International Business Machines Corporation

Patent Trials and Appeals Board

Dec 1, 2020

2020001870 (P.T.A.B. Dec. 1, 2020)

UNITED STATES PATENT AND TRADEMARK OFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
14/170,373 01/31/2014 STEPHEN K BOYER ARC920130141US1 2577
67232 7590 12/01/2020
CANTOR COLBURN LLP - IBM ARC DIVISION
20 Church Street
22nd Floor
Hartford, CT 06103
EXAMINER
HARWARD, SOREN T
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
12/01/2020 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):
usptopatentmail@cantorcolburn.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte STEPHEN K. BOYER, JEFFREY T. KREULEN, and
W. SCOTT SPANGLER
__________

Appeal 2020-001870
Application114/170,373
Technology Center 1600
__________

Before JEFFREY N. FREDMAN, JOHN G. NEW, and
RACHEL H. TOWNSEND, Administrative Patent Judges.

TOWNSEND, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) involving claims to a
method for displaying on a graphical user interface information for
discovering a pathway among a plurality of genes, which have been rejected
as being directed to patent ineligible subject matter and as being obvious.
We have jurisdiction under 35 U.S.C. § 6(b).
We affirm.

1 We use the word “Appellant” to refer to “applicant” as defined in 37
C.F.R. § 1.42. Appellant identifies the real party in interest as International
Business Machines Corporation. (Appeal Br. 1.)
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STATEMENT OF THE CASE
Appellant’s invention is concerned with presenting a visual summary
of biological information found in documents. (See, e.g., Spec. 8–9.)
Claims 1–3 and 5–7 are on appeal.2 Claim 1 is representative and
reads as follows:
1. A method for displaying via a graphical user interface
information for discovering a pathway among a plurality of
genes, the method comprising:
a) displaying, on the graphical user interface, a relative
neighborhood graph, the relative neighborhood graph created
from a vector space representation of a set of documents based
on words and/or phrases occurring in the documents, each
document in the documents mentioning at least one gene in the
plurality of genes, at least one of the words and/or phrases
associated with a disease;
b) displaying, on the relative neighborhood graph, a centroid,
for each gene in the plurality of genes, the centroid created in
the vector space based on the vectors corresponding to
documents mentioning that gene;
c) displaying a relative distance network of the plurality of
genes, in view of the centroids, thereby identifying a particular
pathway connecting the centroids;
d) displaying at least one most connected centroid on the
particular pathway,
e) displaying a gene corresponding to the at least one most
connected centroid in (e), and where a drug is designed to treat
the disease, wherein the drug is identified based on the
displayed gene in (f) corresponding to the at least one most
connected centroid.
(Appeal Br. 14.)

2 Claims 8–19 remain pending but are withdrawn from consideration. (Adv.
Action dated May 30, 2019.)
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The prior art relied upon by the Examiner is:
Name Reference Date
Nikolskaya et al. US 2007/0038385 A1 Feb. 15, 2007
G. Salton and C. Buckley, Term-Weighting Approaches in Automatic Text
Retrieval, 24(5) Information Processing & Mgmt., 513–23 (1988)
P. Groth et al., Mining phenotypes for gene function prediction, 9(136)
BMC Bioinformatics, 1–15 (2008)

The following grounds of rejection by the Examiner are before us on
review:
Claims 1–3 and 5–7 under 35 U.S.C. § 101 as being directed to
patent-ineligible subject matter.
Claims 1–3 and 5–7 under 35 U.S.C. § 103(a) as unpatentable over
Groth, Salton, and Nikolskaya.
DISCUSSION
I
Patent Ineligible Subject Matter
Appellant addresses the claims as a group. Thus, we address the
Examiner’s rejection with respect to exemplary claim 1. See 37 C.F.R.
§ 41.37(c)(1)(iv).

