Vinay Varadan et al.Download PDFPatent Trials and Appeals BoardMar 11, 20212020001633 (P.T.A.B. Mar. 11, 2021) 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. 13/983,651 10/09/2013 Vinay Varadan 2011P00166WOUS 3445 24737 7590 03/11/2021 PHILIPS INTELLECTUAL PROPERTY & STANDARDS 465 Columbus Avenue Suite 340 Valhalla, NY 10595 EXAMINER DEJONG, ERIC S ART UNIT PAPER NUMBER 1631 NOTIFICATION DATE DELIVERY MODE 03/11/2021 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): katelyn.mulroy@philips.com marianne.fox@philips.com patti.demichele@Philips.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte VINAY VARADAN, PRATEEK MITTAL, SITHARTHAN KAMALAKARAN, NEVENKA DIMITROVA, ANGEL JANEVSKI, and NILANJANA BANERJEE Appeal 2020-001633 Application 13/983,651 Technology Center 1600 Before RICHARD M. LEBOVITZ, TAWEN CHANG, and MICHAEL A. VALEK, Administrative Patent Judges. CHANG, 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, 2, 4–12, and 15–21. 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 did not identify a real party in interest in the Appeal Brief. Appeal 2020-001633 Application 13/983,651 2 STATEMENT OF THE CASE The Specification states: Several diseases, in particular cancerous diseases, are complex and involve the alteration of multiple gene functions or underlying cellular processes. These diseases constitute severe challenges to clinicians, who struggle for reliable stratification approaches with high sensitivity and specificity. One possibility of improving the stratification process is based on the use of molecular profiles, which are known to correspond to different clinically relevant groups. These profiles are often used for high throughput analyses through the statistical selection of a set of features, which jointly differentiates between clinically relevant classes of patients. . . . . However, the molecular signatures discovered so far typically do not capture the underlying cellular mechanisms and the high throughput and pathway- recognition approaches do not sufficiently capture how genes or proteins interact inside the cell and are therefore limited in their ability to reliably stratify patients. There is, thus, a need for improved diagnostic tools enabling the clinician to use high-throughput data to stratify patients, in particular cancer patients. Spec. 1:24–2:5. Accordingly to the Specification, “[t]he present invention addresses this need and provides means and methods, which implement an enhanced recognition of cellular interactions, and thus allow an improved stratification of patients into clinically relevant groups.” Spec. 2:8–10. Appeal 2020-001633 Application 13/983,651 3 CLAIMED SUBJECT MATTER The claims are directed to a method for assignment of a cancer patient into a clinically relevant group of cancer patients. Claim 1, the only independent claim, is illustrative: 1. A computer-implemented method for flow vector-based assignment of a cancer patient into a clinically relevant group of cancer patients, said computer-implemented method comprising: [(a)] obtaining cancer molecular profiling data from a patient sample of the cancer patient; [(b)] inputting said cancer molecular profiling data onto a processor configured to receive such cancer molecular profiling data; [(c)] obtaining a dataset, for an individual cancer patient, comprising molecular data of expression of one or more of said cancer patient’s genes; [(d)] inputting said patient molecular data onto said processor; [(e)] providing a database of cancer molecular data of known phenotypes; [(f)] applying, by said processor, a statistical analysis to identify a probability of there being altered molecular data within the patient molecular data in comparison to the database of cancer molecular data of known phenotypes, wherein the probability is identified by integrating said altered molecular data using a probabilistic graphical model framework; [(g)] identifying, by said processor, a biological network by calculating activity of said biological network based upon the identified probability; [(h)] identifying, by said processor, a network information flow probability, for said cancer patient by applying statistical techniques to determine a probability of interactions in said biological network based on said probability of altered molecular data; [(i)] applying, by said processor, a statistical analysis to create multiple instances of network information flow vectors Appeal 2020-001633 Application 13/983,651 4 for said cancer patient from a full interaction probability distribution of the biological network; [(j)] calculating, by said processor, a distance of said cancer patient from other cancer patients using said multiple instances of network information flow vectors; [(k)] assigning, by said processor, said cancer patient to the clinically relevant group based on the calculated distance of said cancer patient from the other cancer patients; and [(l)] providing a visualization of the assignment of the cancer patient to the clinically relevant group in the context of the network information flow vectors. Appeal Br. 16–17 (Claims App.) (bracketed alphabetical notations added). REJECTION(S) A. Claims 1, 2, 4–12, and 15–21 are rejected under 35 U.S.C. § 101 as being directed to a judicial exception to patent-eligibility (i.e., a law of nature, a natural phenomenon, or an abstract idea), without significantly more. Ans. 3. B. Claims 1, 2, 4–12, and 15–21 are rejected under 35 U.S.C. § 112 (Pre- AIA), first paragraph, as failing to comply with the written description requirement. Ans. 5. C. Claims 1, 2, 4–12, and 15–21 are rejected under 35 U.S.C. § 112 (Pre- AIA), second paragraph, as being infinite.2 Ans. 7. 2 We note that the Examiner did not list claims 16–21 in the indefiniteness rejection in the Final Rejection or Answer. Final Act. 6; Ans. 7. However, Appellant states in the Appeal Brief that “[o]n page 6-8, the [Final] Office Action rejected all pending claims under 35 U.S.C. § 112 as allegedly indefinite.” Appeal Br. 14. Moreover, each of claims 16–21 depends, Appeal 2020-001633 Application 13/983,651 5 OPINION A. Patent-Ineligible Subject Matter (claims 1, 2, 4–12, and 15–21) 1. Issue The Examiner concludes that [t]he instant claims are directed to a method and related computer system for stratifying a patient into a clinically relevant group. The recited process comprises the steps of obtaining data and analyzing said data. While for a specific purpose, the claims only delineate what patient information is to be gathered and what information is to be distilled therefrom. All recited steps in the instant claims (obtaining information, identifying, inferring, identifying, creating multiple instances of information flow, calculating, and assigning) are abstract steps carried out by employing a configured processor. Ans. 3–4. The Examiner notes that courts have found such a process, which “employs mathematical algorithms to manipulate existing information to generate additional information,” to be patent-ineligible. Id. at 4 (quoting Digitech Image Techs., LLC v. Elecs. for Imaging