Court Opinion

ID: 4671320
Source: CourtListenerOpinion
Date Created: 2021-03-25 15:00:56.997146+00
Date Added: 2024-06-11T08:02:31.658444
License: Public Domain

Case: 20-1288    Document: 46    Page: 1   Filed: 03/25/2021

   United States Court of Appeals
       for the Federal Circuit
                  ______________________

  IN RE: BOARD OF TRUSTEES OF THE LELAND
        STANFORD JUNIOR UNIVERSITY,
                    Appellant
             ______________________

                        2020-1288
                  ______________________

     Appeal from the United States Patent and Trademark
 Office, Patent Trial and Appeal Board in No. 13/486,982.
                   ______________________

                 Decided: March 25, 2021
                 ______________________

     JOEL KAUTH, KPPB LLP, Anaheim, CA, argued for ap-
 pellant. Also represented by DAVID BAILEY, CHRISTIAN
 HANS, MARK YEH.

    MAUREEN DONOVAN QUELER, Office of the Solicitor,
 United States Patent and Trademark Office, Alexandria,
 VA, argued for appellee Andrew Hirshfeld. Also repre-
 sented by THOMAS W. KRAUSE, FRANCES LYNCH, AMY J.
 NELSON.
                 ______________________

   Before PROST, Chief Judge, LOURIE and REYNA, Circuit
                         Judges.
 REYNA, Circuit Judge.
    The Board of Trustees of the Leland Stanford Junior
 University appeals the final rejection of patent claims in
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 2                              IN RE: THE BOARD OF TRUSTEES

 its patent application. The patent examiner reviewing the
 application rejected the claims on the grounds that they in-
 volve patent ineligible subject matter. On review, the Pa-
 tent Trial and Appeal Board affirmed the examiner’s final
 rejection of the claims. As discussed below, the rejected
 claims are drawn to abstract mathematical calculations
 and statistical modeling, and similar subject matter that is
 not patent eligible. Accordingly, we affirm the decision of
 the Patent Trial and Appeal Board.
                        BACKGROUND
      The Board of Trustees of the Leland Stanford Junior
 University (“Stanford”) filed its Application No. 13/486,982
 (“’982 application”) on June 1, 2012. J.A. 39. 1 The ’982
 application is directed to computerized statistical methods
 for determining haplotype phase. A haplotype phase acts
 as an indication of the parent from whom a gene has been
 inherited. Haplotype phasing is a process for determining
 the parent from whom alleles—i.e., versions of a gene—are
 inherited.
     The written description of the ’982 application explains
 that accurately estimating haplotype phase based on geno-
 type data obtained through sequencing an individual’s ge-
 nome “plays pivotal roles in population and medical genetic
 studies.” J.A. 85. The ’982 application is directed to meth-
 ods for inferring haplotype phase in a collection of unre-
 lated individuals. J.A. 65–69. According to the written

     1    The court notes that this case was consolidated for
 purposes of oral argument with In Re: The Board of Trus-
 tees of the Leland Stanford Junior University, Case No. 20-
 1012, in which we concluded that the claims in U.S. Patent
 Application No. 13/445,925 (“’925 application”) are drawn
 to patent ineligible subject matter. Both the ’925 applica-
 tion and the ’982 application involve statistical methods of
 predicting haplotype phase.
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 IN RE: THE BOARD OF TRUSTEES                               3

