Ex Parte Bremel et al

Patent Trials and Appeals Board

May 20, 2019

13052733 - (D) (P.T.A.B. May. 20, 2019)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO.
13/052,733
72960 7590
Casimir Jones, S.C.
FILING DATE
03/21/2011
05/22/2019
2275 Deming Way Ste 310
Middleton, WI 53562
FIRST NAMED INVENTOR
Robert D. Bremel
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
ATTORNEY DOCKET NO. CONFIRMATION NO.
IOGEN-31239/US-3/0RD 7001
EXAMINER
BORIN, MICHAEL L
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
05/22/2019 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):
docketing@casimirjones.com
pto .correspondence@casimirjones.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte ROBERT D. BREMEL and JANE HOMAN
Appeal2018-007657
Application 13/052,733
Technology Center 1600
Before JEFFREY N. FREDMAN, JOHN G. NEW, and JAMIE T. WISZ,
Administrative Patent Judges.
WISZ, Administrative Patent Judge.
DECISION ON APPEAL
Pursuant to 35 U.S.C. § 134(a), Appellants 1 seek review of claims 1,
9-16, 18-31, and 37-50.2 The Examiner rejected the claims as directed to
patent-ineligible subject matter. We have jurisdiction under 35 U.S.C.
§ 6(b ).
For the reasons set forth below, we AFFIRM.
1 Appellants identify the Real Party in Interest as ioGenetics, LLC. App. Br.
3.
2 Claims 2-8, 17, and 90-98 have been cancelled. Claims 32-36 and 51-89
have been withdrawn.
Appeal2018-007657
Application 13/052,733
STATEMENT OF THE CASE
The specification describes "processes for identifying peptide and
polypeptide ligands for a binding partner" through the use of "principal
component analysis of amino acids to derive vectors describing amino acid
subsets corresponding to peptides with known binding affinities." Spec.
153. This information is then used in a "neural network modeling process to
derive binding prediction equations." Id. "These binding prediction
equations are then used in the analysis of subsets of amino acids from a
target source to identify peptides or polypeptides ligands in the target source
that have affinity for a binding partner." Id.
Claim 1, the only independent claim, is set forth below:
1. A computer implemented process of identifying peptide
and polypeptide ligands for a MHC-I or MHC-II binding
partner comprising:
(a) obtaining an amino acid sequence for a target
polypeptide;
(b) providing peptide binding prediction equations for a
MHC-I or MHC-II binding partner polypeptide derived by:
(i) assembling experimentally derived data from a
plurality of experiments comprising a multiplicity of
measurements of amino acid physicochemical properties;
(ii) producing a correlation matrix of the
experimentally derived data;
(iii) deriving by Principal Component Analysis
multiple uncorrelated dimensionless, weighted and ranked
proxy descriptors to describe at least 80% of the variance in
said physicochemical properties of individual amino acids,
(iv) using said proxy descriptors to describe individual
amino acids in peptides with known binding affinities thereby
creating vectors which describe said peptides with known
binding affinities, and
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(v) via neural network modeling, deriving said binding
prediction equations for said MHC-I or MHC-II binding partner
by comparing said vectors with said known binding affinities of
said peptides, wherein said principal components of said amino
acids are utilized as the input layer of a multilayer perceptron
neural network;
( c) in-putting said amino acid sequence from said target
polypeptide into a computer;
( d) applying said proxy descriptors from said Principal
Component Analysis to describe individual amino acids in said
target polypeptide sequence;
( e) deriving vectors to describe a plurality of peptides of
defined length in said target polypeptide;
(f) via said neural network, applying said peptide binding
prediction equations to said plurality of peptides of defined
length from said target polypeptide to predict the ability of said
plurality of peptides of defined length from said target
polypeptide to bind to said binding partner, wherein said neural
network determines the permuted average binding of a peptide
to at least 20 MHC-I or MHC-II binding regions; and
(g) displaying the binding affinity of said peptides of defined
length in said target polypeptide to said binding partner.
App. Br. 20 (Claims Appendix).
The Examiner rejected claims 1, 9-16, 18-31, and37-50under
3 5 U.S. C. § 101 as directed to an abstract idea. Final Act. 3-7.
PRINCIPLES OF LAW
An invention is patent-eligible if it claims a "new and useful process,
machine, manufacture, or composition of matter." 35 U.S.C. § 101.
