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 .
Applicant filed a response dated 10/14/2025 in which claims 1-15 are pending in the application.
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 1-15 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of characterizing a tumor micro environment without significantly more.
Examiner has identified claim 1 as the claim that represents the claimed invention presented in independent claims 1 and 14-15.
Claim 1 is directed to a method, which is one of the statutory categories of invention (Step 1: YES).
The claim 1 recites a series of steps, e.g., using a trained natural language processing machine learning model (NLP-model), extracting facts from biomedical text, the extracted facts comprising relationship information between cell types and found gene names; using a reference database comprising gene names and gene aliases, grouping the extracted facts according to associated genes to generate extracted and grouped information; and generating a matrix from the extracted and grouped information with a first axis representing cell types and second axis representing genes, each value of the matrix being respectively calculated based on an importance of an associated gene taken and an associated weight, the associated weight being based on at least one of associated publication meta information or an associated detection method’s robustness and reliability. These limitations (with the exception of italicized limitations) describe the abstract idea of characterizing a tumor micro environment which may correspond to a certain method of organizing human activity and thus the claim recites an abstract idea. The additional elements of a trained natural language processing machine learning model (NLP-model) do not restrict the claim from reciting an abstract idea. Thus, the claim 1 recites an abstract idea (Step 2A, Prong One: YES).
This judicial exception is not integrated into a practical application because the additional elements of a trained natural language processing machine learning model (NLP-model) result in no more than simply applying the abstract idea using generic computer elements. The additional elements of a trained natural language processing machine learning model (NLP-model) are recited at a high level of generality and under their broadest reasonable interpretation comprises a generic computer arrangement. The presence of a generic computer arrangement is nothing more than to implement the claimed invention by applying the exception using a generic computer element (MPEP 2106.05(f)). Therefore, the recitations of additional elements do not meaningfully apply the abstract idea and hence do not integrate the abstract idea into a practical application. Thus, the claim 1 is directed to an abstract idea (Step 2A-Prong 2: NO).
The claim 1 does not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claim recites the additional elements of a trained natural language processing machine learning model (NLP-model) are recited at a high level of generality in that it result in no more than simply applying the abstract idea using generic computer elements. The additional elements when considered separately and as an ordered combination do not amount to add significantly more as these elements provide nothing more than to simply apply the exception in a generic computer environment (Step 2B: NO). Thus, the claim 1 is not patent eligible.
Similar arguments can be presented for other independent claims 14-15 and hence these claims are rejected on similar grounds as claim 1.
Dependent claims 2-13 further define the abstract idea that is present in the independent claim 1, thus correspond to a certain method of organizing human activity, and hence are abstract in nature for the reason presented above. Dependent claims do not include any additional elements that integrate the abstract idea into a practical application or are sufficient to amount to significantly more than the judicial exception when considered both individually and as an ordered combination. Therefore, the claims 1-15 are not patent-eligible.
Response to Arguments
Applicant's arguments filed dated 10/14/2025 have been fully considered but they are not persuasive due to the following reasons:
With respect to the rejection of claims 1-15 under 35 U.S.C. 101, Applicant states that claims 1-15 are directed to a computer-implemented, automated machine-learning approach for characterizing a tumor microenvironment in a faster, more complete, computationally-efficient and accurate manner.
Examiner respectfully disagrees and notes that the claims do not recite automated, particularly in independent claims 1 and 14-15 and characterizing a tumor microenvironment is only recited in the preamble of independent claims 1 and 14-15 while the body of the independent claims 1 and 14-15 does not recite any positive steps that relate to characterizing a tumor microenvironment. Moreover, faster, efficient and accuracy are associated with the use of a computer and are anticipated when a computer implements a process. These benefits do not originate from the claimed invention as these benefits originate from the use of computer and are available to any computer implemented process. Thus, these arguments are moot.
Applicant also states that not a single step recited in claim 1 covers any human activity whatsoever, much less the certain methods of organizing human activity that are patent ineligible, and primarily are only legal and financial methods. Rather, the steps recited in independent claim 1 reflect complex machine learning processing or complex biomedical information including a sufficient number of cell types, gene names and gene alias to characterize a tumor micro environment. The recited machine learning approach for charactering the tumor microenvironment is nothing like any other method which was found to be one of the certain methods of organizing human activity.
Examiner respectfully disagrees and notes that under Step 2A, Prong One, the claim limitations are initially considered in the absence of additional elements to determine if the claim recites an abstract idea. In this case, when considered in the absence of additional elements, the claim recites steps that can be performed manually by a human. This interpretation is supported by Applicant’s specification in paragraph [0012] (a manual process executed by human experts). The additional elements do not restrict the claim from reciting an abstract idea. Thus, under Step 2A, Prong One, the claim recites an abstract idea. The additional elements are then further considered in detail under Step 2A, Prong Two and Step 2B to determine if the additional elements integrate the abstract idea into a practical application or amount to add significantly more.
Applicant also states that for example, paragraphs [0039]-[0046] of the published specification describes that “[e]mbodiments of the present disclosure address the technical problem of how to build a computer-based tool that effectively characterizes a patient’s TME, diagnoses the patient, and outputs treatment protocols for cancer patients.
Examiner respectfully disagrees and notes that the computer recitations are present at a high level of generality in that it simply result in applying the abstract idea. There are no technical steps in the claim that address a technical solution to a technical problem. The specification simply states that the present disclosure addresses the technical problem of how to build a computer-based tool that effectively characterize a patient’s TME, diagnoses the patient, and outputs treatment protocols for cancer patient. However, the disclosure and the claim do not go into specific details as to how the computer-based tool performs those steps. For example, the independent claims 1, and 14-15 do not describe a cell-by-cell characterization of the tumor microenvironment by uncovering hidden relationships and patterns. In the absence of any specificity, the computer based tool recited in the claim simply amounts to applying the abstract idea without integrating the abstract idea into a practical application or amounting to add significantly more. Thus, these arguments are not persuasive.
Conclusion
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to RAJESH KHATTAR whose telephone number is (571)272-7981. The examiner can normally be reached M-F 8AM-5PM.
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RAJESH KHATTAR
Primary Examiner
Art Unit 3684
/RAJESH KHATTAR/Primary Examiner, Art Unit 3684