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 amendments and remarks, filed 03/30/2026, are acknowledged. Rejections and/or objections not reiterated from previous office actions are hereby withdrawn.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.
Status of Claims
Claims 1, 3-13, 15-18, 20 are under examination.
Claims 14 and 19 are withdrawn. Claim 2 has been cancelled.
Priority
Applicant’s claim for the benefit of priority under 35 U.S.C. 119(a)-(d) is acknowledged. Receipt is acknowledged of the certified copy of foreign priority to application EP19186032, filed 07/12/2019. However a U.S. non-provisional utility application containing a foreign priority claim, or its earliest parent application under 35 U.S.C. 120, must have been filed within 12 months of the FIRST filed foreign application disclosing the claimed invention. See MPEP 213 (37 CFR 1.55). This is not the case, as the instant application was filed 01/11/2022.
This application is also the National Stage filing under 35 USC 371 of PCT/EP2020/068611, filed 07/02/2020. However, contrary to applicant’s response, the issue remains that the examiner cannot find a certified copy of PCT/EP2020/068611 as required by 35 U.S.C. 119(b) (only PCT written opinions and search strategies filed 01/11/2022). Accordingly, the effective filing date is 01/11/2022.
Withdrawn Rejections
The rejection of claims 1, 3-13, 15-18, 20 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, is withdrawn in view of applicant’s amendments.
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.
The following rejection is modified in view of applicant’s amendments.
Claims 1, 3-13, 15-18, 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.
The United States Patent and Trademark Office published revised guidance on the application of 35 U.S.C. § 101. USPTO’s 2019 Revised Patent Subject Matter Eligibility Guidance (“Guidance”). Under the Guidance, in determining what concept the claim is “directed to,” we first look to whether the claim recites:
(1) any judicial exceptions, including certain groupings of abstract ideas (i.e., mathematical concepts, certain methods of organizing human activity such as a fundamental economic practice, or mental processes) (Guidance Step 2A, Prong 1); and
(2) additional elements that integrate the judicial exception into a practical application (see MPEP § 2106.05(a)-(c), (e)-(h)) (Guidance Step 2A, Prong 2).
Only if a claim (1) recites a judicial exception and (2) does not integrate that exception into a practical application, do we then look to whether the claim contains an “‘inventive concept’ sufficient to ‘transform’” the claimed judicial exception into a patent-eligible application of the judicial exception. Alice, 573 U.S. at 221 (quoting Mayo, 566 U.S. at 82). In so doing, we thus consider whether the claim:
(3) adds a specific limitation beyond the judicial exception that are not “well-understood, routine and conventional in the field” (see MPEP § 2106.05(d)); or 2019 Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50-57 (January 7, 2019).
(4) simply appends well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception.(Guidance Step 2B). See Guidance, 84 Fed. Reg. at 54-56.
Guidance Step 1:
The instant invention (claim 1 being representative) is directed to a method for monitoring bacterial outbreak that performs a process. Thus, the claims are directed to one of the statutory categories of invention. MPEP 2106.03.
A. Guidance Step 2A, Prong 1
The Revised Guidance instructs us first to determine whether any judicial exception to patent eligibility is recited in the claim. The Revised Guidance identifies three judicially-excepted groupings identified by the courts as abstract ideas: (1) mathematical concepts, (2) certain methods of organizing human behavior such as fundamental economic practices, and (3) mental processes. Regarding claim(s) 1, the claimed steps that are part of the abstract idea are as follows:
calculating a genomic distance of the digital genome obtained from a digital genome of a database, called epidemiological database, comprising at least one digital genome of a bacterial strain belonging to the bacterial species and sampled within the geographical zone;
calculating a first threshold and a second threshold by:
constructing or providing a learning database of genomes of bacterial strains belonging to the bacterial species, the learning database comprising…;
selecting a binary predictor variable configured for predicting that two bacterial strains are related or unrelated by comparing a genomic distance between the two bacterial strains against a fifth threshold…;
calculating (i) a confusion matrix of the binary predictor as a function of the learning database; (ii) a first quality index of the binary predictor as a function of the confusion matrix, the first quality index being different from a sensitivity and specificity of the binary predictor; (iii) a second quality index…;
finding a first value of fifth threshold that optimizes the first quality index and a second value of the fifth threshold that optimizes the second quality index;
setting the first threshold equal to a minimum of the first and second values of the fifth threshold…;
predicting: (i) that the bacterial strain sampled and the bacterial strain of the epidemiological database belong to a bacterial outbreak if their genomic distance is below the first predetermined threshold; or (ii) that the bacterial strain sampled and the bacterial strain of the epidemiological database do not belong to the bacterial outbreak…; or (iii) that the bacterial strain sampled and the bacterial strain of the epidemiological database possibly belong to the bacterial outbreak if their genomic distance is between the first and the second threshold…;
Mental Processes
With regards to said calculating, these steps are recited at a high level of generality (without any technological details directed to how they are performed) and do not explicitly require a computer. Notably, the mere mention of “computer-implemented” in the preamble is merely suggestive language and does not require a computer. In addition, scientists routinely perform calculations, e.g. with a pencil and paper. As such, these steps encompass a mental process of observing data and performing analysis. MPEP 2106.04(a)(2), section III.