 description, although high-throughput DNA sequencing
 methods provide genotype data for individuals, those meth-
 ods do not provide haplotype information. J.A. 65–66.
 Though difficult, it is possible to infer haplotype phase,
 even without information about relatives, using statistics-
 based algorithms. J.A. 66. Prior art methods for perform-
 ing this analysis include PHASE, fastPHASE, and Beagle.
 J.A. 67–68, 81–82. These methods involve using, among
 other things, a hidden Markov model (“HMM”), which is a
 statistical tool used in various applications to make proba-
 bilistic determinations of latent variables. See, e.g.,
 J.A. 73, 82.
     The written description of the ’982 application discloses
 an embodiment in which a statistical model called PHASE-
 EM is used to predict haplotype phase. PHASE-EM is al-
 legedly a modified version of the preexisting PHASE model
 and operates more efficiently and accurately than the
 PHASE model. J.A. 68. Like prior art statistical models,
 including the fastPHASE model, PHASE-EM uses “a pa-
 rameterization [expectation maximization] algorithm” in
 predicting haplotype phase. J.A. 68–69. PHASE-EM “per-
 form[s] optimization on haplotypes rather than MCMC
 [Markov chain Monte Carlo] sampling,” which is used in
 PHASE. J.A. 68–69. According to the written description,
 the computational intensiveness of MCMC sampling
 makes it difficult to use PHASE to analyze large datasets
 like those generated in genome-wide association studies.
 J.A. 68.

     The written description further explains that PHASE-
 EM improves accuracy over existing methods by using a
 particular type of HMM to predict haplotype phase. See
 J.A. 82–84; id. at 50–51 (figures 5–6) (showing PHASE-
 EM’s allegedly reduced error rate). The HMM features
 variables including a hidden state sequence, an emitted se-
 quence, and jump variables. J.A. 75–76. Increased accu-
 racy is purportedly accomplished by using imputed
 haplotypes as the hidden states. J.A. 45, 68–69, 74–75, 77.
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 4                               IN RE: THE BOARD OF TRUSTEES

 According to the written description, “[t]his increase in ac-
 curacy becomes more pronounced with increasing sample
 size.” E.g., J.A. 69.

     The examiner issued a final rejection of claims 1 and
 22–43 of the ’982 application on grounds that the claims
 cover patent ineligible abstract mathematical algorithms
 and mental processes. See J.A. 10–12. The Patent Trial
 and Appeal Board (“Board”) affirmed the final rejection of
 the claims. Claim 1 is representative and recites:

     1. A computerized method for inferring haplotype
     phase in a collection of unrelated individuals, com-
     prising:
     receiving genotype data describing human geno-
     types for a plurality of individuals and storing the
     genotype data on a memory of a computer system;
     imputing an initial haplotype phase for each indi-
     vidual in the plurality of individuals based on a sta-
     tistical model and storing the initial haplotype
     phase for each individual in the plurality of indi-
     viduals on a computer system comprising a proces-
     sor a memory [sic];
     building a data structure describing a Hidden Mar-
     kov Model, where the data structure contains:
         a set of imputed haplotype phases compris-
         ing the imputed initial haplotype phases
         for each individual in the plurality of indi-
         viduals;
         a set of parameters comprising local recom-
         bination rates and mutation rates;
     wherein any change to the set of imputed haplotype
     phases contained within the data structure auto-
     matically results in re-computation of the set of pa-
     rameters comprising local recombination rates and
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 IN RE: THE BOARD OF TRUSTEES                              5

     mutation rates contained within the data struc-
     ture;
     repeatedly randomly modifying at least one of the
     imputed initial haplotype phases in the set of im-
     puted haplotype phases to automatically re-com-
     pute a new set of parameters comprising local
     recombination rates and mutation rates that are
     stored within the data structure;
     automatically replacing an imputed haplotype
     phase for an individual with a randomly modified
     haplotype phase within the data structure, when
     the new set of parameters indicate that the ran-
     domly modified haplotype phase is more likely than
     an existing imputed haplotype phase;
     extracting at least one final predicted haplotype
     phase from the data structure as a phased haplo-
     type for an individual; and
     storing the at least one final predicted haplotype
     phase for the individual on a memory of a computer
     system.
 J.A. 30. 2

     2   The only other independent claim is claim 32,
 which contains essentially the same limitations as those in
 claim 1, except that claim 32 sets forth the “conditional
 probabilities” defining the HHM. See J.A. 33–34. Claims
 22–24 and 26–31, which depend from claim 1, recite the
 same limitations as corresponding claims 33–35, 37–41,
 and 43. See J.A. 30–36. These limitations add or further
 define features of the claimed model. See id. The same is
 true for remaining claims 25, 36, and 42, although those
 dependent claims do not contain limitations corresponding
 to other dependent claim limitations. See id. at 31, 35, 36.
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 6                              IN RE: THE BOARD OF TRUSTEES

