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’s Response
Applicant’s response, filed 08/06/2025, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Claims Status
Claims 1, 2, 4-6, 8, 9, 11-13, 15, 16, 18, and 19 are pending.
Claims 1, 2, 4-6, 8, 9, 11-13, 15, 16, 18, and 19 are examined.
Withdrawn Objections/Rejections
The rejection of claims 1, 2, 4, 6, 8, 9, 11, 13, 15, 16, and 19 under 35 USC 103 over Biswas et al. (“Relation Prediction of Co-Morbid Disease Using Knowledge Graph Completion”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, published July 2019, cited in prior Office Action) in view of Halevy et al. (“Managing Google’s data lake: an overview of the GOODS system”, IEEE 2016, cited in prior Office Action) is withdrawn in view of the amendments submitted.
The rejection of claims 5, 12, and 18 under 35 USC 103 over Biswas et al. in view of Halevy et al. and further in view of Costabello et al. (“AmpliGraph: a Library for Representation Learning on Knowledge Graphs”, published March 2019, cited in prior Office Action).
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.
Claims 1, 2, 4-6, 8, 9, 11-13, 15, 16, 18, and 19 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. This is a new grounds of rejection as necessitated by claim amendment.
With respect to claims 1, 8, and 15, the claims recite the limitation of “wherein, to predict the target link between the target gene and the target disease, the KnowGene model uses a functional association score to compare a joint probability of the target gene and a known disease gene of the at least one gene occurring together in a disease of the at least one disease against a probability of the target gene and the known disease gene occurring independently in the disease”. The claims are indefinite because it is unclear if “a disease” for which the joint probability of the target gene and a known disease is the same as the target disease, or instead a different one. Additionally, it is unclear if the known disease gene is a gene known for the target disease or the “a disease”.
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 1-2, 4-6, 8, 9, 11-13, 15, 16, 18, and 19 are rejected under 35 U.S.C. 101 because the claimed inventions are directed to an abstract idea of mental steps, mathematic concepts, or a natural law without significantly more. Any newly recited portion is necessitated by claim amendment.
The MPEP at MPEP 2106.03 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of
matter?
(2A)(1) Are the claims directed to a judicially recognized exception, i.e. a law of nature,
a natural phenomenon, or an abstract idea?
(2A)(2) If the claims are directed to a judicial exception under Prong One, then is the
judicial exception integrated into a practical application?
(2B) If the claims are directed to a judicial exception and do not integrate the judicial
exception, do the claims provide an inventive concept?
With respect to step (1): Yes, the claims are directed to a system, a method, and a non-transitory computer-readable medium.
With respect to step (2A)(1): The claims recite an abstract idea of mathematic concepts and mental processes. “Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection” (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 (procedures for observing, evaluating, analyzing/judging and organizing information (MPEP 2106.04(a)(2)). Laws of nature or natural phenomena include naturally occurring principles/relations that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature (MPEP 2106(b)).
Mathematic concepts recited in claims 1, 8, and 15:
generate graph-based datasets based on the data lake, each of the graph-based datasets comprising a subject, an object, and a predicate
generate a knowledge graph based on the data lake, the knowledge graph representing a plurality of links related to at least one gene and at least one disease
generate embedding spaces based on compressed representation of data of the knowledge graph
predict, using a network based model including a KnowGene model, a target link between the target gene of the at least one gene and the target disease of the at least one disease, wherein the target link is predicted based on the weights and the embedding spaces
wherein, to predict the target link between the target gene and the target disease, the KnowGene model uses a functional association score to compare a joint probability of the target gene and a known disease gene of the at least one gene occurring together in a disease of the at least one disease against a probability of the target gene and the known disease gene occurring independently in the disease
Mental processes recited in claims 1, 8, and 15:
determine weights for the plurality of links in the knowledge graph based on the extracted datasets, wherein the weights indicate degrees of importance of corresponding genes of the at least one gene for existence of corresponding diseases of the at least one disease
apply the prediction of the target link between the target gene and the target disease for drug discovery of the target disease, wherein applying the prediction for the drug discovery of the target disease comprises generating new formulations resulting from replacement of a drug compound with discovery compound related to the drug discovery
Dependent claims --4-6, 11-13, and 18-19 recite additional steps that either are directed to abstract ideas or further limit the judicial exceptions in independent claims 1, 8, and 15 and as such, are further directed to abstract ideas. Hence, the claims explicitly recite numerous elements that individually and in combination constitute abstract ideas. The relevant recitations are:
Claims 4 and 11: “the KnowGene model is a knowledge-graph based model for predicting gene-disease association”
Claims 5 and 12: “the target link is further predicted using an AmpliGraph model by: generating the embedding spaces with a neural architecture, and predicting the target link with a scoring function based on the generated embedding spaces”
Claims 6, 13, and 19: “the knowledge graph includes…”, “the target link is predicted using a link-prediction model based on the numerical values”
Claim 18: “the KnowGene model is a knowledge-graph based model for predicting gene-disease associations”, “the target link is further predicted using an AmpliGraph model by: generating the embedding spaces with a neural architecture, and predicting the target link with a scoring function based on the generated embedding spaces”
The abstract ideas recited in the claims are evaluated under Broadest Reasonable Interpretation (BRI) and determined herein to each cover mathematical concepts because the claims recite no more than graphing data and using calculations to find links between the data graphed. The dependent claims further limit how the link predictions are calculated and how the data is graphed.
