Kim, Seungchan et al.Download PDFPatent Trials and Appeals BoardOct 24, 201914078994 - (D) (P.T.A.B. Oct. 24, 2019) Copy Citation UNITED STATES PATENT AND TRADEMARK OFFICE UNITED STATES DEPARTMENT OF COMMERCE United States Patent and Trademark Office Address: COMMISSIONER FOR PATENTS P.O. Box 1450 Alexandria, Virginia 22313-1450 www.uspto.gov APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO. 14/078,994 11/13/2013 Seungchan Kim 91482.203 9723 54434 7590 10/24/2019 BOOTH UDALL FULLER, PLC 1255 W. Rio Salado Pkwy. Suite 215 Tempe, AZ 85281 EXAMINER BRUSCA, JOHN S ART UNIT PAPER NUMBER 1631 NOTIFICATION DATE DELIVERY MODE 10/24/2019 ELECTRONIC Please find below and/or attached an Office communication concerning this application or proceeding. The time period for reply, if any, is set in the attached communication. Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the following e-mail address(es): PATENT@BOOTHUDALL.COM aho@boothudall.com reception@boothudall.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE __________ BEFORE THE PATENT TRIAL AND APPEAL BOARD __________ Ex parte SEUNGCHAN KIM and SUNGWON JUNG __________ Appeal 2019-003840 Application 14/078,994 Technology Center 1600 __________ Before DEMETRA J. MILLS, RICHARD M. LEBOVITZ, and DEBORAH KATZ, Administrative Patent Judges. MILLS, Administrative Patent Judge. DECISION ON APPEAL Pursuant to 35 U.S.C. § 134(a), Appellant1 appeals from the Examiner’s decision to reject claims 1–5 and 8–22. We have jurisdiction under 35 U.S.C. § 6(b). We affirm. 1 We use the word “Appellant” to refer to “applicant” as defined in 37 C.F.R. § 1.42. Appellant identifies the real party in interest as The Translational Genomics Research Institute. Appeal Br. 3. Appeal 2019-003840 Application 14/078,994 2 NATURE OF THE INVENTION This invention relates to systems and methods for evaluating the differentiality of a set of discrete random variables between two or more conditions, such as two different disease conditions. In particular embodiments, the systems and methods more specifically relate to comparisons of multiple conditions by evaluating the probability distributions of dependency networks from random variables and for identifying and evaluating the relationships between a plurality of genes. Spec. ¶2. The invention Evaluates the probability distribution of P(G I Dc) of a discrete random variable G requires computing the posterior probability Pr(gi I Dc) of each dependency network structure, where gi (1 ≤ i ≤ N) for the condition C. The direct computation of the posterior probability of a model (gi) given observation (Dc) is not necessarily straightforward. As such, the approach uses these likelihoods to compute the posterior probability using Bayes’ theorem. Spec. ¶57. In particular, once the probability distributions of dependency network structures P (G I Dc1) and P (G I Dc2) are computed, the divergence between the conditions C1 and C2 is measured using JS divergence, which is a popular method of measuring the divergence between two discrete probability distributions. Once the JS divergence[2]value, JS, is obtained, the statistical significance of JS is computed using a permutation approach. Spec. ¶66. 2 The Jensen-Shannon divergence equation: JSπ (Pi, P2) = H (π1P1 + π2P2) - π1H (P1) - π2H (P2). Reply Br. 6. Appeal 2019-003840 Application 14/078,994 3 STATEMENT OF CASE The following claim 1 is representative. 1. A bioinformatics method for identifying or evaluating relationships between a plurality of genes, comprising: receiving, with a processor, a target gene set across a plurality of conditions, wherein the target gene set comprises a plurality of genes having differing expression patterns; evaluating each gene as a discrete random variable; identifying a plurality of likely dependency network structures for the plurality of genes for each condition, wherein the number of the likely dependency network structures is at least 50; generating, with the processor, a probability distribution of the likely dependency network structures for each condition; measuring, with the processor, a first Jensen-Shannon (JS) divergence to generate an overall differential dependency relationship between genes in the target gene set across the plurality of conditions; building, with the processor, a plurality of permuted data sets using randomly permuted conditions from the target gene set; measuring, with the processor, a second JS divergence to generate an overall differential dependency relationship for each permuted data set; comparing, with the processor, the first JS divergence to the second JS divergence; generating, with the processor, a statistical significance of the first JS divergence; identifying a plurality of biological functions and pathways that show genetic relationships across the plurality of conditions using the overall differential dependency relationships; and displaying one or more of the identified pathways using a network diagram, displaying the statistically significant gene sets using a chart, or both. Appeal 2019-003840 Application 14/078,994 4 Appeal Br. 31–32 (Claims