     In its analysis of the examiner’s rejections, the Board
 applied the two-step framework established by the Su-
 preme Court for determining patent eligibility. See Alice
 Corp. Pty. Ltd. v. CLS Bank Int’l, 573 U.S. 208 (2014);
 J.A. 9–20. Addressing step one of the Alice inquiry, the
 Board determined that representative claim 1 is directed
 to patent ineligible abstract ideas in the form of mathemat-
 ical concepts, i.e., mathematical relationship, formulas,
 equations, and calculations. J.A. 10–11. Specifically, the
 Board explained, claim 1 recites an initial step of receiving
 genotype data, followed by the mathematical operations of
 building a data structure describing an HMM and ran-
 domly modifying at least one imputed haplotype to auto-
 matically recompute the HMM’s parameters. Id.
     The Board also determined that claim 1 recites two ab-
 stract mental processes. J.A. 11. First, claim 1 recites the
 step of “imputing an initial haplotype phase for each indi-
 vidual in the plurality of individuals based on a statistical
 model,” which, according to the Board, does not require a
 computer implementation. See id. Second, claim 1 recites
 the step of automatically replacing an imputed haplotype
 phase with a randomly modified haplotype phase when the
 latter is more likely correct than the former. See J.A. 11–
 12. The Board thus concluded that claim 1 recites abstract
 ideas.
     The Board noted that the additional elements in claim
 1 recited generic steps of receiving and storing genotype
 data in a computer memory, extracting the predicted hap-
 lotype phase from the data structure, and storing it in a
 computer memory. J.A. 12–13. Stanford argued that, here
 as in Enfish, the application of the steps in claim 1 results
 in improved computer functionality. Enfish, LLC v. Mi-
 crosoft Corp., 822 F.3d 1327 (Fed. Cir. 2016). The Board
 determined that the evidence does not support that argu-
 ment. J.A. 13. The Board explained that Stanford failed
 to identify any specific disclosures in the specification
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 IN RE: THE BOARD OF TRUSTEES                               7

 asserting that claim 1 results in improved computer func-
 tionality. J.A. 12.
      The Board also rejected Stanford’s argument that
 claim 1 is patent eligible under McRO, Inc. v. Bandai
 Namco Games America Inc., 837 F.3d 1299, 1315 (Fed. Cir.
 2016). See J.A. 13. Stanford argued that haplotype phas-
 ing is a computer implemented field, and that under
 McRO, “improvements to computer implemented fields are
 considered technological improvements.” J.A. 14. The
 Board distinguished McRO on the basis that the claimed
 process there used “a combined order of specific rules that
 renders information into a specific format that is then used
 and applied to create desired results: a sequence of syn-
 chronized, animated characters.” J.A. 14 (quoting McRO,
 837 F.3d at 1315). The Board noted that claim 1 merely
 recites a series of computations to produce mathematically
 predicted haplotype information but does not include steps
 that apply that information in a practical way. See J.A. 14.
 The Board further acknowledged that claim 1 “may be use-
 ful in medical or population genetics studies,” but nonethe-
 less claim 1 is devoid of any specific step that applies the
 information in a useful way, such that the claimed calcula-
 tions are “integrated” into a practical application. J.A. 15.
 The Board concluded that claim 1 is directed to an abstract
 idea that is patent ineligible subject matter under § 101.
 See 35 U.S.C. § 101; Alice, 573 U.S. at 217–18; J.A. 10, 16.
     Turning to step two of the Alice inquiry, the Board re-
 viewed whether claim 1 included additional limitations
 that, when taken individually or in combination, provided
 an inventive concept that transformed the abstract idea
 into patent eligible subject matter. The Board determined
 that the claim 1 steps of receiving, storing, and extracting
 data were well-known, routine, and conventional. See
 J.A. 17–19. The Board rejected Stanford’s argument that
 specific computational steps themselves establish patent
 eligibility. J.A. 18. The Board explained that, although the
 abstract computational steps “might be a highly significant
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 8                               IN RE: THE BOARD OF TRUSTEES