Inc., 758 F.3d 1344, 1351 (Fed. Cir. 2014)). The Examiner further finds that “the claims . . . rely on the use of generic computer serving as conventional computational vehicle on which to apply the recited data analysis procedure.” Ans. 4. The Examiner finds that, accordingly, the claims “fail to amount to something significantly more than a recitation of generic computer components and implementation as the vehicle to simply ‘apply’ the abstract ideas and functionally defined directly or indirectly, from claim 1, which is the subject of an indefiniteness rejection. Thus, we understand that the indefiniteness rejection encompasses claims 16–21 as well. Appeal 2020-001633 Application 13/983,651 6 computer operations as set forth in the instant claims.” Id. With specific reference to claim 17, the Examiner finds that, although the claim recites certain physical steps of data collection, these steps do not “improve[] or alter[] . . .data collection procedures that are . . . routine and conventional in the art” and thus “do not . . . present something significantly more than the judicial exception[s]” recited in the claim. Id. at 4–5. Appellant contends that the Examiner failed to follow the PTO’s 2019 Revised Patent Subject Matter Eligibility Guidance (“Revised Guidance”). Appeal Br. 4–6. Appellant does not separately argue the claims. We thus focus our analysis on claim 1 as representative. The issue with respect to this rejection is whether a preponderance of evidence of record supports the Examiner’s determination that claim 1 is directed to a judicial exception to patent- eligible subject matter, without significantly more. 2. Analysis We analyze this case under the framework set forth by the Supreme Court in Mayo Collaborative Services v. Prometheus Laboratories, Inc., 566 U.S. 66 (2012), and applied by our reviewing court in Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371 (Fed. Cir. 2015). As the Ariosa court explained: In Mayo . . . , the Supreme Court set forth a framework for distinguishing patents that claim laws of nature, natural phenomena, and abstract ideas from those that claim patent-eligible applications of those concepts. First, we determine whether the claims at issue are directed to a patent-ineligible concept. . . . If the answer is yes, then we next consider the elements of each claim Appeal 2020-001633 Application 13/983,651 7 both individually and “as an ordered combination” to determine whether additional elements “transform the nature of the claim” into a patent-eligible application. . . . The Supreme Court has described the second step of this analysis as a search for an “inventive concept”—i.e., an element or combination of 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 1375. Step 2A of the Revised Guidance: Whether Claim 1 Is Directed to Patent-Ineligible Concept We begin with the first step of the Mayo test, namely whether a claim is “directed to” a patent-ineligible concept. On January 7, 2019, the Director of the USPTO issued the “2019 Revised Patent Subject Matter Eligibility Guidance” (“Revised Guidance”), which provides further details regarding how the Patent Office analyzes patent-eligibility questions under 35 U.S.C. § 101. 84 Fed. Reg. 50–57 (Jan. 7, 2019). Under the Revised Guidance, the first step of the Mayo test (i.e., Step 2A of the Revised Guidance) is “a two- prong inquiry.” Id. at 54. In prong one, we evaluate whether the claim recites a judicial exception, such as laws of nature, natural phenomena, or abstract ideas. Id. The Revised Guidance explains that the abstract idea exception includes the following groupings of subject matter, when recited as such in a claim limitation(s) (that is, when recited on their own or per se): (a) Mathematical concepts—mathematical relationships, mathematical formulas or equations, mathematical calculations; (b) Certain methods of organizing human activity— fundamental economic principles or practices (including hedging, insurance, mitigating risk); commercial or legal Appeal 2020-001633 Application 13/983,651 8 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); and (c) Mental processes—concepts performed in the human mind (including an observation, evaluation, judgment, opinion). Id. at 52 (footnotes omitted). The Guidance states that, except in rare circumstances, “[c]laims that do not recite matter that falls within these enumerated groupings of abstract ideas should not be treated as reciting abstract ideas” and thus would be patent-eligible. Id. at 53. If the claim recites a judicial exception, the claim is further analyzed under prong two, which requires “evaluat[ion of] whether the claim recites additional elements that integrate the exception into a practical application of that exception.” Id. The Revised Guidance explains that, “[i]f the recited exception is integrated into a practical application of the exception, then the claim is eligible at Prong Two of . . . Step 2A [of the Revised Guidance].” Id. Prong One of Step 2A of Revised Guidance With respect to the first prong of Step 2A of the Revised Guidance, we agree with the Examiner that claim 1 recites patent-ineligible subject matter. In particular, mathematical concepts are abstract, 84 Fed. Reg. at 52, and steps (f)–(j) of claim 1 recite such mathematical concepts. For instance, step (f) recites “applying . . . a statistical analysis to identify a probability . . . by . . . using a probabilistic graphical model framework”; step (h) recites “identifying . . . a network information flow probability . . . by applying statistical techniques to determine a probability of interactions in said . . . Appeal 2020-001633 Application 13/983,651 9 network”; step (i) recites “applying . . . a statistical analysis to create multiple instances of network information flow vectors . . . from a full interaction probability distribution of the . . . network”; and step (j) recites “calculating . . . a distance . . . using said multiple instances of network information flow vectors.” Appeal Br. 16–17 (Claims App.). Finally, step (g) recites “identifying . . . a biological network by calculating activity of said biological network based upon the identified probability” of there being altered molecular data.” Appeal Br. 16 (Claims App.). The Specification teaches that “the activity of a biological network may be inferred on the basis of the probability of an alteration within the one or more sets of molecular data.” Spec. 11:9–11. The Specification further states that “[t]he term ‘inferred’ as used herein relates to a suitable derivation or calculation activity resulting in the identification of biological networks” and further states that “suitable algorithms such as the junction tree inference algorithm, preferably with HUGIN updates, the Belief Propagation with sequential updates, or the expectation-maximization (EM) algorithm may be used.” Id. at 11:27–31. Our reviewing court has held that similar claims directed to methods for performing certain statistical analyses are patent-ineligible because “[t]heir subject is nothing but a series of mathematical calculations based on selected information and the presentation of the results of those calculations (in the plot of a probability distribution function).” SAP Am., Inc. v. InvestPic, LLC, 898 F.3d 1161, 1163 (Fed. Cir. 2018). In that case, the selected information was investment information, id., while in the instant appeal the information analyzed is molecular data. Nevertheless, the same rationale articulated in SAP applies here. As the SAP court noted, Appeal 2020-001633 Application 13/983,651 10 “limitation of the claims to a particular field of information . . . does not move the claims out of the realm of abstract ideas.” Id. at 1169. Likewise, mental processes such as observation, evaluation, judgment, and opinion are abstract ideas. 