Ex Parte Zidan et al

Patent Trial and Appeal Board

Mar 29, 2017

13185849 (P.T.A.B. Mar. 29, 2017)

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.
13/185,849 07/19/2011 M. Affan Zidan 821109-1020 3141
24504 7590 03/31/2017
THOMAS I HORSTEMEYER, LLP
400 INTERSTATE NORTH PARKWAY SE
SUITE 1500
ATLANTA, GA 30339
EXAMINER
SKIBINSKY, ANNA
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
03/31/2017 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):
uspatents @ tkhr.com
ozzie. liggins @ tkhr.com
docketing @ thomashorstemeyer. com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte M. AFFAN ZIDAN, TALAL BONNY,
and KHALED N. SALAMA
Appeal 2016-0074821
Application 13/185,849
Technology Center 1600
Before DONALD. E. ADAMS, RICHARD M. LEBOVITZ, and MELANIE
L. McCOLLUM, Administrative Patent Judges.
LEBOVITZ, Administrative Patent Judge.
DECISION ON APPEAL
This appeal involves claims directed to a computing device
comprising a computer application for processing database sequences. The
Examiner rejected the claims as patent ineligible subject matter under
35 U.S.C. § 101. We have jurisdiction under 35 U.S.C. § 134. The rejection
is reversed.
STATEMENT OF CASE
Appellants appeal from the Examiner’s final rejection of claims 13—
28. The Examiner withdrew the rejection of the claims as obvious under
1 The Appeal Brief (“Appeal Br.”) lists King Abdullah University of Science
and Technology as the real-party-in-interest.
Appeal 2016-007482
Application 13/185,849
pre-AIA 35 U.S.C. § 103(a). Final Rej. 5. The only remaining rejection is
under 35 U.S.C. § 101. The Examiner found that independent claims 13 and
21, and dependent claims 14—20 and 22—28 are ineligible for a patent
because they are directed to an abstract idea. Id. at 2.
Claim 13 is representative and reads as follows:
13. A system, comprising:
at least one computing device; and
an application executed in the at least one computing
device, the application comprising:
logic that obtains a plurality of database
sequences;
logic that orders the plurality of database
sequences;
logic that determines a splitting ratio associated
with the ordered plurality of database sequences, where
the splitting ratio separates the ordered plurality of
database sequences into a first portion of the ordered
plurality of database sequences associated with at least
one central processing unit (CPU) and a second portion
of the ordered plurality of database sequences associated
with a graphical processing unit (GPU), where the length
of the database sequences of the first portion of the
ordered plurality of database sequences are shorter than
the length of the database sequences of the second
portion of the ordered plurality of database sequences;
logic that assigns the first portion of the ordered
plurality of database sequences to the at least one CPU
for sequencing by the at least one CPU; and
logic that assigns the second portion of database
sequences to the GPU for sequencing by the GPU.
Claim 21 is directed to a computer-implemented method comprising
the same elements as in claim 13, but recited in the form of steps. Thus,
claim 21 stands or falls with claim 13.
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DISCUSSION
Claims
Claim 13 is directed to a system comprising a computer device and an
application executed in the computer device. The application comprises
three “logics” which we understand to be each a logic function that
comprises computer code (Spec. 1 56). The logics perform the following
functions:
1) obtain a plurality of database sequences;
2) order the plurality of database sequences;
3) determine a splitting ratio associated with the ordered plurality of
database sequences.
The splitting ratio has the following function:
3 a) separates a first portion of the database sequences to be assigned
to a CPU and separates a second portion of the database sequences to be
assigned to a GPU;
3b) where the length of the database sequences of the first portion are
shorter than the length of the second portion of database sequences.
The sequences are then assigned to the CPU and GPU for sequencing.
