DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 6/4/2026 has been entered.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged. Priority of a 371 of PCT/EP2016/074307 filed 10/11/2016 is acknowledged.
Status of Claims
Claims 12, 14, 16, 18 are cancelled;
Claims 1-11, 13, 15, 17 and 19-20 are pending;
Claims 9-11 are withdrawn;
Consequently claims 1-8, 13, 15, 17 and 19-20 are examined on the merits.
Claim Rejections - 35 USC § 101
This rejection is maintained from a previous Office Action.
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-8, 13, 15, 17 and 19-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Step 1: Process, Machine, Manufacture or Composition
Claims 1-4 are to “a computer-implemented method” for compression of genome sequence data, with a series functional steps. So a process.
Claims 5, 13, 15, 17 and 19-20 are to another “computer-implemented method” for decompression of a genomic stream, with a series functional steps. So another process.
Claim 6 is to a "encoder," which is not, in all embodiments within a BRI, interpreted as belonging to any category listed in 101. In a BRI, the claim reads on data and/or software comprising no structure other than data and/or software. The claim is not recited as a process, and the claim is not limited to any particulars structure as a 101 machine (A machine is a "concrete thing, consisting of parts, or of certain devices and combination of devices." MPEP $2106.03) or ma manufacture (A manufacture is "a tangible article that is given a new form, quality, property, or combination through man-made or artificial means." MPEP $2106.03). The claim reads on transitory propagating signals which are not proper patentable subject matter because it does not fit within any of the four statutory categories of invention (In Nuijten, Federal. Circuit, 2006).
It is suggested that the claim be amended to recite an encoder on non-transitory computer readable media or a computer comprising a processor and storage comprising an encoder.
Similarly Claims 7-8 are to a "decoder," which is not, in all embodiments within a BRI, interpreted as belonging to any category listed in 101. In a BRI, the claim reads on data and/or software comprising no structure other than data and/or software. The claim is not recited as a process, and the claim is not limited to any particulars structure as a 101 machine (A machine is a "concrete thing, consisting of parts, or of certain devices and combination of devices." MPEP $2106.03) or ma manufacture (A manufacture is "a tangible article that is given a new form, quality, property, or combination through man-made or artificial means." MPEP $2106.03). The claim reads on transitory propagating signals which are not proper patentable subject matter because it does not fit within any of the four statutory categories of invention (In Nuijten, Federal. Circuit, 2006).
It is suggested that the claim be amended to recite a decoder on non-transitory computer readable media or a computer comprising a processor and storage comprising a decoder.
Step 2A Prong One: Identification of an Abstract Idea
Claim 1 recites:
Aligning said reads to one or more reference sequences thereby creating aligned reads.
----Human mind is equipped to align and to compare two sequences. “Creating aligned reads” reads on data manipulation based on data observation. The claims don't really give any information about the size of the reads or the size of the reference sequences in the claim. Although recited as a job performed by an aligner unit, under a broadest reasonable interpretation (BRI) and in its simplest embodiment, nothing can stop a human from performing sequence mapping with the help of a pen and paper. Hence step a) recites an abstract idea of mental activities.
Classifying said aligned reads into different classes comprising at least:
a first class, where said aligned reads match said one or more reference sequences without any mismatch,
a second class, where said aligned reads match a region in said one or more reference sequences with a number of mismatches constituted by a number of positions in which the sequencing machine was not able to call any base,
a third class, where said aligned reads match a region in said one or more reference sequences with a number of mismatches constituted by a number of positions in which the sequencing machine was not able to call any vase or it called a different base than the one reported in the reference genome,
a fourth class, where said aligned reads match a region in said one or more reference sequences with a number of mismatches constituted by a number of positions in which the sequencing machine was not able to call any base, or called a different base than the one reported in the reference genome and by the presence of insertions, deletions, or clipped nucleotides, and
a fifth class, where said aligned reads do not find any valid mapping on said one or more reference sequences according to specified alignment constraints, thereby creating classes of aligned reads: and
----This step equates to data observation of aligned reads followed by a decision-making (classifying, or groping the reads alignment in to five different classes). “Classifying said aligned reads into different classes” is a judgement/decision-making activity that can be performed in human mind, therefore this step is directed to an abstract idea of mental activities. The claims don't really give any information about the size of the reads or the size of the reference sequences in the claim, under a BRI and at its simplest embodiment, this job can be achieved in the human mind, with the help of a pen and paper.