However, the Supreme Court has long interpreted 35 U.S.C. § 101 to include
implicit exceptions: "[l]aws of nature, natural phenomena, and abstract
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ideas" are not patentable. See, e.g., Alice Corp. v. CLS Bank Int 'l, 573 U.S.
208, 216 (2014).
In determining whether a claim falls within an excluded category, we
are guided by the Supreme Court's two-step framework, described in Mayo
and Alice. Id. at 217-18 ( citing Mayo Collaborative Servs. v. Prometheus
Labs., Inc., 566 U.S. 66, 75-77 (2012)). In accordance with that framework,
we first determine what concept the claim is "directed to." See Alice, 573
U.S. at 219 ("On their face, the claims before us are drawn to the concept of
intermediated settlement, i.e., the use of a third party to mitigate settlement
risk."); see also Bilski v. Kappas, 561 U.S. 593, 611 (2010) ("Claims 1 and 4
in petitioners' application explain the basic concept of hedging, or protecting
against risk.").
Concepts determined to be abstract ideas, and thus patent ineligible,
include certain methods of organizing human activity, such as fundamental
economic practices (Alice, 573 U.S. at 219-20; Bilski, 561 U.S. at 611);
mathematical formulas (Parker v. Flook, 437 U.S. 584, 594-95 (1978)); and
mental processes (Gottschalkv. Benson, 409 U.S. 63, 69 (1972)). Concepts
determined to be patent eligible include physical and chemical processes,
such as "molding rubber products" (Diamond v. Diehr, 450 U.S. 175, 192
(1981 )); "tanning, dyeing, making waterproof cloth, vulcanizing India
rubber, smelting ores" (id. at 184 n.7 (quoting Corning v. Burden, 56 U.S.
252, 267-68 (1854))); and manufacturing flour (Benson, 409 U.S. at 69
(citing Cochrane v. Deener, 94 U.S. 780, 785 (1876))).
In Diehr, the claim at issue recited a mathematical formula, but the
Supreme Court held that "[a] claim drawn to subject matter otherwise
statutory does not become nonstatutory simply because it uses a
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mathematical formula." Diehr, 450 U.S. at 176, 192 ("We view
respondents' claims as nothing more than a process for molding rubber
products and not as an attempt to patent a mathematical formula."). Having
said that, the Supreme Court also indicated that a claim "seeking patent
protection for that formula in the abstract ... is not accorded the protection
of our patent laws,[] and this principle cannot be circumvented by
attempting to limit the use of the formula to a particular technological
environment." Id. ( citing Benson and Flook), 187 ("It is now commonplace
that an application of a law of nature or mathematical formula to a known
structure or process may well be deserving of patent protection.").
If the claim is "directed to" an abstract idea, we tum to the second
step of the Alice and Mayo framework, where "we must examine the
elements of the claim to determine whether it contains an 'inventive
concept' sufficient to 'transform' the claimed abstract idea into a patent-
eligible application." Alice, 573 U.S. at 221 ( quotation marks omitted). "A
claim that recites an abstract idea must include 'additional features' to
ensure 'that the [claim] is more than a drafting effort designed to
monopolize the [abstract idea]."' Id. (quoting Mayo, 566 U.S. at 77).
"[M]erely requir[ing] generic computer implementation[] fail[ s] to transform
that abstract idea into a patent-eligible invention." Id.
The United States Patent and Trademark Office published revised
guidance on the application of 35 U.S.C. § 101. USPTO's 2019 Revised
Patent Subject Matter Eligibility Guidance ("Guidance"). 3 Under the
3 2019 Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg.
50-57 (January 7, 2019).
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Guidance, in determining what concept the claim is "directed to," we first
look to whether the claim recites:
(1) any judicial exceptions, including certain groupings
of abstract ideas (i.e., mathematical concepts, certain methods
of organizing human activity such as a fundamental economic
practice, or mental processes) (Guidance Step 2A, Prong l);
and
(2) additional elements that integrate the judicial
exception into a practical application (see MPEP § 2106.05(a)-
(c), (e)-(h)) (Guidance Step 2A, Prong 2).
Only if a claim (1) recites a judicial exception and (2) does not
integrate that exception into a practical application, do we then look to
whether the claim contains an "'inventive concept' sufficient to 'transform"'
the claimed judicial exception into a patent-eligible application of the
judicial exception. Alice, 573 U.S. at 221 (quoting Mayo, 566 U.S. at 82).