84 Fed. Reg. at 52. “[I]dentifying . . . a biological network” based on network activity, as recited in the first part of step (g), falls within this category of abstract idea. Similarly, claim 1 recites “assigning . . . cancer patient to the clinically relevant group based on the calculated distance of said cancer patient from the other cancer patients” (step (k)). Although the calculation of the distance of a cancer patient from other cancer patients using multiple instances of network information flow vectors (i.e., step (j)) may not be practically performed in the mind, the assignment in step (k) of a patient to a group based on the calculated distance is a step involving observation, evaluation and/or judgment that could be “performed in the human mind[] or by a human using a pen and paper.” CyberSource Corp. v. Retail Decisions, Inc., 654 F.3d 1366, 1372 (Fed. Cir. 2011). Thus, claim 1 also recites mental processes. Prong Two of Step 2A of Revised Guidance With respect to the second prong of Step 2A of the Revised Guidance, we find that claim 1 does not recite sufficient additional elements that integrate the recited judicial exception(s) into a practical application of the exception(s). 84 Fed. Reg. at 54. More specifically, the additional elements of claim 1 that are not either mathematical concepts or mental processes include (1) “obtaining cancer molecular profiling data from a patient sample” (step (a)); (2) “inputting said . . . data” (step (b)); (3) “obtaining a dataset . . . comprising molecular data of expression of one or more of said Appeal 2020-001633 Application 13/983,651 11 cancer patient’s genes” (step (c)); (4) “inputting said patient molecular data” (step (d)); (5) “providing . . . cancer molecular data of known phenotypes” (step (e)); and (6) “providing a visualization of the assignment of the cancer patient to the clinically relevant group in the context of the network information flow vectors” (step (l)). Appeal Br. 16–17 (Claims App.). Certain steps of claim 1 (see, e.g., steps (b), (d), and (f)–(k)) also recite a “processor,” and step (e) recites a “database” (i.e., a “database of cancer molecular data of known phenotypes”). Id. These additional elements, individually and in combination, do not suffice to integrate the recited judicial exceptions into a practical application. More specifically, steps (a)–(e) merely gather the data to be used in the claimed method, and step (l) presents a result based on the recited abstract mental processes and mathematical calculations. Thus, they are “insignificant extra-solution activity.” 84 Fed. Reg. at 55 (explaining that an additional element that adds insignificant extra-solution activity to the judicial exception does not integrate the exception into a practical application); see also In re Meyer, 688 F.2d 789, 794 (CCPA 1982) (a claimed step that “test[s] for a response . . . is nothing more than a data gathering step,” which “cannot make an otherwise nonstatutory claim statutory”); In re Richman, 563 F.2d 1026, 1030 (CCPA 1977) (holding that antecedent steps that “merely determine values for the variables used in the mathematical formulae used in making the calculations . . . do not suffice to render the claimed methods, considered as a whole, statutory subject matter”); Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d at 1350, 1353– 1354 (Fed. Cir. 2016) (holding that claims involving “merely presenting the results of abstract processes of collecting and analyzing information, without Appeal 2020-001633 Application 13/983,651 12 more . . . , is abstract as an ancillary part of such collection and analysis”). Similarly, the recitation of a “database” and “processor” in claim 1 merely recites using these computer elements “as a tool to perform an abstract idea,” which does not integrate a judicial exception into a practical application. 84 Fed. Reg. at 55. Step 2B of the Revised Guidance: Whether Claim 1 Amounts to “Significantly More” Having determined that claim 1 is directed to a patent-ineligible abstract idea, we next consider whether claim 1 recites “an element or combination of elements that is ‘sufficient to ensure that the patent in practice amounts to significantly more than a patent upon the [ineligible concept] itself.’” Ariosa, 788 F.3d at 1375 (citation omitted). We agree with the Examiner that it does not. As discussed above, the additional elements in claim 1 that are not either mental processes or mathematical concepts include (1) “obtaining cancer molecular profiling data from a patient sample” (step (a)); (2) “inputting said . . . data” (step (b)); (3) “obtaining a dataset . . . comprising molecular data of expression of one or more of said cancer patient’s genes” (step (c)); (4) “inputting said patient molecular data” (step (d)); (5) “providing a database of cancer molecular data of known phenotypes” (step (e)); (6) “providing a visualization of the assignment of the cancer patient to the clinically relevant group in the context of the network information flow vectors” (step (l)); and (7) a processor that receives a patient’s “cancer molecular profiling data” and “molecular data comprising molecular data of expression of one or more . . . genes” (steps (b) and (d)) and further Appeal 2020-001633 Application 13/983,651 13 performs various mathematical/statistical analysis (steps (f)–(k)). Appeal Br. 16–17 (Claims App.). These limitations, however, are recited at a high level of generality and/or are described in the Specification as well known, routine, and conventional. For example, as for obtaining and inputting a cancer patient’s molecular profiling data or data set comprising molecular data of expression of one or more of said cancer patient’s genes (steps (a)–(d)), the Specification states that “‘molecular data’ as used herein refers to data on a genetic, medical, biochemical, chemical, biological or physical condition or modality linked to a subject” and include, e.g., presence or absence or amount/level of transcripts “as well as further conditions or modalities known to the person skilled in the art.” Spec. 9:17–32 (emphasis added). The Specification states that “molecular data may be obtained by any suitable technique, method or approach known to the person skilled in the art.” Id. at 20:5–6 (emphasis added). In the same vein, the Specification states that “‘datasets comprising one or more sets of molecular data’” may be provided “in any suitable form known to the person skilled in the art, e.g. in suitable input formats for bioinformatic applications.” Id. at 9:33–10:10 (emphasis added). The Specification further states, in the context of stratifying cancerous disease, that “molecular profiles . . . are known to correspond to different clinically relevant groups” and “are often used for high throughput analyses through the statistical selection of a set of features.” Spec. 1:24–31. Likewise, the limitations relating to a database (step (e)), to inputting data into a processor (steps (b) and (d)), and to using the processor to perform various statistical and/or mathematical calculations (steps (f)–(k)) Appeal 2020-001633 Application 13/983,651 14 merely recite a generic and/or already available computer component performing generic/already available computer functions, such as storing, receiving and/or analyzing data and performing mathematical calculations. For example, as a preferred embodiment, the Specification generically describes “a database of molecular data of known phenotypes” as “a biological annotation database, a pathway database, a database on biological processes and/or a database on biological functions” and refers to such known databases as “the National Cancer Institute Pathway interaction database, the KEGG pathway database, the BioCarta database, the Panther database, the Reactome database, and/or the DAVID database” as examples. Spec. 3:14–19. Similarly, the Specification generically describes a “clinical decision support system” for carrying out the disclosed method, Spec. 39:3– 12, and points to Philips’ iSite PACS systems as an example of such a clinical decision support system, id. at 40:22–29.3 3 The Specification does state that clinical decision support systems such as the Philips’ iSite PACS system may be “adjusted or modified” to “comply with the requirements of the methods of the present invention and/or in order to be able to carry out a computer program or algorithm as described herein, and/or in order to store expression or other molecular parameters or patient data or parts of patient databases as defined herein.” Spec. 40:25–29. However, as discussed above, the Specification teaches that the molecular data are provided in suitable formats known to a skilled artisan. Spec. 9:33– 10:10. Likewise, the Specification describes the various algorithms used in the method as generic statistical calculations and/or algorithms well known to the skilled artisan. See, e.g., Spec. 10:25–28 (probability of alteration in molecular data may be determined by algorithm known to skilled artisan); 24:32–34 (citing known probabilistic graphical model frameworks including Bayesian networks and Markov random fields); 11:27–34 (biological networks may be identified by algorithms known to skilled artisan); 12:4–7, 31–34 (network information flow probability and vector refer generically to, Appeal 2020-001633 Application 13/983,651 15 As our reviewing court has explained with respect to similar claims, where database and processor limitations “require no improved computer resources,” but rather rely on “already available computers, with their already available basic functions, to use as tools in executing the claimed process,” such limitations “are insufficient to pass the test of an inventive concept in the application of an abstract idea.” SAP, 898 F.3d at 1170. Put another way, “an invocation of already-available computers that are not themselves plausibly asserted to be an advance, for use in carrying out improved mathematical calculations, amounts to a recitation of what is ‘well-understood, routine, [and] conventional.’” Id. (quoting Mayo, 556 U.S. at 73). respectively, “information provided by interactions amongst genes or other factors captured in the identified network” and “vector of probabilities, where each probability is the likelihood that a particular interaction in the biological network was activated in the patient”); 13:17–20 (“sample states or sample state vectors may be generated from the probabilities in the network information flow vector” with algorithms known to skilled artisans, such as “Metropolis-Hastings sampling algorithm, Gibbs sampling, slice sampling, or any Monte Carlo sampling methods”); 15:24–30 (distance of patient from other subjects in patient database “refers to a mathematical or statistical distance between two or more instances of the network information flow” and “may be calculated with any suitable method, process or algorithm known to the person skilled in the art”). The Specification similarly states that “visualization [in the context of the information flow in the networks and other clinically relevant groups and healthy subjects] may be implemented with suitable algorithms known to the person skilled in the art.” Id. at 40:11–19. Thus, we find that the already available systems, such as Philips’ iSite PACS system, together with any needed adjustments or modifications, would nevertheless be well-known, routine, and/or conventional. Appeal 2020-001633 Application 13/983,651 16 Finally, considered as an ordered combination, the components of claim 1 add nothing that is not already present when they are considered separately. Viewed as a whole, claim 1 simply recites the abstract mathematical calculations and/or mental processes used to assign a cancer patient to a clinically relevant group, as performed by generic computer components and/or conventional, already available systems, obtaining the necessary data inputs for the algorithms, and displaying the results. In sum, the combination of elements recited in claim 1 does not amount to significantly more than the judicial exceptions themselves, and under 35 U.S.C. § 101 the claimed method is not eligible for patenting. Appellant’s Arguments Appellant contends that the Examiner’s § 101 rejection should be reversed because the Examiner failed to follow the steps set out in the Revised Guidance for supporting a § 101 rejection. Appeal Br. 4–9; Reply Br. 2–3. Appellant first argues that the Examiner “unreasonably broadened the scope of” and “‘abstracted’ . . . Appellant’s claim language”; “failed to identify the specific limitations in the claim . . . that . . . recites an abstract idea”; and “made no attempt to determine whether the claimed subject matter fell within the subject matter groupings of abstract ideas” set out in the Revised Guidance. Appeal Br. 5–6; Reply Br. 2. Appellant contends that the claims do not recite limitations falling within any of the groupings of abstract ideas – i.e., mathematical concepts, certain methods of organizing human activity, and mental processes – set forth in the Revised Guidance. Appeal Br. 6. Appeal 2020-001633 Application 13/983,651 17 We are not persuaded. The Examiner notes in the rejection that the claims recite steps of obtaining and analyzing data (e.g., “obtaining information, identifying, inferring, identifying, creating multiple instances of information flow, calculating, and assigning”) and more specifically notes that, with regard to such claims, the courts have been clear that “a process that employs mathematical algorithms to manipulate existing information to generate additional information is not patent eligible” without additional limitations. Ans. 3–4 (quoting Digitech Image Techs., LLC v. Elecs. for Imaging, Inc., 758 F.3d 1344, 1351 (Fed. Cir. 2014)). As noted above, mathematical concepts is one of the categories of abstract ideas enumerated in the Revised Guidance. 