Because the claims do recite judicial exceptions, direction under (2A)(2) provides that the claims must be examined further to determine whether they integrate the abstract ideas into a practical application (MPEP 2106.04(d). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d).I; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim is said to fail to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
With respect to the instant recitations, claims 1, 8, and 15 recite the following additional elements:
a memory to store executable instructions
a processor adapted to access the memory, the processor further adapted to execute the executable instructions stored in the memory
extract datasets from a plurality of databases, the extracted datasets comprising historical datasets for a genetic mutation in a human DNA dataset, and/or a gene expression dataset, and/or a gene interaction dataset, and/or a drug dataset, and a disease dataset
store the extracted datasets in a data lake, the data lake is stored in the memory
the compressed representation of the data of the knowledge graph indicates the data being compressed
The steps of extracting datasets and storing the extracted datasets in a data lake are directed to data gathering as these steps gather the data on which the abstract idea, the generation of a knowledge graph, is performed. Data gathering steps are not abstract ideas but represent extra-solution activity, as said steps collect the data needed to carry out the abstract idea. Data gathering does not impose any meaningful limitation on the abstract idea, or how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application (MPEP 2106.05(g)).
Steps directed to additional non-abstract elements of “processor; computer; system; storage medium”, etc. do not describe any specific computational steps by which the “computer parts” perform or carry out the abstract idea, nor do they provide any details of how specific structures of the computer, such as the computer-readable recording media, are used to implement these functions. The claims state nothing more than a generic computer which performs the functions that constitute the abstract idea. Hence, these are mere instructions to apply the abstract using a computer, and therefore the claim does not integrate that abstract idea into a practical application. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc. … are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (see MPEP 2106.05(f)).
Dependent claims 2, 9, and 16 are directed to displaying the knowledge graph, are ancillary to the recited judicial exception and provide means for “showing” the result of the judicial exception rather than providing and integration of that exception. Thus, said steps are extra-solution.
None of these dependent claims recite additional elements, alone or in combination, which would integrate a judicial exception into a practical application.
With respect to step (2B): Because the claims recite an abstract idea, and do no integrate that abstract idea into a practical application, the claims lack a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements of above do not rise to the level of significantly more than the judicial exception. As set forth in the MPEP at 2106.05(d)(I), determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to claims 1, 8, and 15: The additional elements of a memory to store executable instructions, a processor adapted to access the memory, the processor further adapted to execute the executable instructions stored in the memory, extract datasets from a plurality of databases, the extracted datasets comprising historical datasets for a genetic mutation in a human DNA dataset, and/or a gene expression dataset, and/or a gene interaction dataset, and/or a drug dataset, and/or disease dataset, store the extracted datasets in a data lake, the data lake stored in the memory, and the compressed representation of the data of the knowledge graph indicates the data being compressed do not rise to the level of significantly more than the judicial exception. With respect to the computer elements, as exemplified in the MPEP at 2106.05(f) with reference to Alice Corp. 573 US at 223, 110 USPQ2d at 1983 “claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible”. Therefore, the programmed computer constitutes no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than an abstract idea (see MPEP 2105(b)I-III). With respect to extracting datasets from databases, as exemplified in the MPEP at 2106.05(d)(II) with reference to Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362, using the internet to gather data is a routine add conventional technique. Furthermore, with respect to storing the extracted datasets in a data lake, as exemplified in the MPEP at 2106.05(d)(II) with reference to Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015) and OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, storing and retrieving information stored in memory is a routine and conventional activity. Furthermore, with respect to the data lake being stored in graph-based datasets and each graph-based dataset comprising a subject and an object and a predicate, the prior art Halevy et al. (“Managing Google’s data lake: an overview of the GOODS system, IEEE 2016, cited in prior Office Action) discloses the managing of Google’s data lake using the GOODS system (Abstract), that stores the data lake in graph-based datasets (page 9, Section 3). Halevy et al. further discloses that each of these graph-based datasets comprises a subject, and object, and a predicate, as exemplified by the example of the query “Tom Hanks played a role in ‘Forrest Gump’” wherein Tom Hanks is the subject, “Forrest Gump” is the object, and “played a role” is the predicate (page 9, Section 3, paragraph 2). Therefore, a graph-based governance of a data lake is a system used by a large company to manage the datasets in their data lake and used by the Google engineers. Therefore, this is considered to be a conventional element. As such, the prior art recognizes that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, it does not require or set forth a particular machine, it does not affect a transformation of matter, nor does it provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
In combination, the collection or generation of the data, acted upon by the judicial exception, fail to rise to the level of significantly more. The data gathering steps provide the data for the judicial exception. No non-routine step or element has clearly been identified.
