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 .
Status of the Claims
Claims 1 and 3-18 are pending and examined herein.
Claim 2 is canceled.
Priority
As detailed on the 20 August 2021 filing receipt, the application claims priority as early as 14 August 2020 to application DE 102020210357.7. At this point in examination, all claims have been interpreted as being accorded this priority date as the effective filing date.
Withdrawn Objections
The objection to claims 1 and 10 is overcome in view of correction of the placement of the conjunction joining the final list elements.
The objection to claims 7-8 are withdrawn in view of correction of the typographical error.
The objection to claim 8
The following objections and/or rejections constitute the complete set of objections and/or rejections applied to the instant application.
Claim Interpretation under 35 USC 112(f)
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 limitations are:
A: device configured in claim 9.
Because this claim limitation is being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it is being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof. The following indicates the corresponding structure identified in the specification for each 112(f) limitation:
A: method carried out by training device 141 may be stored,
implemented as a computer program, on a machine-readable memory
medium 146 and executed by a processor 145. (Page 19, Last 3 lines). In addition, The specification discloses “the present invention relates to a device
and a computer program which are each configured to carry out
the above methods and a machine-readable memory medium on which
this computer program is stored. (Page 4, Lines 15-18).
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 § 112(b)
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 11-18 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. Claims 11-18 recite the determined primary RNA sequence is used for synthesizing an RNA molecule (claims 11-14) and for use in synthetic biology or biotechnology (claims 15-18). These claims recite intended use of the sequence determined by their parent claims. That is, the claims merely recite a use without any active, positive steps delimiting how this use is actually practiced (Ex parte Erlich, 3 USPQ2d 1011 (Bd. Pat. App. & Inter. 1986)). Although a claim should be interpreted in light of the specification disclosure, it is generally considered improper to read limitations contained in the specification into the claims. See In re Prater, 415 F.2d 1393, 162 USPQ 541 (CCPA 1969) and In re Winkhaus, 527 F.2d 637, 188 USPQ 129 (CCPA 1975), which discuss the premise that one cannot rely on the specification to impart limitations to the claim that are not recited in the claim. MPEP 2173.05(q) pertains. Amending the claims to positively recite a step implementing the sequence, such as synthesizing the sequence, may overcome the rejection.
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 3-18 are rejected under 35 USC § 101 because the claimed inventions are directed to an abstract idea without significantly more. "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 § I). Abstract ideas include mathematical concepts, and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2)). The claims as a whole, considering all claim elements individually and in combination, are directed to a judicial exception at Step 2A, Prong 2, and the additional elements of the claims, considered individually and in combination, do not provide significantly more at Step 2B than the abstract idea of ascertaining an RNA sequence.
MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter (MPEP 2106.03)?
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of
nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
The claims are directed to methods (claims 1, 3-8, 11-12, 15-16), a device interpreted as a computer system (claims 9, 13, and 17), and a non-transitory machine-readable medium (claim 10, 14, and 18), each of which falls within one of the categories of statutory subject matter. [Step 1: Yes]
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. MPEP § 2106.04(a)(2) further explains that abstract ideas are defined as:
• mathematical concepts (mathematical formulas or equations, mathematical relationships
and mathematical calculations) (MPEP 2106.04(a)(2)(I));
• certain methods of organizing human activity (fundamental economic principles or practices, managing personal behavior or relationships or interactions between people) (MPEP 2106.04(a)(2)(II)); and/or
• mental processes (concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) (MPEP 2106.04(a)(2)(III)).
The step of “initializing the strategy” (claims 1 and 8-10) is interpreted as deciding to begin the method, which is a step practically performed by the human mind.
