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 .
Priority
This application filed 01/10/2023 is a National Stage entry of PCT/EP2021/069341, with an International Filing Date of 07/12/2021, and claims foreign priority to EP 20185779.4, filed 07/14/2020. The claims are therefore examined as filed on 07/14/2020, 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).
Claim Status
Claims 1-15 are pending.
Claims 4 and 8-10 are objected to as being dependent on a rejected claim.
Claims 1-15 are examined.
Claims 1-3, 5-7, and 11-15 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 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 14 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 14 is indefinite as it is a “use claim”, as described in MPEP 2173.05(q), which explains that attempts to claim a process without setting forth any steps involved in the process generally raises an issue of indefiniteness. Claim 14 is indefinite because it merely recites a use without any active, positive steps delimiting how this use is actually practiced.
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, 5-7, and 11-15 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of mental processes and mathematical concepts, without significantly more.
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?): Yes. The claims are directed to one of the statutory classes. Claims 1-3, 5-7, 11, and 14-15 are directed to a process (computer implemented method), claim 12 is directed to a computer system for performing the method of claim 1, and claim 13 is directed to a non-transitory computer program product comprising instructions to be executed by a computer for performing the steps of claim 1.
With regard to step (2A)(1) (Do the claims recite a judicially recognized exception?): Yes. The claims recite the abstract ideas of processing data using mental steps and mathematical concepts. Claims that recite nothing more than abstract ideas, natural phenomena, or laws of nature are not eligible for patent protection (see MPEP 2106.04).
Abstract ideas include mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (including procedures for collecting, observing, evaluating, and organizing information (See MPEP 2106.04(a)(2)). In particular, these abstract ideas include but are not limited to:
Determining a presentation likelihood for sets of neoantigens using a model (mental process/mathematical concept; the human mind is capable of determining a likelihood using a model, inputting data into a mathematical model and receiving an output is equivalent to performing a calculation; claim 1, 12, 13)
Associating a confidence score to genomic events based on a number of reads and comparing a confidence score of a set of genomic events to a threshold value (mental process/mathematical concept; the human mind is capable of associating a score based on data and of comparing a value to a threshold, determining scores and comparing values is a mathematical process; claim 2)
Determining a treatment by selecting a subset of neoantigens based on determined presentation likelihood by comparing the likelihood to a threshold value, and identifying T-cells that are antigen specific for neoantigens in the subset (mental process/mathematical concept; the human mind is capable of making a determination based on data, making a selection based on data, and comparing a value to a threshold value; comparing values is a mathematical concept; claims 14-15)
Therefore, the claims recite elements that constitute one or more judicial exceptions.
With regard to step (2A)(2) (Do the claims recite additional elements that integrate the judicial exception into a practical application?): No. The claims recite the additional elements of obtaining data for use in an analysis, and of training and using a deep learning model for the analysis. Claims 3, 5, and 11 further describe the datasets used in training the model, and claims 6-7 describe the type of model used. Claim 1 also recites the additional element of the method being computer implemented, claim 12 recites the additional element of a computer system, and claim 13 recites a non-transitory computer program product with instructions executed by a computer.
While the claims recite the additional element of obtaining/receiving data, such steps that only amount to necessary data gathering , without any technical details of how the data is obtained that integrate the judicial exception, are insignificant extrasolution activities that do not add a meaningful limitation to the claims (see MPEP 2106.05(g)). As a result, the judicial exception is not integrated into a practical application. In addition, while the claims recite additional elements related to the use of computers, they do not provide any specific details by which the computer, computer system, or program product performs or carries out the judicial exception listed in step (2A)(1), nor do they provide any details of how specific structures of the computer are used to implement these functions. The judicial exception is therefore not integrated into a practical application because the generically recited computer elements do not add a meaningful limitation to the abstract idea, as they amount to simply implementing the abstract idea on a computer (see MPEP 2106.05(f)). This also applies to the general recitation of training and using of a deep learning model to process data, as such a model, without additional recited structure or training steps that integrates the judicial exception, is also analogous to implementing an abstract idea of data analysis on a computer. Because the claims do not recite any additional elements that integrate the judicial exception into a practical application, the claims as a whole are directed to an abstract idea.
With regard to step (2B) (Do the claims recite additional elements that provide an inventive concept and amount to significantly more than the judicial exception?): No. The claims recite an abstract idea with additional elements; however, these additional elements are general computer elements added to abstract ideas, and non-particular instructions to apply the abstract idea by linking it to a field of use or extrasolution activity (see MPEP 2106.05(f-h)). General computer elements used to perform an abstract idea do not provide an inventive concept, and similarly, non-particular instructions to gather data do not provide an inventive concept. Non-particular instructions to gather data using general computer elements are also considered well-understood, routine and conventional activities (see MPEP 2106.05(d), which indicates that limitations such as “Receiving or transmitting data over a network” from Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362, and “Storing and retrieving information in memory” from Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93 are recognized as conventional activities). The claims therefore do not include additional elements that are sufficient to amount to significantly more than the judicial exception. As a result, the claims as a whole do not provide an inventive concept.
Claims Not Rejected Under 35 USC § 101
It should be noted that claims 4, and 8-10 are not rejected under 35 USC § 101. These claims expand upon the additional elements of training the deep learning model and the structure of the resulting deep learning model. The specific steps involved in training the model, and the model’s specific structure, amount to a technological improvement and significantly more than the abstract idea.
Claims Without an Art Rejection
No art rejection is applied to claims 1-15. Similar art, for example CHEN 2019 and WU 2019 (as cited on form 892), while teaching deep learning methods for neoantigen presentation prediction, do not teach at least the limitation of claim 1 of training a deep learning model on a positive data set comprising a plurality of input-output pairs, wherein each of the input-output pairs comprises an entry of an epitope sequence as input, said epitope sequence being identified or inferred from a surface bound or secreted HLA/peptide complex encoded by a corresponding HLA allele expressed by a training cell, wherein each of the input-output pairs further comprises an entry of a peptide sequence of an alpha-chain encoded by the corresponding HLA allele as output. No combinable art before the effective filing date could be found to render the claims as obvious.
Allowable Subject Matter
Claims 4, and 8-10 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure:
CHEN 2019 “Predicting HLA class II antigen presentation through integrated deep learning” teaches a multimodal recurrent neural network for predicting the likelihood of antigen presentation from a gene of interest in the context of specific HLA class II alleles
WU 2019 “DeepHLApan: A Deep Learning Approach for Neoantigen Prediction Considering Both HLA-Peptide Binding and Immunogenicity” teaches deep learning techniques to predict neoantigens considering both the possibility of HLA-peptide binding and the potential immunogenicity of the peptide-HLA complex
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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/MARY C LEVERETT/ Examiner, Art Unit 1687
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