Appendix). Grounds of Rejection Claims 1–5 and 8–22 are rejected under 35 U.S.C. §101 as directed to patent ineligible subject matter. Ans. 3; Advisory Act. p. 1. FINDINGS OF FACT The Examiner’s findings of fact are set forth in the Answer at pages 3–9. PRINCIPLES OF LAW In making our determination, we apply the preponderance of the evidence standard. See, e.g., Ethicon, Inc. v. Quigg, 849 F.2d 1422, 1427 (Fed. Cir. 1988) (explaining the general evidentiary standard for proceedings before the Office). §101 Rejection ANALYSIS I. Patent Eligible Subject Matter, Principles of Law To determine whether claims are patent eligible under 35 U.S.C. § 101, we apply the Supreme Court’s two-step framework articulated in Alice Corp. v. CLS Bank Int’l, 573 U.S. 208 (2014). First, we determine whether the claims are directed to a patent-ineligible concept: laws of nature, natural phenomena, and abstract ideas. Id. at 216–17. If so, we then proceed to the second step to consider the elements of the claims “individually and ‘as an ordered combination’” to determine whether there are additional elements that “‘transform the nature of the claim’ into a patent-eligible application.” Id. at 217. In other words, the second step is to “search for an ‘inventive concept’—i.e., an element or combination of Appeal 2019-003840 Application 14/078,994 5 elements that is ‘sufficient to ensure that the patent in practice amounts to significantly more than a patent upon the [ineligible concept] itself.’” Id. at 217–18 (alteration in original). The Federal Circuit has described the Alice step-one inquiry as looking at the “focus” of the claims, their “character as a whole,” and the Alice step-two inquiry as looking more precisely at what the claim elements add—whether they identify an “inventive concept” in the application of the ineligible matter to which the claim is directed. See Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016); Enfish, LLC v. Microsoft Corp., 822 F.3d 1327, 1335–36 (Fed. Cir. 2016); Internet Pat. Corp. v. Active Network, Inc., 790 F.3d 1343, 1346 (Fed. Cir. 2015). A. 2019 Revised Guidance The PTO has published revised guidance that governs all patent- eligibility analysis under Alice and § 101 effective as of January 7, 2019. See USPTO, 2019 Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50 (January 7, 2019) (“2019 Revised Guidance”). According to the 2019 Revised Guidance and under Alice step 1 (abstract idea), we first look to whether the claim recites: (1) any judicial exceptions, including certain groupings of abstract ideas (i.e., mathematical concepts, mental processes, or certain methods of organizing human activity such as a fundamental economic practice or managing personal behavior or relationships or interactions between people); and Appeal 2019-003840 Application 14/078,994 6 (2) additional elements that integrate the judicial exception into a practical application (see Manual of Patent Examining Procedure (“MPEP”) §§ 2106.05(a)–(c), (e)–(h)).3 See id. at 51–52, 55, Revised Step 2A, Prong One (Abstract Idea) and Prong Two (Integration into A Practical Application). A claim that integrates a judicial exception into a practical application applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception, such that the claim is more than a drafting effort designed to monopolize the judicial exception. See id. at 54. When the judicial exception is so integrated, then the claim is not directed to a judicial exception and is patent eligible under § 101. Id. Only if a claim: (1) recites a judicial exception, and (2) does not integrate that exception into a practical application, do we then evaluate whether the claim provides an “inventive concept” under Alice step 2. See id. at 56; Alice, 573 U.S. at 217–18. For example, we look to whether the claim: 1) adds a specific limitation beyond the judicial exception that is not “well-understood, routine, conventional” in the field (see MPEP § 2106.05(d)); or 2) simply appends well-understood, routine, and conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception. See, 2019 Revised Guidance, 84 Fed. Reg. at 56. 3 All references to the MPEP are to the Ninth Edition, Revision 08–2017 (rev. Jan. 2018). Appeal 2019-003840 Application 14/078,994 7 Because there is no single definition of an “abstract idea” under Alice step 1, the PTO has recently recognized, for purposes of clarity, predictability, and consistency, key concepts identified by the courts as abstract ideas to explain the “abstract idea” exception. These concepts include the following three groupings: 1. Mathematical concepts—mathematical relationships, mathematical formulas or equations, mathematical calculations; 2. Mental processes—concepts performed in the human mind (including an observation, evaluation, judgment, opinion); and 3. Certain methods of organizing human activity—fundamental economic principles or practices (including hedging, insurance, mitigating risk); commercial or legal interactions (including agreements in the form of contracts; legal obligations; advertising, marketing or sales activities or