The Dispute
The Examiner finds that claim 1 recites the following mathematical
concepts: “a vector space representation of documents based on words
and/or phrases occurring in the documents,” “a centroid in the vector space,”
“a relative distance network of the plurality of genes, in view of the
centroids,” and “at least one most connected centroid on the particular
pathway.” (Ans. 3.)
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Appellant contends that the claim does not recite mathematical
concepts, certain methods of organizing human activity, or mental processes
and thus should not be treated as reciting abstract ideas. (Appeal Br. 4.)
Appellant also argues, that even if the claim were considered to recite an
abstract idea, the claim is directed toward a practical application because it
improves the prior art problem of unstructured text analysis to infer
biological pathways by connecting a set of proteins via a relationship graph
that is presented for visualization such that “relationships between the nodes
can be easily inferred from interactive queries on the visualization itself”
(Appeal Br. 6–7) and recites that a drug that is identified based on the
display corresponding to the at least one most connected centroid “is
designed to treat the disease” (Id. at 7).
The Analysis
The Supreme Court has established a two-step framework for
“distinguishing patents that claim laws of nature, natural phenomena, and
abstract ideas from those that claim patent-eligible applications of those
concepts.” Alice Corp. Pty. Ltd. v. CLS Bank Int’l, 573 U.S. 208, 217
(2014). “First, we determine whether the claims at issue are directed to” a
patent-ineligible concept. Id. If so, “we consider the elements of each claim
both individually and ‘as an ordered combination’ to determine whether the
additional elements ‘transform the nature of the claim’ into a patent-eligible
application.” Id. (quoting Mayo Collaborative Servs. v. Prometheus Labs.,
Inc., 566 U.S. 66, 78–79 (2012)).
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Applying the 2019 Revised Patent Subject Matter Eligibility Guidance
(“Guidance”), 84 Fed. Reg. 50–57 (Jan. 7, 2019),3 and in accordance with
judicial precedent, we agree with the Examiner’s conclusion that the claims
are addressed to patent-ineligible subject matter.
STEP 2A, Prong One:
Under the Guidance, in determining what concept a claim is “directed
to” in step one of the Supreme Court’s two-step framework, we first look to
whether the claim recites any judicial exceptions, such as (a) mathematical
concepts, (b) methods of organizing human activity including fundamental
economic principles or practices (including hedging, insurance, mitigating
risk), and/or (c) mental processes including an observation, evaluation,
judgment, or opinion. Guidance, 84 Fed. Reg. at 52, 54 (Step 2A, Prong
One).
We agree with the Examiner that the claims recites a number of
mathematical concepts. In particular, the “relative neighborhood graph” that
is displayed is “created from a vector space representation of a set of
documents.” In Appellant’s brief, Appellant argued that
the phrase “vector space representation” is a term of art
associated with vector space models that has a specific
meaning within the field of information retrieval . . .
Applicant’s specification notes that “in such a representation,
each document is represented as a vector of weighted

