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 status
No claim amendments have been filed. Original claims 1-20 filed 4/22/2022 are pending.
Election/Restriction
Applicant's election with traverse of Group II in the reply filed on 1/7/2026 is acknowledged. The traversal is on the ground(s) that the inventions are of overlapping scope and obvious variations of one another. This is found persuasive because upon initial search and consideration, and in view of the teachings of the specification, it does appear that the claims can be examined together without undue burden.
Accordingly, the restriction requirement is withdrawn.
Restriction to one of the following inventions is required under 35 U.S.
Claims 1-20, drawn to a method of selecting candidate drugs using models to assess based on binding predictions, drawn to a system to implement a method to analyze protein-protein interactions and drawn to a computer readable medium with instructions to assess drug compounds using AI and pending and currently under examination.
Priority
This application filed 4/22/2022 claims benefit to foreign application IN 202241012026 filed 3/10/2022 in India.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 8/24/2023 and 4/22/2022 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
It is noted that there are citations of foreign search reports, which have been reviewed, however the file that was reviewed such as the claims are not provided, nor is it clear the reference discussed are provided for context.
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitation(s) is/are: ‘drug identification device’ with several functions outlined for generating, assigning and calculating in claim 1. In view of the guidance of the specification and independent claims directed to a system and CRM, this embodiment appears to encompass a Natural Language Processing algorithm generically that is capable of performing the ascribed steps/analysis and not a physical device. A search of the art of record does not indicate such a device exists or is conventionally known, and generally appears that the device is a general purpose computer with an NLP algorithm.
Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof.
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
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 1-20 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.
Claim analysis
Claim 1 is generally directed to a method for selecting candidate compounds using artificial intelligence. More specifically, the analysis method provides for several steps of extracting ‘relevant data’ of potential lead compounds, generating a knowledge based graph from the extracted data, assigning a rank by correlating any historical clinical information and knowledge based graph data, calculating a binding affinity of a protein-protein interaction and possible interactions, then assigning a final rank based on the analysis. Claim 8 provides for the system on which the method is practiced and claim 15 provides that the method is stored on a computer readable medium. Dependent claims provide an indication of how the steps are performed, but only provide generic probabilistic models, or encoder models to ascribe scores or embedding for computer processing steps.
For step 1 of the 101 analysis, the claims are found to be directed to a statutory category of a method and products.
For step 2A of the 101 analysis, the judicial exception of the claims are the steps of accessing ‘relevant data’ broadly which should represent possible protein-protein interactions as a complex where in the interactions are defined and assessed to identify and rank possible molecules that bind to a target. The steps are generically and broadly provided that they are essentially instructions to use a computer to analyze protein interactions. The method provides using a ‘drug candidate identification device’ which is not conventionally known nor is specifically defined by the specification, and the claims set forth that it performs broad tasks of analysis without any specificity of how it is done. The judicial exception is a set of instructions for analysis of protein-protein interactions and broadly encompasses Mathematical Concepts, that is mathematical formulas or equations for calculating binding affinities and Mental Processes, that is concepts performed in the human mind (including an observation, evaluation, judgment, opinion) because depending on the ‘relevant data’ protein-protein interactions can be observed and ranked by observation, as well as calculating binding constants. The breadth of “extracting”, “generating”, “assigning”, “calculating” and “assigning” encompasses non-transformative visual assessment of ‘relevant data’ that is extracted. The use of a NLP is noted, but there is no specific indication of the starting data nor how the NPL is to analyze or create anything specific, including ‘a semantic knowledge graph’ related to any possible ‘disorder’ for any possible ‘drug’ comprised in the breadth of the claims. This breadth does not impose a meaningful limit on the claim scope, such that all others are not precluded from using the natural principle of assessing protein-protein interactions using a computer or applying generically a NLP. Although the claims recite generating a knowledge graph, the courts have also identified limitations that did not integrate a judicial exception into a practical application; for example, merely including instructions to create new data from other data is considered an abstract idea on a computer, or for the system is merely using a computer as a tool to perform an abstract idea, as discussed in MPEP § 2106.05(f). Computing, constructing datasets and using statistical models was well understood, conventional, and routinely performed in the art at the time the application was filed. See MPEP § 2106.05(g) for a discussion on adding insignificant extra-solution (both pre-solution and post-solution) activity to the judicial exception. See also MPEP § 2106.05(h) for a discussion on generally linking the use of a judicial exception to a particular technological environment or field of use. The claims appear to fall into the category of Mathematical Concepts, as it applies the use of statistics and mathematical relationships in analyzing probabilities/rankings, and also into the category of mental processes, as concepts performed in the human mind (including an observation, evaluation, judgment, opinion) because there is no apparent complexity to or amount of data that is collected and analyzed as presently claimed.
Recent guidance from the office requires that the judicial exception be evaluated under a second prong to determine whether the judicial exception is practically applied. In the instant case, the claims do not have an additional element to which the analysis is applied. It is noted the intended final step is selecting a candidate drug, however this appears to be in silico as the system and CRM only provide for computer implementation as well. This judicial exception requires steps recited at high level of generality and are only stored on a non-transitory, and is not found to be a practical application of the judicial exception as broadly set forth.