Encoding said classified and aligned reads as a multiplicity of syntax elements comprising descriptors which univocally represent said classified and aligned reads,
wherein encoding said classified aligned reads as a multiplicity of syntax elements comprises selecting said syntax elements according to said classes of aligned reads,
----This step reads on an abstract idea because it is interpreted as encoding different syntax element by different algorithms (Fig. 20 step 204) and encoding is drawn to converting data by mathematical algorithms. Therefore this step equates to an abstract idea of mathematical concepts.
wherein the encoding of said classified aligned reads as a multiplicity of syntax elements is adapted according to the statistical properties of the dat
----This step reads on an abstract idea because it further limits “encoding” methods for the syntax elements is affected by the statistical properties of the data. Considering “encoding” is drawn to mathematical concepts, this step recites an abstract idea of mathematical concepts.
wherein the encoding of said classified aligned reads as a multiplicity of layers of syntax elements associates a specific source model to each
layer of the multiplicity of layers of syntax elements, and a specific entropy coder to each layer of the multiplicity of layers of syntax elements to each
element,
----This step reads on an abstract idea because it is interpreted as step 205-2015 in Figure 20. Under a BRI, “entropy coder” refers to popular coding algorithms based on the Shannon’s entropy theory, and the “entropy” refers to mathematical relationship among elements in a layer.
The entropy of the source, denoted H, is defined as:
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(hence “entropy” is defined and measured by math).
“Encoding/Decoding” is classified into abstract ideas by the Court. ("Adding one abstract idea (math) to another abstract idea (encoding and decoding) does not render the claim non-abstract"); Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016). Abstract ideas executed in the computer are still abstract ideas.
Encoding and compression of genomic sequencing reads is achievable in the human mind. For example, when the human sees a lot “A” and only a few “C” in the sequence reads, he can encode “A” using a short bit (such as “1” and encode “C” using a long bit (such as “110”). This all can be achieved in the human mind, with perhaps the aid of a pen and paper. Computer can expedite this process with high accuracy, but that does not change the characteristics that encoding is an abstract idea.
As discussed in above two “wherein” clauses, this is another step of “encoding” and “encoding” is drawn to mathematical concepts. Hence this step recites an abstract idea of mathematical concepts.
and the selection of each of the specific source models and each of the specific entropy coders is based on encoding data in each of the layers of the
multiplicity of layers of syntax elements to reduce a source entropy of each layer,
----This step reads on an abstract idea because it further limits the previous “wherein” clause. Under a BRI, “entropy coders” refers to popular coding algorithms based on the Shannon’s entropy theory and the “entropy” refers to mathematical relationship among elements in a layer. “Entropy coders” are drawn to mathematical concepts. Hence this step recites an abstract idea of mathematical concepts. Further, encoding and compression of genomic sequencing reads is achievable in the human mind. For example, when the human sees a lot “A” and only a few “C” in the sequence reads, he can encode “A” using a short bit (such as “1” and encode “C” using a long bit (such as “110”). This all can be achieved in the human mind, with perhaps the aid of a pen and paper. Computer can expedite this process with high accuracy, but that does not change the characteristics that encoding is an abstract idea. Additionally, “encoding” is classified into abstract ideas by the Court. ("Adding one abstract idea (math) to another abstract idea (encoding and decoding) does not render the claim non-abstract"); Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016). Abstract ideas executed in the computer are still abstract ideas.
wherein there is decomposition of the sequence read data and metadata into homogeneous syntax elements in order to obtain distinct information sources with reduced information entropy.
----This step reads on an abstract idea because it is interpreted as data manipulation (“decomposition of the sequence read data and metadata into homogeneous syntax elements”) in order to draw some conclusion easily. This step reads on a judgement/decision-making activity following a data re-formatting and observation. The processes can be achieved in human mind. Therefore, this step equates to an abstract idea of mental processes.
----“Encoding” under a BRI, this step equates to a conditional data manipulation that convert data from one format into another according to mathematical algorithms (here “specific entropy coders”). The conditions reads on data observation. Therefore this comprehensive step recites abstract ideas of mental activities and mathematical concepts.
Claim 5 recites:
Parsing said compressed genomic stream to obtain multiple blocks of descriptors, said descriptors being representative of a classification of said reads based on specific matching rules that match said reads with one or more reference sequences;
----According to Figure 21, “parsing said compressed genomic stream” steps on data decoding, which is the opposite of data encoding (here the “entropy decoder”). Under a BRI, data decoding follows the mathematical operation applied by data encoding. Therefore, this step equates to abstract ideas of mathematical concepts.