3 “All USPTO personnel are, as a matter of internal agency management,
expected to follow the guidance.” Id. at 51; see also USPTO, October 2019
Update: Subject Matter Eligibility 1 (the “October 2019 Update”) (available
at https://www.uspto.gov/sites/default/files/documents/peg_oct_2019_
update.pdf).
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frequencies of the document features (words and/or
phrases)
(Appeal Br. 9–10.) The Specification describes generally the manner in
which a vector space model is built including the use of weighting schemes
and cites to US Patent 8,606,815 and Salton as examples of effecting such a
representation. (See, e.g., Spec. 10–11.) The mathematical concepts
required are plainly seen in those references. (See ’815 Patent col. 4; Salton
513–14.) Thus, although the claim does not recite a specific vector space
model used, or the particular mathematical equations used to define the
space, we conclude that the recitation that the relative neighborhood graph is
created from a vector space representation of a set of documents, is a
recitation that requires the use of mathematical concepts.
For similar reasons, we conclude that the recitation requiring a
centroid for each gene that is created in the vector space is a recitation that
requires the use of mathematical concepts. (See, e.g., Spec. 9 (“These
vectors can then be averaged . . . to create a centroid (see for example, U.S.
8,606,815, also assigned to International Business Machines Corporation,
for an example of how such centroids are calculated).” (emphasis added);
’815 Patent col. 8.)
The claim also requires “a relative distance network” to be displayed.
In order to be displayed, such a network must be created. The Specification
does not use the term “relative distance network.” Rather, it describes a
“distance matrix,” that is the distance “(e.g., cosine distance)” between any
two pairs of centroids, that is created after the centroids are created which
matrix is then used to create links between centroids. (Spec. 12.) The
determination of the distance matrix thus involves mathematical concepts.
(See also ’815 patent col. 8.) A process for providing the relative distance of
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a plurality of entities so as to represent a network is described in the
Specification, which process involves comparing distance information and
identifying the shortest distance. (Spec. 12.) Such comparison and
identification are mental processes. We conclude from the foregoing that
the displaying of the relative distance network recites a mathematical
concept as well as mental processes.
In light of the above, we conclude that claim recites mathematical
processes as well as mental processes which are abstract ideas, and thus, we
proceed to the next step of the eligibility analysis under the Guidance.
STEP 2A, Prong Two:
Following the Guidance, we next consider whether “the claim as a
whole integrates the recited judicial exception into a practical application of
the exception,” i.e., whether the claim “appl[ies], rel[ies] on, or use[s] the
judicial exception in a manner that imposes a meaningful limit on the
judicial exception.” Guidance, 84 Fed. Reg. at 54. This analysis includes
“[i]dentifying whether there are any additional elements recited in the claim
beyond the judicial exception(s)” and “evaluating those additional elements
individually and in combination to determine whether they integrate the
exception into a practical application.” Id. at 54–55.
Here, most of the additional elements are “displaying” information.
Namely, display a relative neighborhood on a graphical user interface,
display a centroid, display a relative distance network in view of the
centroids, display “at least one most connected centroid,” and display a gene
that corresponds to that at least one most connected centroid. The display is
to be effected on a graphical user interface (GUI).
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We agree with the Examiner that the claim does not specify any
structures or functions of the GUI other than it displays information. (See
Advisory Action May 30, 2019, at 3 (“The claim does not specify any
structures or functions of that interface, other than that it displays
information to the user, which is what any GUI does.”).) In other words, the
invention is not limited by a particular GUI. Nor are any technical details
