DETAILED ACTION
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 .
Claim Rejections - 35 USC § 112
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.
Claim 1-4 and 6-20 are rejected under 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph, as based on a disclosure which is not enabling. The disclosure does not enable one of ordinary skill in the art to practice the invention without the ESM2 protein language model, which is/are critical or essential to the practice of the invention but not included in the claim(s). See In re Mayhew, 527 F.2d 1229, 188 USPQ 356 (CCPA 1976).
In regard to claims 1, 19, and 20, the applicant recites a pLM. However, in the specification, a specific protein language model is used—ESM2. Evidence from the specification dictates that other models collapse when used, and that ESM2 was critical to the applicant’s success. This specific model appears critical to the claims.
Claims 2-4 and 6-18 are further rejected for depending on claim 1.
Claim 1-20 are rejected under 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph, as based on a disclosure which is not enabling. The disclosure does not enable one of ordinary skill in the art to practice the invention without a use case, which is/are critical or essential to the practice of the invention but not included in the claim(s). See In re Mayhew, 527 F.2d 1229, 188 USPQ 356 (CCPA 1976).
In regard to claims 1, 19, and 20, the applicant recites a mathematical model, but fails to delimit a use case. What is this invention actually doing besides abstract classification of data? The independent claims must recite a usage for the model
Claims 2-18 are further rejected for depending on claim 1.
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 1-20 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.
In regard to claim 1, 19, and 20, the applicant recites “a gene” and “a plurality of genes”. This is unclear. The claim should make a distinction between a “target gene” and the “neighbor” or “local” genes in the plurality of genes.
Claims 2-18 are further rejected for depending on claim 1.
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.
In regard to claims 1-20, the claimed invention is directed to a mathematical model without significantly more. The claim(s) recite(s) a processor, a protein language model, and a genome protein model. This judicial exception is not integrated into a practical application because the model does not execute on any particular task. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because processors, protein language models, and genome language models are all known features.
Claims 2-18 are further rejected for depending on claim 1.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure:
Hannigan et al (US 2020/0194098 A1) disclose identifying genes.
Davis et al (US 2022/0139498 A1) disclose contextual embedding.
Szalma et al (US 2002/0072887 A1) disclose protein structure models.
Ji et al (DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome) discloses contextual embedding using a gLM.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CHRISTOPHER E DUNAY whose telephone number is (571)270-1222. The examiner can normally be reached 7:00 am - 6:00 pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, James (Jong-Suk) Lee can be reached at 571-272-7044. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/CHRISTOPHER E DUNAY/Primary Examiner, Art Unit 2875
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