In so doing, we thus consider whether the claim:
(3) adds a specific limitation beyond the judicial
exception that are not "well-understood, routine and
conventional in the field" (see MPEP § 2106.05(d)); or
(4) simply appends well-understood, routine,
conventional activities previously known to the industry,
specified at a high level of generality, to the judicial exception.
(Guidance Step 2B). See Guidance, 84 Fed. Reg. at 54-56.
ANALYSIS
Applying the Revised Guidance to the facts on this record, we find
that Appellants' claims are directed to patent-ineligible subject matter.
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A. Guidance Step 2A, Prong 1
The Revised Guidance instructs us first to determine whether any
judicial exception to patent eligibility is recited in the claim. The Revised
Guidance identifies three judicially-excepted groupings identified by the
courts as abstract ideas: (1) mathematical concepts, (2) certain methods of
organizing human behavior such as fundamental economic practices, and (3)
mental processes.
The Examiner finds that the claims are directed to "a computational
method of characterizing peptides as having a putative binding ability to
bind to a binding partner molecule." Final Act. 3. Specifically, the
Examiner finds that the claimed method "is drawn to deriving binding
prediction equations using neural network modeling computational
technique, wherein the neural network uses vectors of mathematical
expressions obtained by Principal Component analysis." Id. The Examiner
concludes that:
Id.
As such, the claims are directed to processing information,
converting one form of numerical representation into another,
and extracting and categorizing information by organizing
information through mathematical concepts such as
mathematical algorithms; all of these concepts relate to
organization and processing information which can be
performed mentally and is an idea of itself. Therefore, the
claims are directed to an abstract idea which is a judicial
exception.
Appellants argue that the asserted abstract ideas are not directed to a
judicial exception because "the claims define specific steps where
information is rendered into a specific format (i.e., PCA (Principal
Component Analysis) is used to describe amino acids and then that
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information is used to generate vectors representing peptides with known
binding affinities)." App. Br. 8. Appellants assert that this information "is
then used to create desired results (i.e., neural network modeling is used to
derive binding prediction equations which are in tum used to predict binding
by MHC-I and MHC-II binding partners to specific peptide sequences
within a target protein)." Id.
We agree with the Examiner that claim 1 recites patent-ineligible
subject matter. More specifically, claim 1, reproduced above, recites the
following steps: (b) "providing peptide binding prediction equations," (b )(ii)
"producing a correlation matrix," (b )(iii) "deriving by Principal Component
Analysis multiple ... proxy descriptors," (b )(iv) "using said proxy descriptors
... thereby creating vectors," (b)(v) "via neural network modeling, deriving
said binding prediction equations," ( d) "applying said proxy descriptors
from said Principal Component Analysis," (e) "deriving vectors to describe a
plurality of peptides of defined length," and (f) "via said neural network,
applying said peptide binding prediction equations to said plurality of
peptides ... to predict the ability of said plurality ofpeptides ... to bind to said
binding partner." These limitations, under their broadest reasonable
interpretation, recite the mathematical concept of applying peptide binding
prediction equations ( derived by Principal Component Analysis and neural
network modeling) to amino acid sequences, in order to determine the
binding affinity of peptides to a MHC-I or MHC-II binding partner.
The claimed invention is described in the specification as a "computer
implemented system[] and process[] for analyzing all or portions of target
proteome( s )" comprising "a series of mathematical and statistical
processes." Spec. 46-4 7. The specification explains that this analysis can
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be done "on a personal computer, using commercially available statistical
software and database tools." Spec. 46. Furthermore, "Principal
Component Analysis," the use of which is recited in the claims, is described
in the specification as "a mathematical process that is used in many different
scientific fields and which reduces the dimensionality of a set of data."
Spec. 48. In addition, a "neural network," which is also recited in the
claims, is described as "a powerful data modeling tool that is able to capture
and represent complex input/output relationships" and is constructed via a
computer. Spec. 6, 54.
Therefore, the limitations described above require mathematical
calculations, which, without more, are abstract ideas. Intellectual Ventures I
LLC v. Capital One Financial Corp., 850 F.3d 1332, 1340 (Fed. Cir. 2017);
see also Digitech Image Techs., LLC. v. Elecs. For Imaging, Inc., 758 F.3d
1344, 1351 (Fed. Cir. 2014) ("Without additional limitations, a process that
employs mathematical algorithms to manipulate existing information to
generate additional information is not patent eligible"). Accordingly, we
conclude that these steps of claim 1 recite the judicial exception of a
mathematical concept.