supplied as to the display of information. As such, the recited displaying is
insignificant extrasolution activity, not a practical application. SAP Am.,
Inc. v. InvestPic, LLC, 898 F.3d 1161, 1167 (Fed. Cir. 2018) (“[M]erely
presenting the results of abstract processes of collecting and analyzing
information . . . is abstract as an ancillary part of such collection and
analysis.”); see also University of Fl. Research Foundation, Inc. v. GE Co.,
916 F.3d 1363, 1368 (Fed. Cir. 2019); Move, Inc. v. Real Estate Alliance
Ltd., 721 F. App’x 950, 955–956 (Fed. Cir. 2018) (holding a method of
using a computer for locating available real estate properties that did not
recite any technical details as to the database created, the display of
information on a map, or the identification of available real estate was not
directed to a technological improvement but rather was focused on “the
performance of an abstract idea ‘for which computers are invoked merely as
a tool.’”).
“Information as such is an intangible” and collecting, analyzing, and
displaying that information, without more, is an abstract idea. See Interval
Licensing LLC v. AOL, Inc., 896 F.3d 1335, 1344–45 (Fed. Cir. 2018)
(quoting Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353–54
(Fed. Cir. 2016).) Appellant’s limitations that require simply displaying
information without more are abstract.
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Appellant’s argument that the claim integrates any abstract idea into a
practical application because the relationships between nodes can be “easily
inferred from interactive queries on the visualization itself” (Appeal Br.
7) is not persuasive given that the claim does not recite any interactivity
elements. As just discussed, the claim simply requires that information that
is determined from calculations and observations is displayed. Furthermore,
that information can be “easily inferred” based on its display does not
establish an improved user interface or an improvement in the functioning of
computers; it simply establishes the claim is merely directed to displaying
information on a graphical user interface. Even if the display allows
assessments to be made more quickly, such does not establish a
technological advance. See, e.g., In re Rosenberg, 813 F. App’x. 594, 597
(Fed. Cir. 2020) (“Because the purported advance ‘is a process of gathering
and analyzing information of a specified content, then displaying the results,
and not any particular assertedly inventive technology for performing those
functions,’ the claimed method is directed to an abstract idea. . . .The ability
to make assessments more quickly to provide instructions on whether to
modify a clinical trial is at best an improvement on an abstract process itself
and not a technical improvement, given the broad, non-specific nature of the
claim.”).
We also disagree with Appellant that the limitation requiring “a drug
is designed to treat the disease, wherein the drug is identified based on
the displayed gene” (Appeal Br. 7) is not a practical application. That is
because the limitation is simply a results oriented recitation that does not
describe how to meet the objective; it simply encompasses a generic process
in the abstract no matter how implemented. Interval Licensing, 896 F.3d at
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1343. Not only is the claim language itself generic, but the Specification
does not identify a method of implementing the design of a particular drug
based on the displayed gene. All that the Specification provides regarding
drug design is a singular statement that where there is a gene that is
determined from the display of information to be central in the pathway of a
particular disease, such indicates a “key target to go after in designing a new
drug to treat this disease.” (Spec. 13.) “A claimed invention must embody a
concrete solution to a problem having ‘the specificity required to transform a
claim from one claiming only a result to one claiming a way of achieving
it.’” (Id. (quoting SAP, 890 F.3d at 1021–22).)
In sum, we find that the claimed invention does not integrate the
abstract idea into a “practical application,” as that phrase is used in the
Guidance. See Guidance, 84 Fed. Reg. at 55. Thus, we conclude that the
claim is directed to an abstract idea. We next turn to the second step of the
Alice analysis, i.e., whether the claim includes an “inventive concept.”