behaviors; business relations); managing personal behavior or relationships or interactions between people (including social activities, teaching, and following rules or instructions). See id. at 52. According to the 2019 Revised Guidance, “[c]laims that do not recite [subject] matter that falls within these enumerated groupings of abstract ideas should not be treated as reciting abstract ideas,” except in rare circumstances. Id. at 53. Even if the claims recite any one of these three groupings of abstract ideas, these claims are still not “directed to” a judicial exception (abstract idea), and thus are patent eligible, if “the claim as a whole integrates the recited judicial exception into a practical application of that exception.” Id. Appeal 2019-003840 Application 14/078,994 8 For example, limitations that are indicative of “integration into a practical application” include: 1. Improvements to the functioning of a computer, or to any other technology or technical field — see MPEP § 2106.05(a); 2. Applying the judicial exception with, or by use of, a particular machine — see MPEP § 2106.05(b); 3. Effecting a transformation or reduction of a particular article to a different state or thing — see MPEP § 2106.05(c); and 4. Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception — see MPEP § 2106.05(e). In contrast, limitations that are not indicative of “integration into a practical application” include: 1. Adding the words “apply it” (or an equivalent) with the judicial exception, or merely include instructions to implement an abstract idea on a computer, or merely uses a computer as a tool to perform an abstract idea — see MPEP § 2106.05(f); 2. Adding insignificant extra-solution activity to the judicial exception — see MPEP § 2106.05(g); and 3. Generally linking the use of the judicial exception to a particular technological environment or field of use — see MPEP § 2106.05(h). See 2019 Revised Guidance, 84 Fed. Reg. at 54–55 (“Prong Two”). Appeal 2019-003840 Application 14/078,994 9 B. Rejection of Claims under 35 U.S.C. § 101 The Examiner’s Rejection The Examiner rejects representative claim 1 under 35 U.S.C. § 101 because the claim is directed to a mental process/abstract idea and does not recite additional elements that amount to significantly more than the judicial exception itself. Final Act. 3 The Examiner finds that: Independent claims 1 and 10 recite identifying dependency networks of genes across a plurality of conditions, determining differences between probability distributions of the dependency networks, and identifying biological functions and pathways across a plurality of conditions which is a mental process. Independent claim 9 recites a programmed computer that executes the process, which but for recitation of a generic computer, is a mental process. Dependent claims 2, 8, 11, 15- 17, and 19-21 recite further limitations to the mental process. Independent claims 1, 9, and 10 also recite limitations of using Jensen-Shannon divergences that are mathematical concepts required by the claimed subject matter. Dependent claims 3-5 and 12-14 recite further limitations of Bayesian Dirichlet equivalences or explicit mathematical operations that are mathematical concepts. But for the recitation of a generic computer component of a processor nothing precludes claims 1- 5 and 8-22 from falling within the mental process and mathematical concept groupings of abstract ideas. Ans. 3. The Examiner further finds that: Independent claims 1, 9, and 10 are directed to a judicial exception of identifying dependency networks of genes across a plurality of conditions, determining differences between probability distributions of the dependency networks, and identifying biological functions and pathways across a plurality of conditions, which is similar to the abstract idea of obtaining and comparing intangible data at issue in Cybersource Corp. v. Appeal 2019-003840 Application 14/078,994 10 Retail Decisions, Inc., 654 F.3d 1366, 99 USPQ2d 1690 (Fed. Cir. 2011)). Final Act. 3. The Examiner, thus, finds that the “judicial exception is not integrated into a practical application.” Ans. 3. In particular, the Examiner finds that: The claimed subject matter does not practically apply the recited abstract idea because the steps requiring a computer do not require an improvement to computer technology, instead the computer is a generic computer. The steps of inputting data is a data gathering step that does not apply the abstract idea. The steps of displaying an output of data is an extra-solution step that does not apply the abstract idea. The claims as a whole do not require an improvement to a technology, or use a particular machine, or transform an article to a different state or thing. Ans. 4. Appellant contends that: Claims 1, 9, and 10, however, are not directed to an abstract idea of obtaining and comparing intangible data at issue in Cybersource for at least the following reasons. First, unlike Claim 3 of the ‘154 Patent in Cybersource, present Claims 1, 9, and 10 are not drawn to an unpatentable mental process. Id. at 1371. Second, similar