84 Fed. Reg. at 52. Likewise, for the reasons set forth above, we agree with the Examiner that claim 1 recites mathematical concepts, as well as mental processes. Appellant next contends that the Examiner failed to consider whether any abstract ideas recited in claim 1 has been integrated into a practical application, as required by prong two of Step 2A. Appeal Br. 7–8. Appellant contends that, even if the claims recite an abstract idea, such as mental processes, “the claimed processes include critical . . . physical steps that involve the use of non-abstract tangible components.” Id. at 6. In particular, citing Example 42 in the PTO’s 2019 Patent Eligibility Guidance Examples 37 Through 42 (issued Jan. 7, 2019) (“Guidance Examples”), Appellant contends that “the revised guidance emphasizes that the practical application of computer functions can qualify as patent-eligible subject matter.” Id. at 7. We are not persuaded. Appellant’s citation to Example 42 in the Guidance Examples, which relates to methods for transmission of Appeal 2020-001633 Application 13/983,651 18 notifications when medical records are updated, is inapposite. In the Guidance Examples, the PTO explained that claim 1 of Example 42 “as a whole recites a method of organizing human activity” — one of the enumerated categories of abstract ideas — because “a method that allows for users to access patient’s medical records and receive updated patient information in real time from other users . . . is a method of managing interactions between people.” Guidance Examples 18. Nevertheless, the PTO explains that the claim is patent-eligible because the additional elements in the claims — i.e., “storing information, providing remote access over a network, converting updated information that was input by a user in a non-standardized format to a standardized format, automatically generating a message whenever updated information is stored, and transmitting the message to all of the users” — “recite a specific improvement over prior art systems by allowing remote users to share information in real time in a standardized format regardless of the format in which the information was input by the user.” Id. at 18–19. In contrast, as discussed above, the elements of claim 1 that are not mathematical concepts or mental processes either (1) recite insignificant extra-solution activities because they merely gather the data to be used in the claimed method (steps (a)–(e)) or merely present a result based on the recited abstract mental processes and mathematical calculations (step (l)), or (2) use already available computer elements “as a tool to perform an abstract idea.” Thus, unlike in Example 42, these claim elements do not integrate the recited abstract ideas into a practical application by reciting a specific improvement over prior art. 84 Fed. Reg. at 55. Appeal 2020-001633 Application 13/983,651 19 Appellant contends that “[t]he recited subject matter is directed to a practical application of flow vector-based assignment, which is a format for sharing information, akin to Example 42,” and further argues that “[t]he claimed flow vector-based assignment, like Example 42, has the practical application of providing improved visualization in the context of information flow in the networks.” Appeal Br. 7–8; Reply Br. 2. We are not persuaded. The improvement in claim 1 of Example 42 lay in “allowing remote users to share information in real time in a standardized format regardless of the format in which the information was input by the user,” which was not possible in the prior art systems. Guidance Examples 17–19 (explaining that prior to the invention “medical providers must continually monitor a patient’s medical records for updated information” and that such information is “often-times incomplete since records in separate locations are not timely or readily-shared or cannot be consolidated due to format inconsistencies as well as physicians who are unaware that other physicians are also seeing the patient for varying reasons”). In other words, the improvement lay not in a particular format in which information is presented, but the fact that the information may be shared by remote users, in real time, regardless of its input format. In contrast to claim 1 in Example 42, which recites a specific improvement in the manner in which a networked computer system functions, Appellant’s alleged improvement is at most an improvement to a mathematical algorithm used to stratify a cancer patient into a clinically relevant group. However, abstract ideas such as mathematical algorithms do not confer patent eligibility on a claim even if such abstract ideas are “[g]roundbreaking, innovative, or even brilliant.” buySAFE, Inc. v. Google, Appeal 2020-001633 Application 13/983,651 20 Inc., 765 F.3d 1350, 1352 (Fed. Cir. 2014) (quoting Assoc. for Molecular Pathology v. Myriad Genetics, Inc., 569 U.S. 576, 591 (2013)); see also SAP, 898 F.3d at 1167 (finding “a claimed improvement in a mathematical technique with no improved display mechanism” to be patent-ineligible). In this regard, we note that assigning a cancer patient to a clinically relevant group based on “flow vectors” is less similar to the format conversion recited in patent-eligible claim 1 of Example 42, and more similar to the statistical analysis of investment data found to be patent- ineligible in SAP. For example, the Specification defines “network information flow vector” as “a vector of probabilities, where each probability is the likelihood that a particular interaction in the biological network was activated in the patient.” Spec. 12:31–34. The Specification then teaches calculating “the distance of the patient . . . from other subjects in a patient database” based on “multiple instances of the network information flow,” wherein “distance” refers to “a mathematical or statistical distance between two or more instances of the network information flow.” Id. at 15:24–29. The patient is then assigned to a “clinically relevant group” based on “the results and outcome of the calculation of distance,” where assignment refers to “the determination of a probability that a patient is similar or identical with a subject in a patient database regarding molecular data, phenotypes, symptoms etc.” Id. at 17:31–18:2. In short, in this case as in SAP, “the focus of the claims is not a physical-realm improvement but an improvement in wholly abstract ideas – the selection and mathematical analysis of information, followed by reporting or displaying of the results.” SAP, 898 F.3d at 1168. Appeal 2020-001633 Application 13/983,651 21 