 discovery in the field of haplotype prediction,” that alone is
 insufficient to establish patent eligibility. J.A. 18. The
 Board rejected Stanford’s argument that claim 1 does not
 unduly preempt use of an HMM, noting that “the absence
 of complete preemption does not demonstrate patent eligi-
 bility.” J.A. 20 (citing Ariosa Diagnostics, Inc. v. Se-
 quenom, Inc., 788 F.3d 1371, 1379 (Fed. Cir. 2015)). The
 Board affirmed the examiner’s rejection of claims 1 and 22–
 43 under § 101. Stanford appeals. We have jurisdiction
 pursuant to 35 U.S.C. § 141(a) and 28 U.S.C.
 § 1295(a)(4)(A).
                    STANDARD OF REVIEW
      We review Board decisions in accordance with the Ad-
 ministrative Procedure Act (“APA”). 5 U.S.C. § 706(2);
 Dickinson v. Zurko, 527 U.S. 150, 152 (1999). Under the
 APA, we review the Board’s legal conclusions de novo and
 its factual findings for substantial evidence. ACCO Brands
 Corp. v. Fellowes, Inc., 813 F.3d 1361, 1365 (Fed. Cir.
 2016). Substantial evidence is “such relevant evidence as
 a reasonable mind might accept as adequate to support a
 conclusion.” In re Gartside, 203 F.3d 1305, 1312 (Fed. Cir.
 2000) (quoting Consol. Edison Co. v. NLRB, 305 U.S. 197,
 229 (1938)).
                         DISCUSSION
     The Supreme Court has articulated a two-step analysis
 to determine patent eligibility under 35 U.S.C. § 101. Alice,
 573 U.S. at 217–18. In the first step, we examine whether
 a claim is directed to patent ineligible subject matter, such
 as an abstract idea. Id. If so, we turn to the second step
 and examine whether the claims contain an inventive con-
 cept sufficient to transform the abstract idea into patent
 eligible subject matter. Id. at 221. In this second step we
 consider the claim elements individually and as an ordered
 combination to determine whether any additional limita-
 tions amount to significantly more than the ineligible con-
 cept. Id. at 217–18, 221. A patent eligible claim must do
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 IN RE: THE BOARD OF TRUSTEES                                9

 more than simply recite the abstract idea “while adding the
 words ‘apply it.’” Id. at 221.
     We conclude, at Alice step one, that the reviewed
 claims of the ’982 application are directed to patent ineligi-
 ble abstract ideas. Specifically, the claims are directed to
 the use of mathematical calculations and statistical model-
 ing. Courts have long held that mathematical algorithms
 for performing calculations, without more, are patent inel-
 igible under § 101. See, e.g., Parker v. Flook, 437 U.S. 584,
 595 (1978) (“[I]f 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
 nonstatutory.” (internal citation omitted)); Gottschalk v.
 Benson, 409 U.S. 63, 71–72 (1972) (finding claims patent
 ineligible because they “would wholly pre-empt the mathe-
 matical formula and in practical effect would be a patent
 on the algorithm itself”); In re Schrader, 22 F.3d 290, 294
 (Fed. Cir. 1994) (a data gathering step of entering bids was
 “insufficient to impart patentability to a claim involving
 the solving of a mathematical algorithm”).
     Claim 1 is drawn to a “computerized method of infer-
 ring haplotype phase in a collection of unrelated individu-
 als.” J.A. 30. The mathematical techniques used in the
 method include “building a data structure describing an
 [HMM],” and then “repeatedly randomly modifying at least
 one of the imputed initial haplotype phases” to automati-
 cally recompute the parameters of the HMM until the pa-
 rameters indicate that the most likely haplotype phase is
 found. See J.A. 30. In addition to these mathematical
 steps, claim 1 recites steps of receiving genotype data, im-
 puting an initial haplotype phase, extracting the final pre-
 dicted haplotype phase from the data structure, and
 storing it in a computer memory. See id. These generic
 steps of implementing and processing calculations with a
 regular computer do not change the character of claim 1
 from an abstract idea into a practical application. Claim 1
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 10                              IN RE: THE BOARD OF TRUSTEES