B. Guidance Step 2A, Prong 2
Having determined that the claims are directed to a judicial exception,
the Revised Guidance directs us to next consider whether the claims
integrate the judicial exception into a practical application. Guidance Step
2A, Prong 2. "Integration into a practical application" requires that the
claim recite an additional element or a combination of elements, that when
considered individually or in combination, "apply, rely on, or use the
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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." Guidance at 54
We begin by observing that Appellants' claims do not require that
anything be done with the information generated by the claimed method.
The output of the final step, i.e., "displaying the binding affinity of said
peptides ... to said binding partner," simply recites the providing of
information to the user. In this regard, the claims here are unlike those in
Vanda that required the administration of a treatment in response to a
diagnostic determination. See Vanda Pharm. Inc. v. West-Ward Pharm. Int 'l
Ltd., 887 F.3d 1117, 1133-36 (Fed. Cir. 2018). Indeed, we conclude
Appellants' claims are more similar to those held ineligible in Mayo because
they merely "tell doctors to gather data from which they may draw an
inference" of binding affinities. See 566 U.S. at 79-80.
We also determine that the additional steps recited in claim 1 do not
integrate the judicial exception into a practical application. Claim 1 includes
the additional steps of (a) "obtaining an amino acid sequence for a target
polypeptide," (b )(i) "assembling experimentally derived data from a
plurality of experiments," ( c) "in-putting said amino acid sequence ... into a
computer," and (g) "displaying the binding affinity of said peptides." Steps
(a), (b)(i), and (c) are data collection steps that do not amount to
significantly more than the abstract idea because they are insignificant pre-
solution activities. See Mayo, 566 U.S. at 79 (quoting Flook, 437 U.S. at
590) ("Purely 'conventional or obvious' '[pre]-solution activity' is normally
not sufficient to transform an unpatentable law of nature into a patent-
eligible application of such a law"); see also Guidance, 55, n.31.
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Furthermore, the "displaying" limitation of step (g) also does not integrate
the judicial exception into a practical application because it is an
insignificant post-solution activity. The "prohibition against patenting
abstract ideas 'cannot be circumvented' [by] adding 'insignificant post-
solution activity."' Bilski, 561 U.S. at 610-11 (quoting Diehr, 450 U.S. at
191-92).
Appellants argue that the instant claims are similar to those in McRo,
Inc. dba Planet Blue v. Bandai Namco Games America Inc., 837 F.3d 1299
(Fed. Cir. 2016). App. Br. 11-13. Specifically, Appellants assert that:
Thus, like in McRO, the claims define specific steps
where information is rendered into a specific format (i.e., PCA
is used to describe amino acids and then that information is
used to generate vectors representing peptides with known
binding affinities) that is then used to create desired results (i.e.,
neural network modeling is used to derive binding prediction
equations which are in tum used to predict binding by MHC-I
and MHC-II binding partners to specific peptide sequences
within a target protein). Thus, when considered as a whole as an
ordered combination of steps, the claims are directed to a
specific method that improves the relevant technology.
Id. at 13.
Appellants argue that the claimed invention represents a substantial
improvement in the field of immunology and cite to declarations from Dr.
Splitter, Dr. Malone, and Dr. Bremel to support this proposition. Id. at 14-
16. Appellants also argue that the invention provides a substantial
improvement to the "functioning of a computer" in that it improves
computational efficiency by using amino acid principal components as
proxies for physical properties of amino acids. Id. at 16-18.
The Examiner responds to these contentions by stating that:
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[T]he claims are drawn to data analysis, calculation of a value
(binding affinity) and displaying the value. Mere data analysis
is not an improvement, and no improvement is readily apparent
in the claim language. Applicant argues that the claims
determine whether the peptides in the target protein have a
binding affinity for MHC-I or MHC-II binding regions and then
displaying the binding affinity, and by this, the claims go far
beyond merely retrieving and combining data. In response, as
previously discussed, the claimed steps result in generating
numbers that, presumably, reflect binding affinity of peptide
fragments of a polypeptide. There are no meaningful limitations
in the claims, beyond generally linking the use of an abstract
idea to a particular technological environment, that transform
the judicial exception into a patent-eligible application such that
the claim amounts to significantly more than the exception
itself.