STEP 2B
Step 2B requires that we look to whether the claim, that we have
determined above to set forth the judicial exception of an abstract idea,
“[a]dds a specific limitation [beyond the judicial exception that is] not well-
understood, routine, conventional in the field.” Guidance 84 Fed. Reg. at
56; MPEP § 2106.05(d)).
As discussed above, the additional limitations are the recitation of a
GUI, displaying information, and a generic instruction to design a drug
based on the displayed gene. There is nothing “inventive” about these claim
elements, individually or in combination,
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As for the use of a GUI, “the mere recitation of a generic computer
cannot transform a patent-ineligible abstract idea into a patent-eligible
invention.” Alice, 573 U.S. at 223; DDR Holdings, LLC v. Hotels.com, L.P.,
773 F.3d 1245, 1256 (Fed. Cir. 2014) (“after Alice, there can remain no
doubt: recitation of generic computer limitations does not make an otherwise
ineligible claim patent-eligible.”); SAP, 890 F.3d at 1023 (“we think it fair to
say that 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.’”). Nothing in the claim,
understood in light of the Specification, requires anything other than off-the-
shelf, conventional computer and display technology for gathering and
presenting the desired information. Furthermore, a simple instruction to
display information on a generic GUI is insufficient to provide an inventive
concept. See University of Fl., 916 F.3d at 1369; see also Electric Power
Grp, 830 F.3d at 1356.
Regarding the design a drug step, it is nothing more than a generic
instruction to apply the abstract idea, lacking any implementation details.
Our reviewing court has stated that a fails to satisfy Alice’s second step
where “[t]he claim language does not provide any specific showing of what
is inventive about the [limitation in question] or about the technology used
to generate and process it.” Secured Mail Sols. LLC v. Universal Wilde,
Inc., 873 F.3d 905, 912 (Fed. Cir. 2017); see also ChargePoint, Inc. v.
SemaConnect, Inc., 920 F.3d 759, 769 (Fed. Circ. 2019) (explaining that an
invention may not be patent eligible if the “claims were drafted in such a
result-oriented way that they amounted to encompassing the principle in the
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abstract no matter how implemented”); Bilski v. Kappos, 561 U.S. 593, 612
(2010) (“adding token postsolution components [does] not make the
[abstract] concept patentable.”). The failure to provide any implementation
detail for this step leads to the conclusion that this step is nothing more than
an instruction to apply an abstract idea.
After considering the additional steps of claim 1 individually and as
an ordered combination, we conclude that it is directed to ineligible subject
matter under 35 U.S.C. § 101. See, e.g., Inventor Holdings, LLC v. Bed Bath
& Beyond, Inc., 876 F.3d 1372, 1378 (Fed. Cir. 2017) (holding that sequence
of data retrieval, analysis, modification, generation, display, and
transmission was abstract).
Consequently, we affirm the Examiner’s rejection of claims 1–3 and
5–7 under 35 U.S.C. § 101 as being directed to patent-ineligible subject
matter.
II
Obviousness
We again focus on claim 1 as Appellant does not argue the claims
separately. The Examiner finds that Groth teaches a computer system that
mines text of phenotypes, some of which include diseases, to identify
networks of related genes. (Ans. 6–7 (citing Groth p.12, p. 2); Final Action
9–10.) According to the Examiner, the phenotype database entries are the
required documents mentioning at least one gene. (Ans. 6.) The Examiner
further finds that terms extracted from phenotype descriptions of a gene and
all associated phenotype database documents “were concatenated into
‘phenodocs’ associated with a gene” and that “‘phenodoc vectors’ were
calculated from the frequency of each term in the phenodocs” and that those
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vectors “define a vector space in which each word in the phenotype
description is a dimension of the space.” (Id. at 6–7.) The Examiner finds
that the number of times a term occurs in a phenodoc “is the sum of the
number of times that term occurs in a plurality of related database entries”
and “the frequency of the term in the phenodoc is the mean number of times
that the term occurs in all the related database entries.” (Id. at 7.) The
Examiner recognizes that Groth does not specifically identify the phenodoc
vectors are a “centroid in the vector space.” (Id.) However, the Examiner
concludes that given how the phenodoc vector is derived, i.e., the mean
number of times a term occurs in all of the related database entries, it is
necessarily a centroid.
The Examiner additionally finds that Groth teaches creating a network
of genes using term frequency (TF) and inverse document frequency (IDF)
by determining “TF-IDF score vectors for each gene, thereby identifying
pathway(s) connecting the genes.” (Ans. 7 (citing Groth p.5, p.6, and Figs.
3, 4).) The Examiner concludes from this and Salton’s teachings that using
term frequency to create TF-IDF term weights for document comparison and
that such normalization of term weights is straightforward, indicates that
Groth’s network created with TF-IDF score vectors is the required “relative
distance network of the plurality of genes” that “is generated ‘in view of the
centroids.’” (Id. at 7–8, 9.)
The Examiner finds that Groth does not teach displaying a most
connected centroid, a particular gene, or designing a drug to treat a disease
based on the identified gene. (Id.) However, the Examiner finds that these