We are likewise unpersuaded by Appellant’s argument that “[t]he claimed flow vector-based assignment, like Example 42, has the practical application of providing improved visualization in the context of information flow in the networks.” Id.; Reply Br. 2. While claim 1 does recite a step of “providing a visualization of the assignment of the cancer patient to the clinically relevant group in the context of the network information flow vectors,” the claim lacks specificity as to both the manner of such visualization and how it is achieved. Neither does the claim recite any specific improvement in visualization. Indeed, the Specification states that “[s]uch visualization may be implemented with suitable algorithms known to the person skilled in the art.” Spec. 40:11–19. Finally, Appellant contends that, “[e]ven if the claims are deemed directed to an abstract idea . . . , the claims are directed to an inventive concept under step 2B and, thus, directed to patent eligible subject matter.” Appeal Br. 8. Appellant contends that “the Examiner has not satisfied the requirements as set forth by Berkheimer [v. HP, Inc., 881 F.3d 1360, 1368 (Fed. Cir. 2018),] with regard to step 2B.” Id. at 9; Reply Br. 2–3. We are not persuaded. In particular, as discussed above, the additional elements in claim 1 that are not abstract ideas (i.e., either mental processes or mathematical concepts) include (1) “obtaining cancer molecular profiling data from a patient sample” (step (a)); (2) “inputting said . . . data” (step (b)); (3) “obtaining a dataset . . . comprising molecular data of expression of one or more of said cancer patient’s genes” (step (c)); (4) “inputting said patient molecular data” (step (d)); (5) “providing a database of cancer molecular data of known phenotypes” (step (e)); (6) “providing a visualization of the assignment of the cancer patient to the clinically relevant Appeal 2020-001633 Application 13/983,651 22 group in the context of the network information flow vectors” (step (l)); and (7) a processor that receives a patient’s “cancer molecular profiling data” and “molecular data comprising molecular data of expression of one or more . . . genes” (steps (b) and (d)) and further performs various mathematical/statistical analysis (steps (f)–(k)). As also discussed above, however, these limitations are recited at a high level of generality and/or are described in the Specification as well known, routine, and conventional. See, e.g., supra pp. 12–16 (citing Spec. 1:24–31, 3:14–19, 9:17–10:10, 10:25–28, 11:27–34, 12:4–7, 12:31–34, 13:17–20, 15:24–30, 20:5–6, 24:32–34, 39:3–12, 40:11–19, 40:22–29); MPEP § 2106.05(d) (explaining that, while Berkheimer requires “[a] factual determination . . . to support a conclusion that an additional element (or combination of additional elements) is well understood, routine, conventional activity,” “in many instances[] the specification . . . may indicate that additional elements are well-known or conventional”). Accordingly, we affirm the rejection of claim 1 under 35 U.S.C. § 101. Claims 2, 4–12, and 15–21 are not argued separately and fall with claim 1. 37 C.F.R. § 41.37(c)(1)(iv). B. Lack of Written Description and Indefiniteness (claims 1, 2, 4–12, and 15–21) 1. Issue The Examiner asserts that [a]ll recited steps in the instant claims . . . are carried out by employing a generic computer processor. Lacking any definition, the claims fail to provide for how a general purpose processor is actually configured or specifically Appeal 2020-001633 Application 13/983,651 23 programmed to achieve the functionally defined operations and analytical results set forth in the claims. Ans. 5–6. The Examiner asserts that, similarly, “the instant specification only reiterates the functional language that is correlated to a generic computer implementation (i.e. a ‘processor’) as is recited in the instant claims” and concludes that “the instant disclosure is inadequate as it fails [to] describe any additional algorithms or algorithmic procedures corresponding to the recited computer implemented analytical activities.” Id. at 6. The Examiner concludes that, [s]ince the instant claims only recite generic computer implementation . . . , the claims lack sufficient written support from the instant specification for the algorithm(s) and/or algorithmic procedures that, when executed on a computer system, achieve the results that are functionally defined in the instant claims. Therefore, lacking any specific definition that limits the claimed functions to a specifically described configured computer system, applicant has failed to demonstrate that they were in possession of the full scope of the claimed invention at the time the application was filed. Ans. 7. For the same reasons, the Examiner concludes that “the functionally defined steps implemented ‘by a processor’” render the claims indefinite. Ans. 7–9. More particularly, the Examiner asserts that [t]here is no corresponding disclosure of the algorithm(s) or algorithmic procedures that would limit the scope of the computer implemented analysis to a specific set of the algorithms or algorithmic procedures. Rather, at this time the computer implemented steps are bounded only Appeal 2020-001633 Application 13/983,651 24 by the results that are to be achieved and not to any specified set of the algorithms or algorithmic procedures. Id. at 9. The Examiner does not cite 35 U.S.C. § 112 (pre-AIA), sixth paragraph, in the Answer. However, in the Final Action the Examiner explicitly refers to 35 U.S.C. § 112 (pre-AIA), sixth paragraph, in both written description and indefiniteness rejections. Final Act. 5–6, 7. With respect to the written description rejection, the Examiner further states that “the instant disclosure is inadequate as it fails [to] specify any structure corresponding to the means as instantly claimed.” Id. at 6. With respect to the indefiniteness rejection, the Examiner further states that “the functionally defined modules causes the metes and bounds of the instant claims to be indefinite because there is no corresponding disclosure of what structures are encompassed by said generic configured processor means.” Id. at 8. Appellant contends that “none of the claims invoke 35 U.S.C. § 112(f).”4 Appeal Br. 11, 14. 2. Principles of Law Whether a specification complies with the written description requirement of 35 U.S.C. § 112 (pre-AIA), first paragraph, is a question of fact and is assessed on a case-by-case basis. See, e.g., Purdue Pharma L.P. v. Faulding, Inc., 230 F.3d 1320, 1323 (Fed. Cir. 2000) (citing Vas-Cath Inc. v. Mahurkar, 935 F.2d 1555, 1561 (Fed. Cir. 1991)). The specification does not need to describe the claimed subject matter in haec verba in order to 4 35 U.S.C. § 112(f) corresponds to 35 U.S.C. § 112 (pre-AIA), sixth paragraph. Appeal 2020-001633 Application 13/983,651 25 satisfy the written description requirement; however, it must convey with reasonable clarity to those skilled in the art that, as of the filing date, Appellant was in possession of the claimed invention. See id. On January 7, 2019, the Director of the USPTO issued specific guidance on “Examining Computer-Implemented Functional Claim Limitations for Compliance With 35 U.S.C. 112 (“2019 § 112 Guidance”). 