Rejection
The Examiner found that the claims are directed to an abstract idea
because “the method relies on the abstract ideas of comparing information,
categorizing, organizing and transmitting information and organizing
information through mathematical correlations.” FinalRej.3. The
Examiner found that the claims “do not include additional elements that are
sufficient to amount of significantly more than the judicial exception
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because it is routine and conventional to perform the acts of using a
computing device to order information such as sequence data and using a
computer to assign data to various processors.” Id. The Examiner found
that splitting sequences into a first portion and second portion (3a above)
and “assigning short sequences to the CPU and long sequences to the GPU
[3b above] is . . . part of the abstract idea.” Ans. 6. The Examiner also
found that it was known to process sequence data on a CPU and GPU. Id.
The Examiner also stated that the claims are directed to an abstract idea
because the splitting ratio (3 above) is a mathematical algorithm.
Analysis
The determination of patent eligibility under 35 U.S.C. § 101 is a two-
step analysis. First, it must be determined whether the claims are directed to
an abstract idea or other judicial exception. DDR Holdings, LLC v.
Hotels.com, L.P., 773 F.3d 1245, 1255 (2014). Second, the elements of the
claims, “both individually and as an ordered combination,” are considered
“to determine whether the additional elements transform the nature of the
claim into a patent-eligible application of that abstract idea.” Id. “This
second step is the search for an ‘inventive concept,’ or some element or
combination of elements sufficient to ensure that the claim in practice
amounts to ‘significantly more’ than a patent on an ineligible concept.” Id.
(quoting from Alice Corp. v. CLS Bank Int'l, 134 S.Ct. 2347, 2355 (2014)).
The Federal Circuit has acknowledged that it is difficult to discern
when claims are directed to an abstract idea. DDR Holdings, 773 F.3d at
1255. Because of this difficulty, the courts have taken a case-by-case
approach:
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Instead of a definition, then, the decisional mechanism courts
now apply is to examine earlier cases in which a similar or
parallel descriptive nature can be seen—what prior cases were
about, and which way they were decided.
Amdocs (Israel) Limited v. Openet Telecom, Inc., 841 F.3d 1288, 1294
(2016). In other words, the courts look to the similarities and differences
between claims subject to a patent eligibility analysis in earlier decided cases
to determine whether the claims at issue constitute subject matter eligible for
a patent.
As indicated by the Examiner, the claims in this case involve
“comparing information, categorizing, organizing and transmitting
information and organizing information” utilizing a mathematical algorithm.
Final Rej. 3. We thus turn to the recent cases to determine whether the
subject matter is eligible for a patent under § 101.
In Digitech Image Technologies, LLC v. Electronics for Imaging, Inc.,
758 F.3d 1344, 1348 (2014), the claims were directed to “a process of taking
two data sets and combining them into a single data set, the device profile.
The two data sets are generated by taking existing information-—/’, e.,
measured chromatic stimuli, spatial stimuli, and device response
characteristic functions—and organizing this information into a new form.”
The court found that the method claims were drawn to “an abstract idea
because it describes a process of organizing information through
mathematical correlations and is not tied to a specific structure or machine.”
Id. at 1350. The claims in this case are distinguishable because they require
a CPU and GPU which ties them to a specific structure and machine.
In In re TLI Commc ’ns LLC Patent Litig., 823 F.3d 607, 610 (Fed.
Cir. 2016), the claims involved a method for recording and administering
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digital images having the steps, inter alia, of recording images from a
telephone unit, storing the images in a digital form, transmitting the digital
image data, extracting classification information, and storing the digital
information taking into account the classification information. The court
found that the claims were directed to an abstract method of classifying and
storing digital images in an organized manner, lacking “an inventive solution
to any problem presented by combining the two.” Id. at 612—613.
Again, we find that the claims in this proceeding are distinguishable
because the claimed use of CPU and GPU processing, while not new when
each step is considered alone, the combination — particularly of processing
short and long sequences differentially on the CPU and GPU was described
in the Specification as a solution to a computing problem and was
considered inventive by the Examiner as evidenced by the withdrawal of the
§103 rejection (Final Rej. 5). Specifically, the claimed subject matter is
described in the Specification as a technique to reduce computer processing
time when comparing DNA and protein sequences. Spec. 115. The
Specification teaches:
Increasing interest in studying the structure and the function of
DNA, RNA and proteins, and correlating this information with
diseases is driving exponential growth in the bioinformatics
market. Such information helps researchers to identify drug
leads and other therapeutic modalities. However, as the amount
of sequence data being examined increases, the computation
time of the sequencing applications grows at a staggering rate.