steps would have been obvious in view of Nikolskaya. (Id. at 8–9 (citing
Nikolskaya ¶¶ 158, 167, 170–171, Figs. 2, 49–54).) The Examiner explains
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that “Nikolskaya teaches that biological pathway information is valuable for
identifying prospective drug targets.” (Id. at 8.) Nikolskaya further teaches
that the pathway information can be identified from text mining protein
interaction descriptions, constructing a network from the mined data, and
identifying hubs of highly connected members, where the hubs “are usually
valuable targets for designing new drugs.” (Id.) The Examiner notes further
that Nikolskaya teaches using a GUI to display the pathway information
generated by the method, including highlighting hubs within the network,
which is considered to be the claimed displaying of a centroid, and edge
lengths that reflect the relative distance between connected nodes. (Id.) The
Examiner concludes that it would have been obvious to one of ordinary skill
in the art to use the Groth method of creating biological pathways and
combine it with the display methodology described in Nikolskaya to
determine targets for drug design to treat disease related to the pathways
identified in Groth. (Id. at 9.) The Examiner further concludes that one of
ordinary skill in the art would have had a reasonable expectation of success
because “the combination merely requires performing one method . . . and
then using the output from that method as the input to a second method.”
(Id.)
We agree with the Examiner’s findings and conclusion of
obviousness.
Appellant argues that the Examiner’s rejection is in error because
Groth’s phenodoc is concatenated data from all texts including the relevant
term in the phenotype database. (Appeal Br. 8.) Appellant argues that this
is different from the description in the “Application-As-Filed” which depicts
“creating a biological pathway from unstructured information (NOT
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concatenation of structure information in a database)” and where the vector
space representation is created from the documents, i.e., unstructured
information, and a graph is displayed according to the relative position of the
document in space. (Appeal Br. 8–9.) We do not find this argument
persuasive, even accepting Appellant’s further argument that “vector space
representation” is a term of art which requires more than just any
representation based on mere words or phrases in a document (Appeal Br.
9). Appellant argues that the Specification provides for a particular
understanding at pages 10–11 of vector space representation: namely that
“in such a representation, each document is represented as
a vector of weighted frequencies of the document features
(words and/or phrases)” where the “words and/or phrases
that make up the document feature space are determined by
first counting which words occur most frequently (in the
most documents) in the text.”
(Appeal Br. 9–10.)
However, there is insufficient evidence that the term of art is limited
to the Specification notation describing “an example of how documents may
be represented in a vector space model.” (Spec. 10.) “Attorney argument is
not evidence.” Icon Health & Fitness v. Strava, 849 F.3d 1034, 1043 (Fed.
Cir. 2017). Appellant does not point us to any evidence supporting the
Specification’s exemplification of one vector space model as the only
definition for “vector space representation.” And, we find the claim
language “the relative neighborhood graph created from a vector space
representation of a set of documents based on words and/or phrases
occurring in the documents” does not preclude Groth’s concatenation of
information from a plurality of documents to make a phenodoc. As the
Examiner explained the phenodoc is a compilation of text information from
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multiple docs, i.e., the phenodoc which is a single “document,” as the
Examiner noted, “does not represent a single document.” (Ans. 13.) And as
the Examiner explained, to which Appellant does not respond, each
phenodoc is transformed into a vector representation with TF-IDF scores for
each word based on the frequency of the term in the phenodoc that is a
compilation of a plurality of documents. Thus, we conclude that the vector
space representation of the phenodocs of Groth is a representation of a set of
documents based on words occurring in the documents, which meets the
requirements of the claim.
Appellant’s additional argument that the combination of references
does not teach a centroid as claimed rests on Appellant’s position that a
phenodoc is a single document. (Appeal Br. 12.) However, as the Examiner
explained in the Answer, to which Appellant does not respond, the phenodoc
concatenates information from a plurality of documents, thus it is a
representation of a plurality of documents. Moreover, the Examiner further
explains in the Answer, to which Appellant does not respond, how “the
centroid of the term frequency vectors of a set of documents j is
mathematically equivalent to the term frequency vector of a document that is
the concatenation of the j individual documents.” (Ans. 13–14.)
In light of the foregoing, we affirm the Examiner’s rejection of claims
1–3 and 5–7 under 35 U.S.C. § 103 as being obvious over Groth, Salton, and
Nikolskaya.

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DECISION SUMMARY
In summary:
Claims
Rejected
35 U.S.C.
§
Reference(s)/Basis Affirmed Reversed
1–3, 5–7 101 Eligibility 1–3, 5–7
1–3, 5–7 103(a) Groth, Salton,
Nikolskaya
1–3, 5–7
Overall
Outcome
1–3, 5–7

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