84 Fed. Reg. 57 (Jan. 7, 2019). The 2019 § 112 Guidance explains that, where a claim limitation recites “a term and associated functional language, the examiner should determine whether the claim limitation invokes 35 U.S.C. 112(f).” Id. at 58. This determination involves a 3-prong analysis, which evaluates (1) whether “[t]he claim limitation uses the term ‘means’ (or ‘step’) or a generic placeholder,” (2) whether “the term is modified by functional language,” and (3) whether “the term is not modified by sufficient structure, material or acts for performing the function.” Id. If the answer to all three questions is yes, then 35 U.S.C. § 112(f) applies to the limitation. Id. As further explained in the 2019 § 112 Guidance, the broadest reasonable interpretation (“BRI”) of a claim limitation subject to 35 U.S.C. 112(f) “is the structure . . . described in the specification as performing the entire claimed function and equivalents to the disclosed structure.” 84 Fed. Reg. at 59. For a computer-implemented 35 U.S.C. § 112(f) claim limitation, moreover, “the corresponding structure . . . is not simply a general purpose computer by itself but a special purpose computer as programmed to perform the . . . algorithm” disclosed for performing the specific computer function. Id. Thus, the specification must disclose such Appeal 2020-001633 Application 13/983,651 26 an algorithm, “or else the claim is indefinite under 35 U.S.C. 112(b).”5 Id. Finally, the 2019 § 112 Guidance explains that, “[w]hen a claim containing a computer-implemented 35 U.S.C. 112(f) claim limitation is found to be indefinite under 35 U.S.C. 112(b) for failure to disclose sufficient corresponding structure . . . in the specification that performs the entire claimed function, it will also lack written description under 35 U.S.C. 112(a).”6 Id. at 61. The 2019 § 112 Guidance emphasizes that, “[e]ven if a claim is not construed as a means-plus-function limitation under 35 U.S.C. 112(f), computer-implemented functional claim language must still be evaluated for sufficient disclosure under the written description and enablement requirements of 35 U.S.C. 112(a).” 84 Fed. Reg. at 61. For example, “a specification must describe the claimed invention in sufficient detail (e.g., by disclosure of an algorithm) to establish that the applicant had possession of the claimed invention as of the application filing date.” Id. The 2019 § 112 Guidance notes that “[t]he written description requirement is not met if the specification merely describes a ‘desired result.’” Id. (citing Vasudevan Software, Inc. v. MicroStrategy, Inc., 782 F.3d 671, 682 (Fed. Cir. 2015)). In the context of “computer-implemented, software-related claims,” therefore, examiners should determine whether the specification discloses the computer and the algorithm(s) that achieve 5 35 U.S.C. § 112(b) corresponds to 35 U.S.C. § 112 (pre-AIA), second paragraph. 6 35 U.S.C. § 112(a) corresponds to 35 U.S.C. § 112 (pre-AIA), first paragraph. Appeal 2020-001633 Application 13/983,651 27 the claimed function in sufficient detail that one of ordinary skill in the art can reasonably conclude that the inventor possessed the claimed subject matter at the time of filing. An algorithm is defined, for example, as “a finite sequence of steps for solving a logical or mathematical problem or performing a task.” Microsoft Computer Dictionary (5th ed., 2002). Applicant may “express that algorithm in any understandable terms including as a mathematical formula, in prose, or as a flow chart, or in any other manner that provides sufficient structure.” Finisar [Corp. v. DirecTV Grp., Inc.], 523 F.3d [1323,] 1340 [(Fed. Cir. 2008)] (internal citation omitted). It is not enough that one skilled in the art could theoretically write a program to achieve the claimed function, rather the specification itself must explain how the claimed function is achieved to demonstrate that the applicant had possession of it. See, e.g., Vasudevan, 782 F.3d at 682–83. 84 Fed. Reg. at 61–62. 3. Analysis Based on the principles of law set forth above, we are not persuaded that the Examiner has sufficiently articulated a prima facie case that the claims are lacking in written description and/or are indefinite. As an initial matter, although the Examiner cites to 35 U.S.C. § 112 (pre-AIA), sixth paragraph, in the Final Action, this reference is not present in the Answer. Thus, it is not clear to us whether the Examiner is continuing to base the rejections on a construction of the claims as including means- plus-function limitations. To the extent the Examiner’s rejections are based on construing the claims as containing means-plus-function limitations, we are not persuaded Appeal 2020-001633 Application 13/983,651 28 that the Examiner has sufficiently articulated his reasoning with respect to the analysis set forth in the 2019 § 112 Guidance. For example, the 2019 § 112 Guidance requires consideration of whether “[t]he claim limitation uses the term ‘means’ (or ‘step’) or a generic placeholder.” 84 Fed. Reg. at 58. In this case, because the claims do not use the terms “means” or “step,” the question is whether a skilled artisan would consider “processor” to be a generic placeholder in the context of the claims. The Examiner asserts that “the claims fail to provide for how a general purpose processor is actually configured or specifically programmed to achieve the functionally defined operations and analytical results set forth in the claims.” Ans. 6. However, we note that disclosure of an algorithm is not required where a claim recites only the general purpose functions of a computer, because in such a case the recited functions are “coextensive with the structure disclosed, i.e., a general purpose processor,” and in such a case “processor” would not be a “generic placeholder.” In re Katz Interactive Call Processing Patent Litig., 639 F.3d 1303, 1316 (Fed. Cir. 2011). The Examiner has not made findings as to whether, for example, the step of “receiv[ing] . . . cancer molecular profiling data”7 and/or the analytical steps 7 It is unclear whether the Examiner construes “processor configured to receive . . . cancer molecular profiling data” as a means plus function claim limitation and/or otherwise find that limitation to be lacking in adequate written description. On the one hand, the Examiner states in the Answer that “[a]ll recited steps in the instant claims,” including obtaining information, “are carried out by employing a generic computer processor,” but that “the claims fail to provide for how a general purpose processor is actually configured or specifically programmed to achieve the functionally defined operations and analytical results set forth in the claims.” Ans. 5–6 (emphasis added). On the other hand, in another portion of the Answer, the Appeal 2020-001633 Application 13/983,651 29 recited in the claims, such as “applying . . . a statistical analysis,” are those