With regards to constructing, this step is recited at a high level of generality (without any technological details or rules directed to how it is performed) and does not explicitly require a computer. As such, this step encompasses a mental process of observing data. MPEP 2106.04(a)(2), section III.
With regards to said finding, setting, and predicting, these steps are recited at a high level of generality (without any technological details directed to how they are performed) and do not explicitly require a computer. In addition, scientists routinely perform comparative analysis, e.g. in their mind or with a pencil and paper. As such, these steps encompass a mental process of observing data, performing analysis, and making a decision. MPEP 2106.04(a)(2), section III.
Applicant is reminded that the Office's eligibility guidance does not set limit on the number of calculations that can or cannot be performed mentally. MPEP § 2106.04(a)(2)III. In addition, the specification provides sufficient evidence that the claims are directed to an abstract idea since the specific descriptions provided for accomplishing these tasks include mathematical equations for performing said calculations [pages 6-12]. Accordingly, the above steps clearly fall within the mental process groupings of abstract ideas because they cover concepts performed in the human mind, including observation, evaluation, judgment, and opinion. See MPEP 2106.04(a)(2), subsection III [Step 2A, Prong 1: YES].
Mathematical Concept
With regards to calculating said genomic distance, thresholds, confusion matrix, and indexes, these step are recited at a high level of generality (without any technological details or rules directed to how it is performed) and do not explicitly require a computer. In addition, the specification also teaches mathematical equations for performing said calculations [pages 6-12]. Accordingly, when read in light of the specification, this step also encompasses a mathematical concept of manipulating information through mathematical correlations or calculations. MPEP 2106.04(a)(2) Section I.
B. Guidance Step 2A, Prong 2
This part of the eligibility analysis evaluates whether the claim as a whole integrates the recited judicial exception into a practical application of the exception or whether the claim is “directed to” the judicial exception. This evaluation is performed by (1) identifying whether there are any additional steps/elements recited in the claim beyond the judicial exception, and (2) evaluating those additional steps/elements individually and in combination to determine whether the claim as a whole integrates the exception into a practical application. See MPEP 2106.04(d).
In this case, the additional steps/elements recited in the claim beyond the judicial exception are as follows:
obtaining a genome in digital form of a bacterial strain sampled within the geographic zone and belonging to the bacterial species;
With regards to said obtaining, this step is recited at a high level of generality and results in gathering data for use by the abstract idea. Accordingly, this step amounts to insignificant extra-solution activity and are not indicative of an integration into a practical application. See MPEP 2106.05(g). With regards to the claimed database, this feature is generically recited and Applicant is reminded that “generic computer components such as a computer and database do not satisfy the inventive concept requirement.” See MPEP 2106.05(h). Even when viewed in combination, these additional steps/elements do not integrate the recited judicial exception into a practical application. [Step 2A, Prong 2: NO].
C. Guidance Step 2B:
This part of the eligibility analysis evaluates whether the claim as a whole amount to significantly more than the recited exception i.e., whether any additional element, or combination of additional elements, adds an inventive concept to the claim. See MPEP 2106.05.
As discussed above, the non-abstract steps/elements amount to nothing more than insignificant extra-solution activity. A review of the specification teaches a plurality of routine and conventional elements and devices for obtaining and storing genomic data [page 9 and Figure 6]. Furthermore, Kluytmans et al. (Journal of Clinical Microbiology, 2016, Vol. 54, No. 12, pp. 2919-27) teaches a Web-accessible epidemiological database for the global surveillance of bacterial outbreaks. Therefore, even upon reconsideration, there is nothing unconventional with regards to the above non-abstract elements/steps. See MPEP 2106.05(d)(Part II). Thus, the independent claim(s) as a whole do not amount to significantly more than the exception itself. Therefore, the claim(s) is/are not patent eligible. [Step 2B: NO].