The claims have all been examined to identify the presence of one or more judicial exceptions. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether the additional limitations integrate the judicial exception into a practical application. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether those additional limitations provide an inventive concept which provides significantly more than those exceptions. Individually, the limitations of the claims and the claims as a whole have been found to not meet the eligibility requirements.
Response to Arguments
Applicant states that “claimed features such as ‘generate embedding spaces based on compressed representation of data of the knowledge graph, wherein the compressed representation of the data of the knowledge graph indicates the data being compressed, and predict, using at least one of a graph convolutional network model or a network based model including a KnowGene model, a target link between a the target gene of the at least one gene and a the target disease of the at least one disease, wherein the target link is predicted based on the weights and the embedding spaces, and wherein, to predict the target link between the target gene and the target disease, the KnowGene model uses a functional association score to compare a joint probability of the target gene and a known disease gene of the at least one gene occurring together in a disease of the at least one disease against a probability of the target gene and the known disease gene occurring independently in the disease, and apply the prediction of the target link between the target gene and the target disease for drug discovery of the target disease, wherein applying the prediction for the drug discovery of the target disease comprises generating new formulations resulting from replacement of a drug compound by discovery compound related to the drug discovery’ essentially require computing resources, and hence cannot be practically performed in a human mind. Further, contrary to the Office's assertion, claim 1 does not cover any mathematical relationships, mathematical formulas or equations Accordingly, the claim 1 does not set forth or describe the alleged abstract idea of mathematical concepts. In contrast, the invention claimed here is predicting unknown link in a knowledge graph in a field of discovering new relationships between diseases and genes, a concept inextricably tied to computer technology and distinct from the types of concepts found by the courts to be abstract. Further, the claimed method generates gene-specific predictions enabling formulation of therapies that target the genetic underpinnings of a disease, potentially increasing efficacy and reducing off-target effects. Accordingly, the claimed steps do not recite an abstract idea of mental process or mathematical concept. Instead, the claimed method is necessarily rooted in computer technology to overcome a problem specifically arising in predicting unknown disease gene associations in a field of new drug discovery. Therefore, the Applicant submits that the claimed features do not merely recite an abstract idea, law of nature or natural phenomenon, thus fail to satisfy prong 1 of step 2A.”
It is respectfully submitted that this is not persuasive. It is the steps of “determine weights for the plurality of links in the knowledge graph based on the extracted datasets, wherein the weights indicate degrees of importance of corresponding genes of the at least one gene for existence of corresponding diseases of the at least one disease” and “apply the prediction of the target link between the target gene and the target disease for drug discovery of the target disease, wherein applying the prediction for the drug discovery of the target disease comprises generating new formulations resulting from replacement of a drug compound with discovery compound related to the drug discovery” that are interpreted as mental processes. Furthermore, the use of a computer does not disqualify a limitation from being directed to an abstract idea (see MPEP 2106.04(a)(2).III.C). Additionally, mathematical concepts are described in the MPEP at 2106.04(a)(2).I. Mathematical concepts need not be expressed in mathematical symbols and words used in a claim operating on data to solve a problem can serve the same purpose as a formula. The claims are directed to identifying a target gene associated with a target disease using mathematical models to predict and association and recite numerous elements that comprise a mathematical step and thus the claim elements are determined to be abstract. The generation of new formulations is also interpreted as an abstract idea. Lastly, the courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc. … are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (see MPEP 2106.05(f)). Thus, the rejection under 35 USC 101 is maintained.