that may be performed by a general purpose processor. See, e.g., Ans. 4 (stating, in the context of the § 101 analysis, that “the claims still rely on the use of generic computer serving as conventional computational vehicle on which to apply the recited data analysis procedure”). Similarly, although we agree with the Examiner that the term “processor” is modified by functional language in several claim limitations — e.g., “receiv[ing] . . . cancer molecular profiling data,” “applying . . . a statistical analysis to identify a probability,” “identifying . . . a biological network,” “identifying . . . a network information flow probability,” “calculating . . . a distance . . . using . . . multiple instances of network information flow vectors,” “assigning . . . cancer patient to the clinically relevant group” (Appeal Br. 16–17 (Claims App.); Ans. 8), we are not persuaded that the Examiner has sufficiently analyzed whether the term is also, in one or more instances, modified by further structure, in addition to “processor,” for performing the function. For example, claim 1 recites applying, by said processor, a statistical analysis to identify a probability of there being altered molecular data within the patient molecular data in comparison to the database of cancer molecular data of known phenotypes, wherein the probability is identified by Examiner states only that “the instant disclosure is inadequate as it fails [to] describe any additional algorithms or algorithmic procedures corresponding to the recited computer implemented analytical activities (i.e.[,] the recited series of computer implemented analytical steps . . . ).” Id. at 6 (emphasis added). Appeal 2020-001633 Application 13/983,651 30 integrating said altered molecular data using a probabilistic graphical model framework. Appeal Br. 16 (Claims App.) (emphasis added). The Specification further explains that [i]n a specific embodiment said probability of an alteration may be estimated by using a probabilistic graphical model framework, i.e. the probability of an alteration within the one or more sets of molecular data may be identified by estimating altered molecular values as defined herein above (gene expression, copy number etc.) by integrating said molecular data using a probabilistic graphical model framework. The term “probabilistic graphical model” as used herein refers to an approach to characterize joint probability distributions where nodes in the graph are random variables and edges in the graph represent probabilistic relationships between these variables. The graph may accordingly represent the way in which the joint probability of all the variables can be decomposed into a product of factors, each depending on only a subset of all the variables. Suitable examples of probabilistic graphical model frameworks . . . include Bayesian networks and Markov random fields. Spec. 24:22–34. To the extent the application of statistical analysis as claimed cannot be performed by a generic processor, the Examiner does not explain why the claim limitation that “the probability is identified by integrating . . . altered molecular data using a probabilistic graphical model framework” would not, in the view of a ordinarily skilled artisan at the time of the invention, be a structure (i.e., algorithm) that further modifies the generic processor so as to remove the particular limitation from the realm of means-plus-function claiming. Similarly, to the extent the Examiner is not construing the claim limitations as means-plus-function limitations, but nevertheless finds the Appeal 2020-001633 Application 13/983,651 31 claims to be lacking in written description because the Specification has not “disclose[d] the computer and the algorithm(s) that achieve the claimed function in sufficient detail that one of ordinary skill in the art can reasonably conclude that the inventor possessed the claimed subject matter at the time of filing,” 84 Fed. Reg. at 61, we are not persuaded that the Examiner has sufficiently considered the algorithms that appear to be described in the Specification as performing certain claimed functions. For example, we have discussed above the disclosure in the Specification relating to algorithms that may be used to “identify a probability of their being altered molecular data,” as recited in claim 1. Similarly, with respect to the limitation of “identifying . . . a biological network by calculating activity of said biological network based upon the identified probability,” the Specification states: In a further step of the method of the present invention the activity of a biological network may be inferred on the basis of the probability of an alteration within the one or more sets of molecular data as defined above. . . . The term “inferred” as used herein relates to a suitable derivation or calculation activity resulting in the identification of biological networks. For example, suitable algorithms such as the junction tree inference algorithm, preferably with HUGIN updates, the Belief Propagation with sequential updates, or the expectation- maximization (EM) algorithm may be used. These and further suitable algorithms would be known to the person skilled in the art, or could be derived from suitable scientific documents, such as Vaske et al., 2010, Bioinformatics, 26(12): i237-i245, which is incorporated herein by reference in its entirety. Spec. 11:9–34; see also supra n. 3 (citing additional algorithms described in the Specification as useful for performing various claimed steps). Appeal 2020-001633 Application 13/983,651 32 We acknowledge that, as a general matter, the Examiner establishes an adequate prima facie case of lack of written description so long as the Examiner “sufficiently explain to the applicant what, in the examiner’s view, is missing from the written description.” Hyatt v. Dudas, 492 F.3d 1365, 1370 (Fed. Cir. 2007). Nevertheless, because of the lack of clarity in this case as to (1) whether the written description rejection is based on construing certain claim limitations as means-plus-function limitations and (2) the specific limitations the Examiner finds to be lacking in description, and because the Examiner has not adequately articulated his reasoning as to the factors set forth in the 2019 § 112 Guidance, we reverse the Examiner’s rejection of the claims as lacking in written description. The Examiner’s indefiniteness rejection is essentially identical to the written description rejection. Accordingly, we reverse the indefiniteness rejection for the same reasons. CONCLUSION In summary: Claim(s) Rejected 35 U.S.C. § Reference(s)/Basis Affirmed Reversed 1, 2, 4–12, 15–21 101 Eligibility 1, 2, 4–12, 15–21 1, 2, 4–12, 15–21 112 first paragraph Written Description 1, 2, 4–12, 15–21 1, 2, 4–12, 15–21 112 second paragraph Indefiniteness 1, 2, 4–12, 15–21 Overall Outcome 1, 2, 4–12, 15–21 Appeal 2020-001633 Application 13/983,651 33 TIME PERIOD FOR RESPONSE No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a). See 37 C.F.R. § 1.136(a)(1)(iv). AFFIRMED Copy with citationCopy as parenthetical citation