D. Dependent Claims
Dependent claims 3-13, 15-18, 20 have also been considered under the two-part analysis but do not include additional steps/elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons. In particular, claims 3-13, 15-18, 20 are entirely directed to limitations that further limit the specificity of the abstract idea or the nature of the data being used by the abstract idea. Accordingly, these claims are also directed to an abstract idea for the reasons set forth above (Step 2A, prong 1 analysis). Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea (and/or natural correlation) without significantly more.
Response to Arguments
Applicant’s arguments, filed 03/03/2026, have been fully considered but are not persuasive for the following reasons.
Applicant argues that the claims are patent eligible because they are similar to the claims in Example 39 (USPTO SME Guidelines, 2019). In response, 2019 Revised Patent Subject Matter Eligibility Guidance (2019 PEG) clearly states: “the examples are hypothetical and only intended to be illustrative of the claim analysis under the 2019 PEG. These examples should be interpreted based on the fact patterns set forth below as other fact patterns may have different eligibility outcomes.” Moreover, unlike the instant claims, the “Example 39” claims are directed to a method for training a neural network for facial detection. As such, applicant’s arguments are not persuasive because the instant claims are clearly directed to a different fact pattern, namely detecting and monitoring a bacterial outbreak based on threshold calculations and comparisons.
Applicant additionally argues that the claimed invention provides an improvement to the functioning of a computer for detecting and monitoring physical phenomena. In response to aggregate arguments, the MPEP is clear that the word "improvements" in the context of this consideration is limited to improvements to the functioning of a computer or any other technology/technical field, whether in Step 2A Prong Two or in Step 2B. MPEP 2106.04(d)(1). In this case, the amended claims do not integrate the JE into a practical application and still do not even positively require a computer, nor has applicant provided any objective evidence to support the assertion that the claims result in an improvement to the functioning of a computer. Applicant has also failed to identify any steps/elements appended to the abstract idea that provide for a new technology (Step 2A, prong 2 or Step 2B) or provided any evidence of an unconventional combination of steps. Therefore, applicant is essentially arguing that the improvement is entirely in the realm of abstract ideas and that abstract idea is providing the improvement. However, Applicant is reminded that the claimed invention’s use of the ineligible concept to which it is directed (i.e. the abstract idea) cannot supply the inventive concept that renders the invention ‘significantly more’ than that ineligible concept.” BSG Tech LLC v. BuySeasons, Inc., 899 F.3d 1281, 1290 (Fed. Cir. 2018). It is also well settled that mere computer-based efficiency does not save an otherwise abstract method. Bancorp Servs. L.L.C. v. Sun Life Assur. Co. of Canada (US.), 687 F.3d 1266, 1277-78 (Fed. Cir. 2012) (explaining that performance by computer of operations that previously were performed manually or mentally, albeit less efficiently, does not convert a known abstract idea into eligible subject matter). Similarly, the courts have also instructed that “[t]he different use of a mathematical calculation, even one that yields different or better results, does not render patent eligible subject matter.” Board Of Trustees Of Leland Stanford Junior University, 991 F.3d 1245, 1251 (Fed. Cir. 2021). Accordingly, the examiner maintains that the claims do not provide an improvement to the technology (under Step 2A, prong 2, or Step 2B). See MPEP 2106.04(d)(1). Therefore, absent any evidence to the contrary, the rejection is maintained.
Claim rejections - 35 USC § 112, 2nd Paragraph
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.
The following rejection is modified in view of applicant’s amendments.
Claims 1, 3-13, 15-18, 20 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 pre-AIA the applicant regards as the invention. Claims that depend directly or indirectly from claim(s) 1 are also rejected due to said dependency.
Claim 1 recites “calculating a genomic distance of the genome obtained from a genome of a database, called epidemiological database, comprising at least one genome…and sampled within the geographical zone”. In this case, the claim does not provide a discernable boundary on what operation(s) perform the claimed function, i.e. the claim generically reads on doing math. The artisan would understand that calculating a “distance” requires at least two reference points (between which a distance can be measured). However, the claimed calculating step is not limited to any particular reference points (e.g. within a genome) or any particular computational operations (e.g. there are different types of distance calculations). A review of the specification does not provide any limiting definition or clarifying examples. The specification does disclose a genomic distance “between two bacterial strains” [page 5] and an equation for calculating genomic distance for two different bacterial strains based on “Compt” (allelic differences) and the number of loci [page 10]. However, applicant is reminded that it is improper to import narrowing limitations into the claims. MPEP 2111.01. As a result, it is unclear what computational techniques are included or excluded by the claim language such that one of ordinary skill in the art would know how to avoid infringement. In addition, with regard to the phrase “sampled within a geographical zone”, it is unclear in what way this limitation further limits the calculating step. Applicant is reminded that limitations that suggest acts/operations without positively reciting them do not impose any patentable distinction on the claim (i.e. is not limiting). See also MPEP § 2111.04. In each case, clarification is requested via amendment.