Final Act. 6. The Examiner also finds that the use of amino acid principal
components as proxies "is not an improvement to functioning of a
compute[ r ]" and concludes that, "the claims as a whole do not provide
significantly more than a generic computer upon which the claimed method
steps are executed." Final Act. 4.
"We may assume that the techniques claimed are '[g]roundbreaking,
innovative, or even brilliant,' but that is not enough for eligibility." SAP
America, Inc., v. INVESTPIC, LLC, 898 F.3d 1161, 1163 (Fed. Cir. 2018).
We agree with the Examiner and find no evidence of record here to support
the argument that the present situation is like the one in McRO where the
method integrated specific process steps of phenome analysis to obtain facial
expression control of animated characters, thereby integrating the
improvement into the animation process. See McRO, 837 F.3d at 1315. As
found by the Examiner, "[ o ]ther than the manipulation of data, there is no
evidence for an improvement[] to another technology or to the functioning
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of the computer itself, or for applying the judicial exception with, or by use
of, a particular machine." Ans. 3-4. We also agree with the Examiner that,
although Applicants discuss improvements in the field of immunology, the
claims do not recite a particular improvement in this technology but, rather,
recite deducing the binding affinity of certain peptides. Id. at 4.
We find the instant claims similar to those in SmartGene, where the
Federal Circuit held that claims directed to "comparing new and stored
information and using rules to identify medical options" did not
satisfy Alice step one. See SmartGene, Inc. v. Advanced Biological Labs.,
SA, 555 F. App'x 950, 951-52, 955-56 (Fed. Cir. 2014) (nonprecedential).
As in Smartgene, the instantly claimed steps do not rely on an inventive
device or technique for displaying information or new techniques for
analyzing information, but rather constitute a generic recitation of steps for
mathematically manipulating data. See SmartGene, 555 Fed. Appx. at 954
(holding claims were patent ineligible because they did "no more than call
on a 'computing device,' with basic functionality for comparing stored and
input data and rules, to do what doctors do routinely.").
Therefore, on this record, we conclude that the ineligible subject
matter in Appellants' claim 1 is not integrated into a practical application.
C. Guidance Step 2B
Having determined that the judicial exception is not integrated into a
practical application, the Revised Guidance requires us to evaluate the
additional elements individually and in combination to determine whether
they provide an inventive concept, such as a specific limitation beyond the
judicial exception that is not well-understood, routine, conventional in the
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field, 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 84 Fed. Reg. 51.
Appellants argue that the claim, taken as a whole, does not just simply
describe the generation of proxy descriptors and binding equations via
mathematical operations and sending and receiving data, but combine these
steps with steps for describing peptide sequences to determine whether the
peptides in the target protein have a binding affinity. App. Br. 17-8. In
response, the Examiner finds that Appellants are discussing the limitations
that are drawn to the judicial exception rather than "a combination of
elements which are in addition to the elements drawn to the judicial
exception and which either individually or as an ordered combination are not
well understood, routine, or conventional." Ans. 4-5.
We are not persuaded by Appellants' arguments. There is nothing in
the specification indicating that any steps or components recited in the
claims are not generic or conventional. The use of Principle Component
Analysis and neural network modeling is admittedly known. See, e.g., Spec.
48, 54. Furthermore, the invention can be performed on a "personal
computer, using commercially available statistical software and database
tools." Spec. 46. Appellants point to no additional steps that could not be
performed mentally or without using a generic computer. The use of a
generic computer to perform generic computer functions that are "well-
understood, routine, conventional activities" previously known in the
industry is not enough to transform the abstract idea into a patent-eligible
invention. See Alice, 573 U.S. at 225-26.
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Appellants' claims do not require anything other than the use of
conventional and well understood techniques and equipment to gather and
process data according to the recited judicial exception. Accordingly, the
preponderance of evidence of record supports the Examiner's finding that
Appellants' claimed invention is directed to patent-ineligible subject matter.
The rejection of claim 1 under 35 U.S.C. § 101 is affirmed. Claims 9-16,
18-31, and 37-50 are not separately argued and fall with claim 1. See 37
C.F.R. § 41.37(c)(l)(iv).
CONCLUSION
We affirm the Examiner's rejection of claims 1, 9-16, 18-31, and 37-
50 under 35 U.S.C. § 101. No time period for taking any subsequent action
in connection with this appeal may be extended under 37 C.F.R.
§ l.136(a)(l )(iv).
AFFIRMED
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