 recites no application, concrete or otherwise, beyond stor-
 ing the haplotype phase.
     We have also examined, at Alice step one, whether the
 claimed advance alleged in the written description demon-
 strates an improvement of a technological process or
 merely enhances an ineligible concept. See, e.g., Athena
 Diagnostics, Inc. v. Mayo Collaborative Servs., LLC,
 915 F.3d 743, 750 (Fed. Cir. 2019). Stanford suggests that
 one claimed advance is greater efficiency in computing hap-
 lotype phase. See, e.g., Appellant’s Br. 10, 27–28, 46–47.
 But Stanford has forfeited its argument that greater com-
 putational efficiency renders claim 1 patent eligible by fail-
 ing to raise it before the Board. As a result, we will not
 consider it for the first time on appeal. In re Watts,
 354 F.3d 1362, 1367 (Fed. Cir. 2004).
     Stanford separately suggests that another claimed ad-
 vance is that the claim steps result in more accurate hap-
 lotype predictions. See, e.g., Appellant’s Br. 21–22, 29–34,
 43, 46. Specifically, Stanford argues that the alleged in-
 crease in haplotype prediction accuracy renders claim 1 a
 practical application rather than an abstract idea. See id.
 at 30. Stanford’s cited cases do not support its argument
 because the cases involve practical, technological improve-
 ments extending beyond improving the accuracy of a math-
 ematically calculated statistical prediction. See, e.g.,
 McRO, 837 F.3d at 1315 (“The claimed process uses a com-
 bined order of specific rules that renders information into
 a specific format that is then used and applied to create
 desired results: a sequence of synchronized, animated
 characters.”); Finjan, Inc. v. Blue Coat Sys., Inc., 879
 F.3d 1299, 1304 (Fed. Cir. 2018) (finding patent eligible a
 claim drawn to a behavior-based virus scan that protects
 against viruses that have been “cosmetically modified to
 avoid detection by code-matching virus scans”); Enfish,
 822 F.3d at 1330, 1333 (discussing patent eligible claims
 directed to “an innovative logical model for a computer da-
 tabase” that included a self-referential table allowing for
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 IN RE: THE BOARD OF TRUSTEES                                11

 greater flexibility in configuring databases, faster search-
 ing, and more effective storage); CardioNet, LLC v. InfoBi-
 onic, Inc., 955 F.3d 1358, 1368 (Fed. Cir. 2020) (explaining
 that the claims at issue focus on a specific means for im-
 proving cardiac monitoring technology; they are not “di-
 rected to a result or effect that itself is the abstract idea
 and merely invoke generic processes and machinery” (quot-
 ing McRO, 837 F.3d at 1314)). Unlike the technological im-
 provements made in those cases, the improvement in
 computational accuracy alleged here does not qualify as an
 improvement to a technological process; rather, it is merely
 an enhancement to the abstract mathematical calculation
 of haplotype phase itself. See Athena, 915 F.3d at 750; Syn-
 opsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 1151
 (Fed. Cir. 2016) (“[A] claim for a new abstract idea is still
 an abstract idea.”). The different use of a mathematical
 calculation, even one that yields different or better results,
 does not render patent eligible subject matter. Because we
 conclude that claim 1 is directed to patent ineligible subject
 matter, we next turn to step two of the Alice inquiry.
     At step two, we inquire whether any limitations estab-
 lish an inventive concept that transforms the abstract idea
 into patent eligible subject matter. Alice, 573 U.S. at 217–
 18. Step two is like a lifeline: it can rescue and save a claim
 that has been deemed, at step one, directed to non-statu-
 tory subject matter.
     We conclude that claim 1 is not saved. We find no in-
 ventive concept that would warrant treating the use of the
 claimed algorithms and mathematical calculations as pa-
 tent eligible subject matter. Further, the recited steps of
 receiving, extracting, and storing data amount to well-
 known, routine, and conventional steps taken when execut-
 ing a mathematical algorithm on a regular computer. Us-
 ing a conventional computer to receive, extract, and store
 information does not transform an abstract idea into pa-
 tent eligible subject matter. See, e.g., In re Greenstein, 774
 F. App’x 661, 664 (Fed. Cir. 2019) (explaining that the
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 12                             IN RE: THE BOARD OF TRUSTEES