The step of “determining a primary candidate RNA sequence” (claims 1 and 8-10) is interpreted as using a function to determine the order of nucleotides in a nucleotide string, which can performed by the human mind. It is also described in mathematical terms and thus may be understood as a mathematical concept (pg. 3, second paragraph). It is generally noted that a mathematical relationship may be expressed in words and there is no particular word or set of words that indicates a claim recites a mathematical calculation. That is, a claim does not have to recite the word "calculating" in order to be considered a mathematical calculation. For example, a step of "determining" a variable or number using mathematical methods or "performing" a mathematical operation may also be considered mathematical calculations when the broadest reasonable interpretation of the claim in light of the specification encompasses a mathematical calculation (MPEP 2106.04(a)(2)).
The step of “ascertaining a sequence loss” (claims 1 and 8-10) is disclosed in mathematical terms (pg. 3, second paragraph; pg. 10, first equation) and thus interpreted as a mathematical concept. Determining sequence loss may also be understood as a mental process in comparing two sequence.
The step of “applying a folding algorithm” (claims 1 and 8-10) is disclosed as applying a mathematical function (pg. 6, fourth paragraph) and thus a mathematical concept. The step may also be performed mentally or with pen and paper, and thus may also be a mental step.
The step of “ascertaining a structure loss” (claims 1 and 8-10) is disclosed as applying a mathematical function (pg. 10, second equation) and thus a mathematical concept. The step may also be performed mentally or with pen and paper, and thus may also be a mental step.
The step of “ascertaining a total loss” (claims 1 and 8-10) is disclosed as applying a mathematical function (pg. 10, third equation) and thus a mathematical concept. The step may also be performed mentally or with pen and paper, and thus may also be a mental step.
The step of “adapting the strategy using a reinforcement strategy” (claims 1 and 8-10) is disclosed as a having hyperparameters which may be optimized and thus is interpreted as a mathematical concept. The reinforcement learning steps are described on pg. 12, second paragraph, and formulated in mathematical terms in the last paragraph of pg. 12 and the equations on pg. 13.
The step of “successively determining a candidate RNA sequence” (claim 8) is disclosed in mathematical terms (pg. 4, second paragraph) and thus is interpreted as a mathematical concept. The step may also be performed mentally or with pen and paper, and thus may also be a mental step.
Dependent claim 3 recites use of an indicator function, which is disclosed as applying a mathematical function (pg. 9, last equation) and thus a mathematical concept. The step may also be performed mentally or with pen and paper, and thus may also be a mental step.
Dependent claim 4 recites ascertaining sequence loss using a Hamming distance, which is interpreted as a further limitation on the abstract idea discussed above.
Dependent claim 5 recites dividing total loss by number of restrictions, and where division is a mathematical concept.
Dependent claim 6 recites optimization of hyperparameters and thus describes a mathematical concept.
Dependent claim 7 recites Bayesian optimization and hyperband (BOHB), which is a mathematical concept including a probabilistic model.
Dependent claims 11-18 recite claims interpreted as reciting the intended use of the sequences or what the determined sequence is used to do. However, as explained in the rejection under 35 USC 112(b) above, it is not clear that these claims further limit their respective parent claims as they do not have patentable weight as they recite neither abstract ideas nor additional elements.
Hence, the claims explicitly recite numerous elements that, individually and in combination,
constitute abstract ideas. The claims must therefore be examined further to determine whether they
integrate that abstract idea into a practical application (MPEP 2106.04(d)). [Step 2A: Yes]
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Because the claims recite judicial exceptions, direction under Step 2A Prong Two provides that the claims must be examined further to determine whether they recite elements in addition to the abstract ideas which integrate the judicial exceptions 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 judicial exceptions are integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d)(III)).
The claims recite the following elements which are not abstract ideas: a “computer” (claim 1 and 8-10), “providing a task representation” (claims 1 and 8-10), “a non-transitory device” (claim 9), and “a non-transitory machine-readable memory medium” (claim 10).
Data gathering steps, such as receiving data and descriptions of data including the task representation, are not considered abstract ideas, but perform functions of inputting, collecting, and outputting the data needed to carry out the abstract idea. The claims recite providing data or given a certain type pf data. These steps are considered insignificant extra-solution activity, and are not sufficient to integrate an abstract idea into a practical application as they do not impose any meaningful limitation on the abstract idea or how it is performed. To integrate a judicial exception into a practical application, the additional limitations must not be mere instructions to apply the judicial exception. See MPEP § 2106.04(d) and MPEP § 2106.05(g)).
