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 .
Response to Amendment
The following Office action in response to communications received November 13, 2025. Claims 1 and 4-8 have been amended. Claims 2-3 have been canceled. Therefore, claims 1 and 4-8 are pending and addressed below.
Applicant’s amendments to the claims are sufficient to overcome the first paragraph of pre-AIA 35 U.S.C. 112, 35 U.S.C. 112 (pre-AIA ), second paragraph, and pre-AIA 35 U.S.C. 112, sixth paragraph rejections set forth in the previous office action dated May 22, 2025.
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.
Claims 1 and 4-8 are 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. In particular, how are the components functional (input data processing unit, multiple instance learning model unit and associated genetic variant determination unit) without tying them to a specific tangible means. The amended claim 1 claims one or more processors, while the original claim 7 disclosed a data processing unit. The Examiner does not see an actual computing system or device anywhere mentioned in specification. Having a Data Processing Unit (DPU) does not automatically mean you have a computer. A DPU is a specialized processor designed to handle specific tasks that are typically offloaded from the central processing unit (CPU). While a DPU can be part of a computer system, it is not the sole component that constitutes a computer. A system typically includes a CPU, memory, storage, and other hardware components that work together to perform various computing tasks. None of which are taught by original claims or specification.
Examiner suggest using terminology used within specification for clarity and ease in order to conduct a reasonable prior art search. Specification paragraph [97] mentions computer software, computer program product and computer-readable storage device, however does not explicitly mention any system. Appropriate clarification and correction are required.
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 and 4-8 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more. Based upon consideration of all of the relevant factors with respect to the claims as a whole, the claims are directed to non-statutory subject matter which do not include additional elements that are sufficient to amount to significantly more than the judicial exception because of the following analysis:
Independent Claim(s) 1 and 7 are directed to an abstract idea of correlating genetic information to identify a disease and its causative variant. It processes sets of genetic variant information as input and uses machine learning to determine if a disease is genetic and which variant causes it. This enables automated, accurate genetic diagnosis and variant discovery.
Independent Claim 1 recites “derive identification of a the genetic disease of a patient and discovery of the disease- associated genetic variant together using a multiple instance learning model configured to learn instances which are genetic variant information of the patient and a bag of the instances as input data; process, as a bag label, whether a disease of the patient is a the genetic disease caused by a genetic variant generate first attention weights for the instances which are degrees to which the instances contribute to the identification of the genetic disease of the patient using an attention mechanism; process the input data by reflecting the first attention weights for the instances; embed the respective instances into low-dimensional vectors with a same dimension using respective neural networks; project the low-dimensional vectors onto one manifold using weight matrices and an activation function to obtain embedding vectors identical to each other; generate second attention weights for the embedding vectors using the attention mechanism; and perform a pooling process of treating the embedding vectors as one vector.”
Independent Claim 7 recites “processing input data such that an input data processing unit uses instances which are genetic variant information of a patient and a bag of the instances as input data, and generates attention weights for the instances using an attention mechanism to process the input data; determining, using a multiple instance learning model, whether a disease of the patient is the genetic disease; and based on determining that the disease of the patient is the genetic disease, discovering the disease- associated genetic variant that causes the disease of the patient using the attention weights for the instances, generating first attention weights for the instances which are degrees to which the instances contribute to the identification of the genetic disease of the patient using the attention mechanism; processing the input data by reflecting the first attention weights for the instances; embedding the respective instances into low-dimensional vectors with a same dimension using respective neural networks; projecting the low-dimensional vectors onto one manifold using weight matrices and an activation function to obtain embedding vectors identical to each other; generating second attention weights for the embedding vectors using the attention mechanism; and performing a pooling process of treating the embedding vectors as one vector.”
The limitations of Claims 1 and 7, as drafted, under its broadest reasonable interpretation, covers the performance of a Mental Process concepts performed in the human mind (including an observation, evaluation, judgment, opinion), but for the recitation of generic computer components. That is, other than reciting, “processors, memory, input data processing unit” nothing in the claim element precludes the step from practically being performed in the mind. For example, but for the “system” language, “generating” in the context of this claim encompasses the user manually producing first attention weights. Similarly, the process the input data, covers performance of the limitation in the mind but for the recitation of generic computer components. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then it falls within the “Mental Processes” grouping of abstract ideas. Accordingly, the claim recites an abstract idea.
This judicial exception is not integrated into a practical application. In particular, the claims recite the additional elements of using a “processors, memory, input data processing unit” to perform all of the “obtaining, transforming, parsing, determining, transforming, selecting and storing” steps. The “processors, memory, input data processing unit” is/are recited at a high-level of generality (i.e., as a generic processor performing a generic computer function of executing computer-executable instructions for implementing the specified logical function(s) such that it amounts no more than mere instructions to apply the exception using a generic computer component. Accordingly, this additional element does not integrate the abstract idea into a practical application because it does not impose any meaningful limits on practicing the abstract idea. The claim is directed to an abstract idea.