Id. at 12.
The Specification discloses that “[b]y processing the long sequences
of the sequence database on the GPU and simultaneously processing the
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short sequences on the CPU(s), the speed of the sequence alignment
application may be efficiently increased.” Id. at 116.
Thus, in contrast to TLI, the rejected claims involve an inventive
solution achieved by the combination of CPU and GPU processing upon
application of a splitting ratio.
The claims require the use of a mathematical algorithm, a splitting
ratio. However, the claims are not simply implementing the algorithm
conventionally or abstractly. Rather, the splitting ratio is used to separate
the ordered plurality of sequences into first and second portions which are
assigned, based on length, to a CPU or GPU for sequence processing. The
claims are not directed to the splitting ratio as an abstract idea, but instead
are directed to a specific application of it that achieves the purpose of
reducing computer processing times when implementing sequence analysis.
See Enfish, LLC v. Microsoft Corp., 822 F.3d 1327, 1338—39 (2016)
(discussion of mathematical algorithms).
The court determined in BASCOM Glob. Internet Servs., Inc. v. AT&T
Mobility LLC, 827 F.3d 1341, 1349 (Fed. Cir. 2016) that the claims did not
“readily lend themselves to a step-one finding that they are directed to a
nonabstract idea.” Thus, the court went immediately to the second step of
the analysis for eligibility under 35 U.S.C. § 101. The BASCOM court found
the claims to be patent eligible because the combination of steps in the
claims “was not conventional or generic, and the claims did not preempt all
ways of filtering content on the Internet—instead, the patent claimed and
explained how a particular arrangement of elements was ‘a technical
improvement over prior art ways of filtering such content.’” Amdocs, 841
F.3d at 1299. As discussed above, the claims in this case also involve a
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technical improvement with regards to GPU and CPU processing of
sequence data. The claims also do not preempt all ways of performing
sequence analysis. See, e.g., Manavski and Valle (“CUDA compatible GPU
cards as efficient accelerators for Smith-Waterman sequence alignment,”
BMC Bioinformatics (Suppl. 2):S10 (pages 1—9), 2008) describing a method
of performing Smith-Waterman sequence alignment on GPU cards.
The claims in this case are also similar to those in Amdocs where
patent eligibility was found. Specifically, Amdocs involved claims to a
computer program for processing network accounting information
comprising a) computer code for receiving a first network accounting record,
b) computer code for correlating the record with accounting information
from a second source, and b) computer code for using the correlation to
enhance the first network accounting record. Amdocs, 841 F.3d at 1299.
The court found the claims to be patent eligible:
[T]his claim entails an unconventional technological solution
(enhancing data in a distributed fashion) to a technological
problem (massive record flows which previously required
massive databases). The solution requires arguably generic
components, including network devices and “gatherers” which
“gather” information. However, the claim’s enhancing
limitation necessarily requires that these generic components
operate in an unconventional manner to achieve an
improvement in computer functionality.
Id. at 1300-01.
In our opinion, the claims in this case are similar to those in Amdocs.
Here, computer processing of sequence data is enhanced by generic
components that are operated in an unconventional manner by using a
splitting ratio to separate sequences into first and second portions based on
length and then process them in a CPU or GPU according to length, “where
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the length of the database sequences of the first portion of the ordered
plurality of database sequences [assigned to a CPU] are shorter than the
length of the database sequences of the second portion of the ordered
plurality of database sequences [assigned to a GPU].”
For the foregoing reasons, we conclude that claims 13 and 21 are not
abstract ideas and are not ineligible for a patent under 35 U.S.C. § 101. The
rejection of claims 13 and 21, and dependent claims 14—20 and 22—28, is
reversed.
REVERSED
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