to Claim 17 of the ‘604 Patent at issue in Enfish, the plain focus of Claims 1, 9, and 10 is on an improvement to computer functionality itself, not on economic or other tasks for which a computer is used in its ordinary capacity. Enfish, LLC v. Microsoft Corp., 822 F.3d 1327, 1336 (Fed. Cir. 2016). Third, similar to Claim 1 of the ‘567 Patent at issue in McRO, Claims 1, 9, and 10 improve an inherently computer mediated technological process using specific rules. McRO, Inc. v. Bandai Namco Games Am. Inc., 837 F.3d 1299, 1313-16 (Fed. Cir. 2016). Appeal 2019-003840 Application 14/078,994 11 App. Br. 12. Appellant contends that, the claims recite, “an improvement to a computer-implemented bioinformatics method, i.e., a specific type of data analysis designed to improve the way a computer maps the relationship of genes to particular conditions.” App. Br. 18. Alice/Mayo—Step 1 (Abstract Idea) Step 2A–Prongs 1 and 2 identified in the Revised Guidance Step 2A—Prong 1 The Judicial Exception Viewing the Examiner’s rejection through the lens of the Office’s recent guidance, we first determine whether the claim recites a judicial exception to patentability. Claim 1 is directed to “A bioinformatics method for identifying or evaluating relationships between a plurality of genes.” The relationship between genes is a law of nature4. The claim recites the abstract idea judicial exception of mathematical concepts, including “probability distributions,” “a first Jensen-Shannon (JS) divergence to generate an overall differential dependency relationship between genes in the target gene, and displaying the results in a chart. In re Abele, 684 F.2d 902, 908 (CCPA 1982), found that a claim to displaying data resulting from calculations was not directed to patent eligible subject matter. 4 We do not comment on the law of nature abstract idea, but rely on the mathematical concepts abstract idea for purposes of this Decision. Appeal 2019-003840 Application 14/078,994 12 Thus, representative claim 1 is directed to a judicial exception to patentability. Step 2A—Prong 2 (Integration into Practical Application) See 2019 Revised Guidance, Revised Step 2A, Prong Two. As discussed above, we find that Appellant’s claim 1 recites a judicial exception to patentability of mathematical concepts. Under the Revised Guidance, we next determine “whether the claim recites additional elements that integrate the exception into a practical application of that exception.” 84 Fed. Reg. at 54, italicized emphasis added. Limitations that are indicative of integration into a practical application include applying the natural law to effect a particular treatment or prophylaxis for a disease or medical condition. See, e.g., Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1066–68 (Fed. Cir. 2011); see Vanda Pharms. Inc. v. West-Ward Pharms. Int’l Ltd., 887 F.3d 1117, 1134–35 (Fed. Cir. 2018). (emphasis added). [T]he prohibition against patenting abstract ideas ‘cannot be circumvented by attempting to limit the use of the formula to a particular technological environment’ or adding ‘insignificant postsolution activity’” (quoting Diehr, supra, at 191-192, 101 S.Ct. 1048)). Mayo Collaborative Services v. Prometheus Laboratories, Inc., 566 U.S. 66, 79, 132 S.Ct. 1289, 1297 (2012). In the context of revised Step 2A, the following exemplary considerations are indicative that an additional element (or combination of elements) may have integrated the exception into a practical application: Appeal 2019-003840 Application 14/078,994 13 • An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field; • an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition; • an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim; • an additional element effects a transformation or reduction of a particular article to a different state or thing; • an additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception. 2019 Revised Patent Subject Matter Eligibility Guidance, 84 FR 50-01, at 55 [footnotes omitted]. Evaluation of additional claim elements/specific claim steps The mathematical applications recited in claim 1 do not: (1) improve the functioning of a computer or other technology; (2) are not applied with any particular machine (except for a generic computer); (3) do not effect a transformation of a particular article to a different state; and (4) are not applied in any meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception. See MPEP §§ 2106.05(a)–(c), (e)–(h). The additional elements recited in Appellant’s claims do not transform the abstract mathematical concept into a patent-eligible application, as discussed below. We find that Appellant’s invention does not Appeal 2019-003840 Application 14/078,994 14 (1) provide a technical solution to a technical problem unique to the Internet, i.e., a “solution . . . necessarily rooted in computer technology in order to overcome a problem specifically arising in the realm of computer networks” (see DDR Holdings, LLC v. Hotels.com, L.P., 773 F.3d 1245, 1257 (Fed. Cir. 2014)) or (2) “entail[] an unconventional technological solution (enhancing data