saka et al.
One of ordinary skill in the art would have been motivated to have utilized the Markov models or GPT-2 for pattern recognition like Neumann in order to better characterize the antibody repertoire of Lim et al in view of Saka et al for the advantage of identifying alterative paratopes and/or epitopes from the same antigen and/or structural classification, as noted by Saka et al in the third paragraph at p 9.
One of ordinary skill in the art would have had a reasonable expectation of success in adding GPT-2 or Markov layers to the LSTM model suggested by Lim et al in view of Saka et al since adding further layers has been is a technique well within grasp of a machine learning researcher.
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 are rejected under 35 U.S.C. 101 because under the circumstances that the claimed subject matter concerns physical antibodies the claimed invention is directed to natural phenomena, a judicial exception to patent eligible subject matter without significantly more. Taken individually or in combination as a whole, with an antigen structure constituting a model, said claims are drawn to the natural process of affinity maturation by somatic hypermutation in B cells. As such, this judicial exception is not integrated into a practical application because the natural process does not differ from the method presently claimed, lacking any additional elements whatsoever.
Section 33(a) of the America Invents Act reads as follows:
Notwithstanding any other provision of law, no patent may issue on a claim directed to or encompassing a human organism.
Claims 1-2 rejected under 35 U.S.C. 101 and section 33(a) of the America Invents Act as being directed to or encompassing a human organism. See also Animals - Patentability, 1077 Off. Gaz. Pat. Office 24 (April 21, 1987) (indicating that human organisms are excluded from the scope of patentable subject matter under 35 U.S.C. 101). Claims 1-2 encompass affinity maturation of B cells by somatic hypermutation, a process that occurs in humans.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory obviousness-type double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); and In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on a nonstatutory double patenting ground provided the conflicting application or patent either is shown to be commonly owned with this application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement.
Effective January 1, 1994, a registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37 CFR 3.73(b).
Claims 1,2,4,9,10,11,13,18 are provisionally rejected on the ground of nonstatutory obviousness-type double patenting as being unpatentable over claims 1,2,4-5,7,8,10-11 of copending Application No. 18/060218 in view of Lim et al (2022 mAbs vol 14, NO. 1, e2069075 (eleven pages) -- as cited in IDS; published online 28APR2022).
Although the conflicting claims are not identical, they are not patently distinct from each other because, for example, said present claims represent patentably indistinct method variant of all that is recited in the conflicting claims of ‘218 or, alternatively the subject matter claimed overlaps in scope to a large extent and, as a result, are rendered obvious.
The following is illustrative.
Regarding present claim(s) 2 and 11, ‘218 is likewise directed to pre-processing to create a training set therein claims 2 and 8.
Regarding present claims claim(s) 4 and 13, ‘218 is likewise directed to the same models therein claims 5 and 11.
Regarding present claim(s) 9 and 18, ‘218 is drawn to generating high affinity antibodies therein claims 6 and 12.
Additionally, it would have been obvious to one having ordinary skill in the art at the time the invention was made to modify embodiments of ‘218 that fall outside the scope of the present application to select a specifically disclosed embodiment that falls within the scope of the present application because each set of claims concern materials with similar physiochemical properties in that they all possess a common core structure and accordingly biological activity. Furthermore, one of ordinary skill in the art would have been motivated to make such a modification because such modifications are disclosed as “preferred” since the dependent claims of ‘218 “teach toward” Applicant’s presently claimed method and system, especially in view of Lim et al, who teach: the combining and combining steps of claims 1 and 10 as detailed in the anticipation rejection above; training and test sets like ‘218 claims 4 and 10 and/or selecting like ‘218 claims 6 and 12 (cf pp 2-3,5)
This is a provisional obviousness-type double patenting rejection.
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.
Claims 3,5,9,11,12,14,18 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 pre-AIA the applicant regards as the invention.
Claims 5 and 14 recites the limitation "the autoregressive CNN", each in line 3. Claims 9 and 18 recites the limitation "the plurality of known antibody sequence", each in lines 1-2. Claims 3 and 12 recites the limitation "the antibodies", in lines 14 and 15 respectively.
There is insufficient or no antecedent basis for any of the foregoing limitations in each claim, rendering the metes and bounds of the subject matter claimed uncertain.
Claims 9,11,12 & 18 each recite the phrase “plurality of known antibody sequence” which is deemed grammatically vague since it is unclear if said claims require a single known antibody sequence or multiple known antibody sequences, therein rendering the metes and bounds unascertainable.
In accordance with MPEP 2173.02: If the language of the claim is such that a person of ordinary skill in the art could not interpret the metes and bounds of the claim so as to understand how to avoid infringement, a rejection of the claim under 35 U.S.C. 112, second paragraph, would be appropriate. See Morton Int ’l, Inc. v. Cardinal Chem. Co., 5 F.3d 1464, 1470, 28 USPQ2d 1190, 1195 (Fed. Cir. 1993).
In so far as the metes and bounds of the offending claim(s) may not be interpreted properly for the reasons above, all dependent claims therefrom claim 11 is rejected as being indefinite as well.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CHRISTOPHER M GROSS whose telephone number is (571)272-4446. The examiner can normally be reached M-F 10-6.
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/CHRISTOPHER M GROSS/Primary Examiner, Art Unit 1684