Furthermore, Applicant states that “Even assuming the Examiner's characterization is correct (which Applicant does not concede), Applicant asserts that claim 1, as a whole, integrates the alleged judicial exception into a "practical application" at least because the additional elements of claim 1, apply or use the alleged judicial exception in some other meaningful way beyond generally linking the use of the alleged judicial exception to a particular technological environment, such that claim 1, as a whole, is more than a drafting effort designed to monopolize the alleged judicial exception. The Applicant submits that by using embedding spaces and weight-based learning, the claimed system enables a more nuanced representation of relationships between genes and diseases, and hence improving the predictive accuracy of the KnowGene model. Further, by analyzing real co-occurrence probabilities from disease datasets, the KnowGene model learns patterns grounded in biological data retrieved from various datasets rather than relying solely on predefined rules or pathways.
It is respectfully submitted that this is not persuasive. It is the additional elements of the claims that are analyzed to determine whether the claims are integrated into a practical application (MPEP 2106.04(d).I; MPEP 2106.05(a-h)). The steps of extracting datasets and storing the extracted datasets in a data lake are directed to data gathering as these steps gather the data on which the abstract idea, the generation of a knowledge graph, is performed. Data gathering steps are not abstract ideas but represent extra-solution activity, as said steps collect the data needed to carry out the abstract idea. Data gathering does not impose any meaningful limitation on the abstract idea, or how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application (MPEP 2106.05(g)). Steps directed to additional non-abstract elements of “processor; computer; system; storage medium”, etc. do not describe any specific computational steps by which the “computer parts” perform or carry out the abstract idea, nor do they provide any details of how specific structures of the computer, such as the computer-readable recording media, are used to implement these functions. The claims state nothing more than a generic computer which performs the functions that constitute the abstract idea. Hence, these are mere instructions to apply the abstract using a computer, and therefore the claim does not integrate that abstract idea into a practical application. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc. … are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (see MPEP 2106.05(f)). Thus, the rejection under 35 USC 101 is maintained.
Furthermore, Applicant states that “the claims has been amended to refer to "apply the prediction of the target link between the target gene and the target disease for drug discovery of the target disease, wherein applying the prediction for the drug discovery of the target disease comprises generating new formulations resulting from replacement of a drug compound with discovery compound related to the drug discovery". The Applicant further submits that by generating new formulations resulting from replacement of a drug compound with discovery compound related to the drug discovery, the claimed system allows for automatic generation of new drug compounds which helps discovery scientists prioritize the most promising drug targets before entering costly clinical trials. The more informed and prioritized targets will not only result into better drugs, but also better selection of patients. Please refer to paragraphs [0044], [0045], [0048], and [0050] of the Applicant's specification as filed. Thus, the claimed system not only predicts unknown link between a gene and a disease, but also generates new formulations related to the drug discovery by applying predictions. Therefore, the combination of claimed features of claim 1 integrate the abstract idea into a practical application because the claimed system enables predicting the target link based on embedding spaces, a computing device structures information into embedding spaces, which specifically results in the retrieval of more relevant and accurate information in a shorter amount of time, and hence enhancing the processing speed of a computer. Further, the claimed system enables the computing system to automatically generate new formulations related to drug discovery, and hence reduces significant manual efforts.”
It is respectfully submitted that this is not persuasive. The step of applying the prediction and thus generating new formulations resulting from replacement of a drug compound with discovery compound related to the drug discovery is interpreted as a mental process, as a person can perform the mental step of generating a drug formulation. It is the additional elements of the claims that are analyzed to determine whether the claims are integrated into a practical application (MPEP 2106.04(d).I; MPEP 2106.05(a-h)). Thus, this step does not integrate any judicial exceptions into a practical application as it is a judicial exception itself. Thus, the rejection under 35 USC 101 is maintained.
Conclusion
No claims are allowed.
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 EMILIE A NEULEN whose telephone number is (571)272-7543. The examiner can normally be reached 9am - 5pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Larry D Riggs can be reached at (571)270-3062. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/E.A.N./Examiner, Art Unit 1686
/LARRY D RIGGS II/Supervisory Patent Examiner, Art Unit 1686