in a distributed fashion) to a technological problem (massive record flows which previously required massive databases)” and “improve the performance of the system itself” (see Amdocs Ltd. v. Openet Telecom, Inc., 841 F.3d 1288, 1300, 1302 (Fed. Cir. 2016)). Significantly, unlike the claim in Vanda Pharms. Inc. v. West-Ward Pharms. Int’l Ltd., 887 F.3d 1117, 1135 (Fed. Cir. 2018), claim 1 recites a use of the claimed method at a high level of generality, requiring only “evaluating relationships between genes,” and “identifying biological functions and pathways that show genetic relationships.” In Vanda, the claim was found to be a patent-eligible application because the claimed step of identifying a patient’s CYP2D6 genotype was used to determine how much of a drug to actually administer to the patient experiencing a particular condition, schizophrenia, i.e., the claim was directed to treating a specific patient in a specific way. The court in Vanda found that the genotype of the patient (a naturally-occurring phenomenon) was integrated into a new way of using a specific existing drug, iloperidone, to treat a patient having a specific condition, and thus was patent-eligible. Id. In the present case, there is no practical application of the mathematical result of the method, such as a treatment of a specific condition, set forth in the claim. More specifically, claim 1 recites, “A bioinformatics method for identifying or evaluating relationships between a Appeal 2019-003840 Application 14/078,994 15 plurality of genes.” This preamble suggests mathematical concepts in the process/method steps, and does not describe a specific, practical application of the method. In other words, the method is a theoretical, method of identifying or evaluating relationships between a plurality of genes without a stated, practical purpose for the result of the evaluation, e.g. treating a specific condition. The claimed invention is directed to an abstract idea. The first step of claim 1 recites, “receiving, with a processor, a target gene set across a plurality of conditions, wherein the target gene set comprises a plurality of genes having differing expression patterns.” This step describes the use of a generic computer to receive data. The next step of claim 1 recites, “evaluating each gene as a discrete random variable.” This step includes mathematical concepts because the nature of the gene is characterized as a random variable. The next step of claim 1 recites, “identifying a plurality of likely dependency network structures for the plurality of genes for each condition, wherein the number of the likely dependency network structures is at least 50.” This step describes the process of identifying data related to genes and genetic conditions without reciting a practical application, such as treating the genetic condition. The next step of claim 1 recites, “generating, with the processor, a probability distribution of the likely dependency network structures for each condition.” This step describes the use of a generic computer to run a statistical/mathematical calculation. This step does not recite a practical application of the mathematical concept. The next step of claim 1 recites, “measuring, with the processor, a first Jensen-Shannon (JS) divergence to generate an overall differential Appeal 2019-003840 Application 14/078,994 16 dependency relationship between genes in the target gene set across the plurality of conditions.” This step describes the use of a generic computer to run a statistical/mathematical calculation. This step does not recite a practical application of the mathematical concept. The next step of claim 1 recites, “building, with the processor, a plurality of permuted data sets using randomly permuted conditions from the target gene set.” Mere “[data-gathering] step[s] cannot make an otherwise nonstatutory claim statutory.” In re Grams, 888 F.2d 835, 840 (Fed.Cir.1989) (quoting In re Meyer, 688 F.2d 789, 794 (CCPA 1982)). The next step of claim 1 recites, “measuring, with the processor, a second JS divergence to generate an overall differential dependency relationship for each permuted data set.” This step involves mathematical concepts and calculations. The next step of claim 1 recites, “comparing, with the processor, the first JS divergence to the second JS divergence.” This step involves mathematical calculations. The next step of claim 1 recites, “generating, with the processor, a statistical significance of the first JS divergence.” This step involves statistical analysis of data and mathematical calculations. The final steps of claim 1 recite, “identifying a plurality of biological functions and pathways that show genetic relationships across the plurality of conditions using the overall differential dependency relationships; and displaying one or more of the identified pathways using a network diagram, displaying the statistically significant gene sets using a chart, or both.” In re Abele, 684 F.2d 902, 908 (CCPA 1982), found that a claim to displaying data resulting from calculations was not directed to patent eligible subject