Claim 1 has the following additional elements (i.e., processors, memory). Claim 7 has the following additional elements (i.e., data processor unit). Looking to the specification, these components are described at a high level of generality with no structure. Even with the use of a general-purpose computer if taught, taken alone, does not impose any meaningful limitation on the computer implementation of the abstract idea, so it does not amount to significantly more than the abstract idea. Looking at the limitations as an ordered combination adds nothing that is not already present when looking at the elements individually. The combination of elements does not indicate a significant improvement to the functioning of a computer or any other technology and their collective functions merely provide a conventional computer implementation of the abstract idea. Furthermore, the additional elements or combination of elements in the claims, other than the abstract idea per se, amount to no more than a recitation of generally linking the abstract idea to a particular technological environment or field of use, as the courts have found in Parker v. Flook. Therefore, there are no limitations in the claims that transform the judicial exception into a patent eligible application such that the claims amount to significantly more than the judicial exception.
It is worth noting that the above analysis already encompasses each of the current dependent claims (i.e., claims 4-6 and 8). Particularly, each of the dependent claims also fails to amount to “significantly more’ than the abstract idea since each dependent claim is directed to a further abstract idea, and/or a further conventional computer element/function utilized to facilitate the abstract idea. Accordingly, none of the current claims implements an element—or a combination of elements—directed to an inventive concept (e.g., none of the current claims is reciting an element—or a combination of elements—that provides a technological improvement over the existing/conventional technology). These information characteristics do not change the fundamental analogy to the abstract idea grouping of “Mental Process,” and, when viewed individually or as a whole, they do not add anything substantial beyond the abstract idea. Furthermore, the combination of elements does not indicate a significant improvement to the functioning of a computer or any other technology. Therefore, the claims when taken as a whole are ineligible for the same reasons as the independent claims.
Claims 1 and 4-8 are therefore not drawn to eligible subject matter as they are directed to an abstract idea without significantly more.
Response to Arguments
Applicant’s arguments filed November 13, 2025 have been fully considered but they are not persuasive.
In response to argument, the Examiner has considered Applicant's arguments and traversals. However, the rejection under 35 U.S.C. 101 is MAINTAINED.
Applicant's central argument that the claims are not a mental process because the human mind cannot practically perform the recited steps, misapplies the standard. The inquiry under Step 2A Prong One is not whether a human can perform the specific computational steps (e.g., generating attention weights, embedding vectors), but whether the “underlying focus” of the claim is an abstract concept. Here, the claim is directed to the abstract idea of "correlating genetic information to identify a disease and its causative variant," which is a fundamental data analysis task that aligns with the "mental processes" grouping. The recitation of generic machine learning components (multiple instance learning model, attention mechanisms, neural networks) merely provides a technological environment for automating this abstract process. Applicant's reliance on “SRI Int'l” is distinguishable, as that case involved a specific, non-conventional technological solution to a computer network security problem, whereas the present claims use conventional ML tools to solve a data correlation problem in the biological arts.
Furthermore, regarding Step 2A Prong Two, the claimed combination of ML components does not integrate the abstract idea into a “practical application” that provides an “improvement” to computer technology or another technical field. The claim is directed to the abstract data analysis process itself, and the output—an identification of a disease and variant—is simply the result of that abstract process. The instructions to "derive," "process," "generate," "embed," "project," and "perform a pooling process" describe the use of well-understood, routine, and conventional activities in the field of machine learning to execute the abstract idea. The alleged improvement in the performance of the multiple instance learning model, such as retraining it, is a generic benefit of applying machine learning and is not claimed as a specific, non-conventional technological solution. The claim elements, both individually and as an ordered combination, do not amount to significantly more than the judicial exception, as they merely instruct the application of the abstract idea using generic computer components. Therefore, the claims are directed to non-statutory subject matter.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Pub. No.: US 20210366577 A1; Embodiments of the disclosure include implementing a ML-enabled cellular disease model for validating an intervention, identifying patient populations that are likely responders to an intervention, and developing a therapeutic structure-activity relationship screen. To generate a cellular disease model, data is combined from human genetic cohorts, from the literature, and from general-purpose cellular or tissue-level genomic data to unravel the set of factors (e.g., genetic, environmental, cellular factors) that give rise to a particular disease. In vitro cells are engineered using the set of factors to generate training data for training machine learning models that are useful for implementing cellular disease models.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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 EDWARD B WINSTON III whose telephone number is (571)270-7780. The examiner can normally be reached M-F 1030 to 1830.
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/E.B.W/ Examiner, Art Unit 3683
/ROBERT W MORGAN/ Supervisory Patent Examiner, Art Unit 3683