Claim 1 recites “calculating a first threshold and a second thresholds by: - constructing or providing a learning database of genomes of bacterial strains belonging to the bacterial species, the learning database comprising: (i) pairs of bacterial strains previously determined as belonging to one and the same bacterial outbreak, and tagged as pairs of related strains…; selecting a binary predictor variable configured for predicting that two bacterial strains are related or unrelated by comparing a genomic distance between the two bacterial strains against a fifth threshold.” In this case, the above step recites a “first threshold”, “second thresholds”, and a “fifth threshold”. Firstly, it is unclear what is meant by “second thresholds”, which is plural whereas all other thresholds are singular. This appear to be a grammatic error. Correction is requested. Secondly, as the claim jumps from first and second thresholds to a fifth threshold, it is unclear what happened to the third and fourth thresholds. Clarification is requested via amendment.
Claim 1 recites “for each value of the fifth threshold belonging to…values of the fifth threshold.” One of ordinary skill in the art would understand that a ‘threshold’ is just a numerical value---not a string of multiple values. Moreover, there is nothing in the specification that defines or suggests the fifth threshold as claimed to include “multiple values”. Accordingly, it is unclear what limiting effect is intended by the phrase “for each value of the fifth threshold”. As a result, there is also lack of antecedent basis for this limitation (as there is not previous provision in the claim for multiple values associated with a fifth threshold). Clarification is requested via amendment.
Claim 1 recites “calculating (i) a confusion matrix of the binary predictor as a function of the learning database.” In this case, the claim is not limited to any particular operations for performing said calculating. A review of the specification does not describe, to any appreciable extent, any algorithms, equations, or prose equivalent that correspond to the claimed function. Moreover, the artisan would recognize that a confusion matrix is a table used to evaluate the performance of a classification model. However, this is not commensurate in scope with what is claimed and the claim also does not include any “model” for achieving the claimed function. As a result, it is unclear what computational techniques are included or excluded by the claim language such that one of ordinary skill in the art would know how to avoid infringement, i.e. in what way is the confusion matrix being calculated “as a function of the learning database”. Clarification is requested via amendment.
Claim 1 recites “calculating…a first quality index of the binary predictor as a function of the confusion matrix…; a second quality index…as a function of the confusion matrix…”. In each case, it is unclear in what way the first and second indexes are being calculated “as a function of the confusion matrix”. A review of the specification does not describe, to any appreciable extent, any algorithms, equations, or prose equivalent that correspond to the claimed function. As a result, it is unclear what computational techniques are included or excluded by the claim language such that one of ordinary skill in the art would know how to avoid infringement. Clarification is requested via amendment.
Claim 1 recites “setting the first threshold equal to a minimum of the first and second values of the fifth threshold and setting the second threshold equal to a maximum of the first and second values of the fifth threshold, wherein the second predetermined threshold is strictly higher than the first threshold”. In this case, there is lack of antecedent basis for “the first and second values of the fifth threshold” for reasons discussed above. Clarification is requested via amendment.
Prior Art Rejection of Indefinite Claims
In view of the indefiniteness and lack of clarity in the instant claims, as set forth in the 35 USC 112(b) rejection above, the Examiner has had difficulty in properly interpreting instant claims. However, to avoid piecemeal prosecution and to give applicant a better appreciation for relevant prior art if the claims are redrafted to avoid the 35 USC 112 rejections, the following prior art made of record and not relied upon is considered pertinent to applicant' s disclosure.
Adhikari et al. (International Journal of Computer Science & Information Technology, Vol 10, No 4, August 2018, pp.1-16), which teaches methods for epidemic outbreak prediction using artificial intelligence algorithms, including the use of confusion matrices.
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 extension fee 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 date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PABLO S WHALEY whose telephone number is (571)272-4425. The examiner can normally be reached between 1pm-9pm EST.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Anita Coope can be reached at 571-270-3614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/PABLO S WHALEY/Primary Examiner, Art Unit 3619
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