 claims only invoke a computer as a generic tool to store in-
 formation and record transactions). The written descrip-
 tion further illustrates that the mathematical steps
 performed and the data received are conventional and well
 understood in the prior art. See, e.g., J.A. 65–69, 74–77,
 81–84.
     Nor does claim 1 require or result in a specialized com-
 puter or a computer with a specialized memory or proces-
 sor. Indeed, it is hard to imagine a patent claim that
 recites hardware limitations in more generic terms than
 the terms employed by claim 1. See J.A. 30 (reciting
 method steps carried out by a “computer system” with a
 “processor” and a “memory”); see also Alice, 573 U.S. at 226
 (explaining that the hardware-related terms, “data pro-
 cessing system,” “communications controller” and “data
 storage unit” are “purely functional and generic”); In re TLI
 Commc’ns LLC Pat. Litig., 823 F.3d 607, 614 (Fed. Cir.
 2016) (holding generic computer components insufficient to
 add an inventive concept to an otherwise abstract idea).
      Stanford argues the Board erred by failing to consider
 all the elements of claim 1 as an ordered combination. See,
 e.g., Appellant’s Br. 41–44. Specifically, Stanford argues
 that the Board “oversimplif[ied]” claim 1 by characterizing
 it as “directed to a process of using abstract computation
 methods to obtain a specific type of information” and then
 “effectively subsumed” all the steps into that purportedly
 overgeneralized judicial exception. Id. at 41. According to
 Stanford, it is the specific combination of steps recited in
 claim 1 “that makes the process novel” and “that provides
 the increased accuracy over other methods.” Id. at 43. We
 are not persuaded. The Board correctly determined that
 claim 1 simply appends the abstract calculations to the
 well-understood, routine, and conventional steps of receiv-
 ing and storing data in a computer memory and extracting
 a predicted haplotype. The application of those elements
 results in the mathematical analysis itself, and therefore
 the claimed method subsists in “the basic tools of scientific
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 IN RE: THE BOARD OF TRUSTEES                               13

 and technological work.” See Alice, 573 U.S. at 216. Such
 basic tools are not patent eligible. Nor is novelty the touch-
 stone of patent eligibility. That a specific or different com-
 bination of mathematical steps yields more accurate
 haplotype predictions than previously achievable under
 the prior art is not enough to transform the abstract idea
 in claim 1 into a patent eligible application. See SAP Am.,
 Inc. v. InvestPic, LLC, 898 F.3d 1161, 1170 (Fed. Cir. 2018)
 (holding that an advance in financial mathematical tech-
 niques does not constitute an inventive concept).
     The remaining claims contain no limitations, consid-
 ered individually or as an ordered combination, that trans-
 form the abstract idea into a patent eligible application.
 Instead, claims 22–43 only further define the mathemati-
 cal calculations recited in claim 1, which we have held ab-
 stract.
                         CONCLUSION
     We have considered Stanford’s remaining arguments
 and find them unpersuasive. For the above reasons, the
 Board’s conclusion that claims 1 and 22–43 are drawn to
 patent ineligible subject matter under § 101 is affirmed.
                         AFFIRMED