CTNF 18/471,630 CTNF 100516 Notice of Pre-AIA or AIA Status 07-03-aia AIA 15-10-aia The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA. Priority Application is a continuation of application no.:17/898,662 filed on August 30, 2022 which claims the benefit of PCT Application No. PCT/EP2020/078968, filed on October 14, 2020. Claim Rejections - 35 USC § 112 07-30-01 AIA 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 5 , 11 , and 17 rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. The specification teaches an animo acid being selected with a UCB1 formula however the claims teach the UCB formula to select amino acids . It is not clear from the specification or the claims that these are the same thing and there is no other recitation of a UCB formula that supports the claims in the specification. 07-30-02 AIA 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. 07-34-01 Claim 1-17 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. Regarding claim 1 , 7 , and 13 all recite employing a deep neural network to predict a peptide presentation given Major Histocompatibility Complex (MHC) allele sequences and peptide sequences; extracting a library of peptides from a target virus or tumor cells; training a Variational Autoencoder (VAE) to reconstruct peptides by converting the peptide sequences of variable lengths into continuous embedding vectors of a fixed size; running a Monte Carlo Tree Search (MCTS) to generate a first set of positive peptide vaccine candidates; running a Bayesian Optimization search with the trained VAE (BO-VAE) and a Backpropagation search with the trained VAE (BP-VAE) to generate a second set of positive peptide vaccine candidates; screening and merging the first and second sets of positive peptide vaccine candidates; and outputting qualified peptides for immunotherapy from the screened and merged first and second sets of positive peptide vaccine candidates. The claims fail to particularly point out how the claimed invention functions. The claims specify running a Monte Carlo Tree Search, a Bayesian Optimization search, A Backpropagation search, and using a sampling from a Position Weight Matrix without specifying the input to these algorithms and models. It is unclear as to what data is used for the models and algorithms claimed. The claims are indefinite due to the lack of clarity of what data is used as an input to these models and algorithms. Claims 2-6 , 8-12 , and 14-17 are rejected being dependent on claims 1 , 7 , and 13. Further if the rejection stated above were to be overcome the claims would be rejected further as follows, claims 4 , 11 , and 18 , recite wherein the BP-VAE is employed to learn presentation scores from the deep neural network and generate a portion of the first set of positive peptide vaccine candidates by optimizing the continuous embedding vectors with a gradient ascent. The claims recite that the BP-VAE is generating a portion of the first set of the positive peptide vaccine candidates while claim 1. 8, and 15 which these claims depend on all recite the BP-VAE generating the second set of positive peptides vaccine candidates. It is unclear as to if the BP-VAE is generating a part of the first set of positive peptide vaccine candidates or the second set. The claims are indefinite due to the lack of clarity of the claim language in relation to the independent claims. Further if the rejection stated above were to be overcome the claims would be rejected further as follows, claims 5 , 11 , and 17 , recites and extracting a library of peptides through sequencing and peptide processing pipelines that can uniquely identify the virus or tumor cells. This is indefinite because it is unclear if this is the same or a different library of peptides then the one that is extracted in the independent claim. Further if the rejection stated above were to be overcome the claims would be rejected further as follows, claims 5 , 11 , and 17 recites the limitation "the UCB formula" in line 4. There is insufficient antecedent basis for this limitation in the claim. Conclusion Any inquiry concerning this communication or earlier communications from the examiner should be directed to THOMAS B LANE whose telephone number is (571)272-1872. The examiner can normally be reached M-Th: 6:40am-4:40pm; F: Out of Office. Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, MARIELA REYES can be reached at (571) 270-1006. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. /THOMAS BERNARD LANE/Examiner, Art Unit 2142 /HAIMEI JIANG/Primary Examiner, Art Unit 2142 Application/Control Number: 18/471,630 Page 2 Art Unit: 2142 Application/Control Number: 18/471,630 Page 3 Art Unit: 2142 Application/Control Number: 18/471,630 Page 4 Art Unit: 2142 Application/Control Number: 18/471,630 Page 5 Art Unit: 2142
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