Appeal 2019-003840 Application 14/078,994 17 matter. Here, as in Elec. Power Grp., LLC v. Alstom S.A, “the claims are clearly focused on the combination of those abstract-idea processes. The advance they purport to make is a process of gathering and analyzing information of a specified content, then displaying the results, and not any particular assertedly inventive technology for performing those functions. They are therefore directed to an abstract idea.”5 Essentially the claimed method, when read as a whole, runs complex mathematical calculations on a generic computer with a generic instruction to apply the calculation to a technological field. See MPEP § 2106.05(e). Appellant contends that the claimed method steps are too complicated for the human mind to decipher (App. Br. 15), and are directed to improvements in computer functionality. App. Br. 16. However, Appellant has not met the burden of demonstrating that the method “claims [were] truly drawn to [a] specific apparatus distinct from other apparatus[es] capable of performing the identical functions.” Cybersource Corp. v. Retail Decisions Inc., 654 F.3d 1366, 1374 (Fed. Cir. 2011). Nor has Appellant clearly shown that the claimed subject matter integrates into a practical application the abstract idea, mathematical concepts and calculations. While we acknowledge that the claimed method involves complex mathematical calculations, we note that “[g]roundbreaking, innovative, or even brilliant 5 Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1354 (Fed. Cir. 2016) in which the claims were focused on “gathering and analyzing information of a specified content, then displaying the results, and not any particular assertedly inventive technology for performing those functions” and Sap Am., Inc. v. InvestPic, LLC, 898 F.3d 1161, 1161 (Fed. Cir. 2018) where the claims also were founds to be directed to the analysis of information and display of the information. Appeal 2019-003840 Application 14/078,994 18 discovery does not by itself satisfy the § 101 inquiry.” Ass’n for Molecular Pathology v. Myriad Genetics, Inc., 569 U.S. 576, 591 (2013) (emphasis added). Alice/Mayo—Step 2 (Inventive Concept) Step 2B identified in the Revised Guidance Under the 2019 Revised Guidance, 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 adds a specific limitation beyond the judicial exception that is not “well-understood, routine, conventional” in the field (see MPEP § 2106.05(d)); or, simply appends well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception. See 2019 Revised Guidance, 84 Fed. Reg. at 56. Appellant contends that Claims 1, 9, and 10 recite a number of steps distinguishing EDDY[6]from prior art methods “GSEA” (Gene Set Enrichment Analysis) and “GSCA”(Gene Set Co-Expression Analysis). The prior art methods focus on differentially expressed gene (DEG), where each gene is assumed to have a unimodal distribution in each condition, and differential gene sets are defined according to the amount of DEGs. See, e.g., para. [0091]. The prior art methods compute differential gene expression in the target gene set and summarize the expression data into a single statistic that represents the differentiality of the gene set between conditions. See, e.g., para. [0005]. Because genes in biological pathways can maintain consistent interactions while providing various differing expression patterns, the previous 6 EDDY is a bioinformatics method of evaluating dependency differentiality. App. Br. 13. Appeal 2019-003840 Application 14/078,994 19 methods have inherent limitations in identifying gene sets with differential genetic interactions. Id. App. Br. 17. The Examiner finds that a 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 contain elements in addition to the judicial exception that either individually or as an ordered combination 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. Final Act. 4. As discussed above, the Appellant has not met the burden of showing that claimed bioinformatics method, which employs known mathematical formulas to the gene analysis field, provides significantly more than the judicial exception of the use of well known mathematical concepts. The mathematical concepts used in the claimed method are considered abstract ideas. Parker v. Flook, 437 U.S. 584, 594 (1978) (“[T]he discovery of [a mathematical formula] cannot support a patent unless there is some other inventive concept in its application.”) (See also mathematical concepts - Parker v. Flook, 437 U.S. 584, 594–95 (1978); Diamond v. Diehr, 450 U.S. 175, 191 (1981)). The patent ineligibility rejection under 35 USC §101 is affirmed. Appeal 2019-003840 Application 14/078,994 20 CONCLUSION OF LAW The cited references support the Examiner’s lack of patentable subject matter rejection is affirmed for the reasons of record. All pending, rejected claims fall. CONCLUSION In summary: Claims Rejected Basis Affirmed Reversed 1–5 and 8–22 § 101 1–5 and 8–22 Overall Outcome 1–5 and 8–22 No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a)(1)(iv). AFFIRMED Copy with citationCopy as parenthetical citation