For step 2B of the 101 analysis, each of the independent claims do not recite any additional elements. As such, the claims do not provide for any additional element to consider under step 2B. It is noted that in explaining the Alice framework, the Court wrote that "[i]n cases involving software innovations, [the step one] inquiry often turns on whether the claims focus on the specific asserted improvement in computer capabilities or, instead, on a process that qualifies as an abstract idea for which computers are invoked merely as a tool." The Court further noted that "[s]ince Alice, we have found software inventions to be patent-eligible where they have made non-abstract improvements to existing technological processes and computer technology." Moreover, these improvements must be specific -- "[a]n improved result, without more stated in the claim, is not enough to confer eligibility to an otherwise abstract idea . . . [t]o be patent-eligible, the claims must recite a specific means or method that solves a problem in an existing technological process." As indicated in the summary of the judicial exception above and in view of the teachings of the specification, the steps are drawn to analysis of ‘relevant’ data for protein-protein interaction. While the instruction are stored on a CRM medium and could be implemented on a computer as a system, together the steps do not appear to result in significantly more than a means to compare sequences. The judicial exception of the method as claimed can be performed by hand and in light of the previous claims to a computer medium and in light of the teaching of the specification on a computer. In review of the instant specification the methods do not appear to require a special type of processor and can be performed on a general purpose computer. Dependent claims set forth additional steps which are more specifically define the considerations and steps of calculating, and comparing, and do not add additional elements which result in significantly more to the claimed method for the analysis. No additional steps are recited in the instantly claimed invention that would amount to significantly more than the judicial exception. Without additional limitations, a process that employs mathematical algorithms (aligning sequences) to manipulate existing information (identify a probe that starts at a deletion or insertion) to generate additional information is not patent eligible. Furthermore, if a claim is directed essentially to a method of calculating, using a mathematical formula, even if the solution is for a specific purpose, the claimed method is non-statutory. In other words, patenting abstract idea (defining or analyzing protein interactions) cannot be circumvented by attempting to limit the use to a particular technological environment or purpose and desired result.
One way to overcome a rejection for non-patent-eligible subject matter is to persuasively argue that the claimed subject matter is not directed to a judicial exception. Another way for the applicants to overcome the rejection is to persuasively argue that the claims contain elements in addition to the judicial exception that either individually or as an ordered combination are not well understood, routine, or conventional. Another way for the applicants to overcome the rejection is to persuasively argue that the claims as a whole result in an improvement to a technology. Persuasive evidence for an improvement to a technology could be a comparison of results of the claimed subject matter with results of the prior art, or arguments based on scientific reasoning that the claimed subject matter inherently results an improvement over the prior art. The applicants should show why the claims require the improvement in all embodiments.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-20 are rejected under 35 U.S.C. 103 as being unpatentable over Malas et al. (2019).
Claim 1 provides a method for selecting candidate compounds using artificial intelligence implementing several steps of extracting ‘relevant data’ of potential lead compounds, generating a knowledge based graph from the extracted data, assigning a rank by correlating any historical clinical information and knowledge based graph data, calculating a binding affinity of a protein-protein interaction and possible interactions, then assigning a final rank based on the analysis. The use of artificial intelligence to analyze protein-protein interactions was known and applied to identifying possible interactions which could possibly be therapeutic targets for a variety of disorders. For example, Malas et al. provide methods of drug prioritization using the semantic properties of a knowledge graph. More specifically, Malas et al teach that compounds that are candidates for drug repurposing can be ranked by leveraging knowledge available in the biomedical literature and databases. this knowledge, spread across a variety of sources, can be integrated within a knowledge graph, which thereby comprehensively describes known relationships between biomedical concepts, such as drugs, diseases, genes, etc. and that the use of the semantic information between drug and disease concepts as features, which are extracted from an existing knowledge graph that integrates 200 different biological knowledge sources was done. Malas et al. provide specific examples of targets and analyze Mozavaptan, a vasopressin V2 receptor antagonist that is predicted to be the drug most likely to be approved after a clinical trial, and belongs to the same drug class as tolvaptan, the only treatment for ADpKD that is currently approved. In the analysis they conclude that semantic properties of concepts in a knowledge graph can be exploited to prioritize drug repurposing candidates for testing in clinical trials.
Malas et al. do not specifically state to rank or provide a final rank, but it is clear that they are reviewing potential drugs for repurposing and effectively rank, or provide yes or no criteria during the analysis. Further, it is noted that the present claims for the method and system are generic and do not provide any specific starting data, nor does it provide any specific disorder or means that are used to assess the relevant data that is first extracted. Given the generic nature of the present claims and the specific examples of Malas et al. it would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made to provide target or lead compounds and based on the analysis rank or score them as possible candidates one to the other. One having ordinary skill in the art would have been motivated to provide or rank possible drugs based on the analysis, ultimately to provide for a drug that may be applicable to other conditions or disorders consistent with it’s known function or that known in the art. There would have been a reasonable expectation of success given the results Malas et al. to analyze existing data and apply artificial intelligence to the analysis to provide relevant analysis of properties to assign a compound as a possible lead compound for other disorders.
Thus, the claimed invention as a whole was clearly prima facie obvious.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Joseph T Woitach whose telephone number is (571)272-0739. The examiner can normally be reached Mon-Fri; 8:00-4:00.
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/Joseph Woitach/Primary Examiner, Art Unit 1687
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