The claims comprising computer components do not describe any specific computational steps by which the computer performs or carries out the abstract idea, nor do they provide any details of how specific structures of the computer are used to implement these functions. The claims state nothing more than that a generic computer performs the functions that constitute the abstract idea. Hence, these are mere instructions to apply the abstract idea using a computer, and therefore the claim does not integrate that abstract idea into a practical application (see MPEP 2106.04(d) § I; and MPEP 2106.05(f)). [Step 2A Prong Two: No]
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself. Step 2B of 101 analysis determines whether the claims contain additional elements that amount to an inventive concept, and an inventive concept cannot be furnished by an abstract idea itself (MPEP 2106.05). The claims recite the following elements which are not abstract ideas: a “computer” (claim 1), “providing a task representation” (claims 1 and 8-10), “a non-transitory device” (claim 9), and “a non-transitory machine-readable memory medium” (claim 10). Data collection and implementation of a method on a computer system do not add significantly more than the abstract ideas. Data gathering does not amount to an inventive concept (MPEP 2106.05(g)). Storing data on a computer is a conventional computer function (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; MPEP 2106.05(d)). Therefore, the recited additional elements, alone or in combination with the judicial exceptions, do not appear to provide an inventive concept. [Step 2B: No]
Conclusion: Claims are Directed to Non-statutory Subject Matter
For these reasons, the claims, when the limitations are considered individually and as a whole,
are directed to an abstract idea and lack an inventive concept. Hence, the claimed invention does not
constitute significantly more than the abstract idea, so the claims are rejected under 35 USC § 101 as
being directed to non-statutory subject matter.
Response to the 10 August 2026 Applicant Remarks
Regarding Step 2A Prong Two of the 101 analysis, applicant remarks state the amendment to the independent claims reciting that they are "for designing a functional RNA molecule having the
predefined secondary structure for use in transcription, epigenetics, or translation" where producing a functional RNA molecule according to the claimed method achieves benefits in terms of efficiency while also allowing RNA design to be conducted over a larger search space than in the related art (pg. 8). Applicant remarks state the amended claims links the optimization achieved by the claimed application of an RL algorithm to the design of functional RNA molecules having a predefined secondary structure for use in transcription, epigenetics, or translation (pg. 9).
At Step 2A Prong Two, analyzing the elements in addition to the abstract ideas are analyzed to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). The claims recite the following elements which are not abstract ideas: a “computer” (claim 1 and 8-10), “providing a task representation” (claims 1 and 8-10), “a non-transitory device” (claim 9), and “a non-transitory machine-readable memory medium” (claim 10). Designing an RNA molecule remains an abstract idea as generating the molecule itself is not required. For the reasons stated above, the additional elements are interpreted as instructions to implement the abstract ideas using a general purpose computer and data inputting as data gathering, which is considered insignificant extra solution activity (MPEP 2106(d), (f), and (g). The amended limitations regarding what the RNA sequence is for is interpreted as an intended use limitation. Active, positively claimed limitations such as synthesizing the RNA molecule or using the molecule in synthetic biology or biotechnology is not recited. Furthermore, if positively recited, it is not clear these steps would amount to more than instructions to apply the abstract ideas (MPEP 2106.05(f)). Finally, it is not clear, if the steps were positively recited, how the device (claim 9) and computer-readable medium (claim 10) would perform the synthesis steps of designing the molecule, if designing is interpreted as tantamount to synthesizing, thus necessitating a rejection under 35 USC 112(a).
Therefore, the rejection under 35 USC 101 is maintained.
Conclusion
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 Robert J Kallal whose telephone number is (571)272-6252. The examiner can normally be reached Monday through Friday 8 AM - 4 PM EST.
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/R.J.K./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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