Expanding said blocks of descriptors into classified reads of sequences of nucleotides based on the following classes according to specific matching rules defining the classification of the reads with respect to the one or more reference sequences:
a first class, wherein reads of this class match the one or more reference sequences without any mismatch,
----This step reads on an abstract idea because it reads on data observation of the first class reads that can be achieved in human mind. Therefore step equates to an abstract idea of mental processes.
a second class, wherein reads of this class match a region in the one or more reference sequences with a number of mismatches constituted by a number of positions in which a sequencing machine was not able to call any base,
----This step reads on an abstract idea because it reads on data observation of the second class reads that can be achieved in human mind. Therefore step equates to an abstract idea of mental processes.
a third class, wherein reads of this class match a region in said one or more reference sequences with a number of mismatches constituted by a number of positions in which a sequencing machine was not able to call any base or it called a different base than the one reported in the reference genome,
----This step reads on an abstract idea because it reads on data observation of the third class reads that can be achieved in human mind. Therefore step equates to an abstract idea of mental processes.
a fourth class, wherein reads of this class match a region in one or more reference sequences with a number of mismatches constituted by a number of positions in which a sequencing machine was not able to call any base, or called a different base than the one reported in a reference genome and by the presence of insertions, deletions, or clipped nucleotides, and
----This step reads on an abstract idea because it reads on data observation of the fourth class reads that can be achieved in human mind. Therefore step equates to an abstract idea of mental processes.
a fifth class, wherein reads of this class do not find any valid mapping on one or more reference sequences according to specified alignment constraints, and
----This step reads on an abstract idea because it reads on data observation of the fifth class reads that can be achieved in human mind. Therefore step equates to an abstract idea of mental processes.
---- According to Figure 21, “expanding said blocks of descriptors into classified reads of sequences of nucleotides” steps on layered decoding by layered “decoder”. “Decoder” encompasses mathematical algorithms. “According to specific matching rules defining the classification of the reads with respect to the one or more reference sequences” reads on a decision-making activity based on data observation. Therefore, this step recites abstract ideas of mathematical concepts and mental processes.
Selectively decoding said classified reads of sequences of nucleotides so as to obtain uncompressed reads of sequences of nucleotides, wherein said decoding comprises associating a specific source model and a specific entropy decoder to each block of descriptors.
wherein the selection of the specific source model and the specific entropy decoder is based on genomic layer data contained in each of the classified reads of sequences of nucleotides to reduce a source entropy of each genomic layer.
---- According to Figure 21 and under a BRI, “Selectively decoding said classified reads of sequences of nucleotides so as to obtain uncompressed reads of sequences of nucleotides” steps on data decoding by various classes (here “specific entropy decoder”). Under a BRI, “entropy decoder” refers to popular decoding algorithms based on the Shannon’s entropy theory and the “entropy” refers to mathematical relationship among elements in a layer. Therefore this step recites abstract ideas of mathematical concepts. Additionally, “decoding” is classified into abstract ideas by the Court. ("Adding one abstract idea (math) to another abstract idea (encoding and decoding) does not render the claim non-abstract"); Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016). Abstract ideas executed in the computer are still abstract ideas.
Claim 6 recites:
An aligner unit, configured to align said reads to one or more reference sequences thereby creating aligned reads.
----“To align said reads to one or more reference sequences” is an operation to align two sequences by similarity, usually the reference sequence is on the upper line and the sequence read is in the lower line. This can be achieved by a human being with the help of a pen and paper. Therefore this claim equates to an abstract idea of mental processes.
a data classification unit, configured to classify said aligned reads into different classes comprising at least:
a first class, where said aligned reads match said one or more reference sequences without any mismatch,
This step reads on an abstract idea because it reads on data observation of the first class reads that can be achieved in human mind. Therefore step equates to an abstract idea of mental processes.
a second class, where said aligned reads match a region in said one or more reference sequences with a number of mismatches constituted by a number of positions in which the sequencing machine was not able to call any base,
This step reads on an abstract idea because it reads on data observation of the second class reads that can be achieved in human mind. Therefore step equates to an abstract idea of mental processes.
a third class, where said aligned reads match a region in said one or more reference sequences with a number of mismatches constituted by a number of positions in which the sequencing machine was not able to call any vase or it called a different base than the one reported in the reference genome,
This step reads on an abstract idea because it reads on data observation of the third class reads that can be achieved in human mind. Therefore step equates to an abstract idea of mental processes.
a fourth class, where said aligned reads match a region in said one or more reference sequences with a number of mismatches constituted by a number of positions in which the sequencing machine was not able to call any base, or called a different base than the one reported in the reference genome and by the presence of insertions, deletions, or clipped nucleotides, and
This step reads on an abstract idea because it reads on data observation of the fourth class reads that can be achieved in human mind. Therefore step equates to an abstract idea of mental processes.
a fifth class, where said aligned reads do not find any valid mapping on said one or more reference sequences according to specified alignment constraints, thereby creating classes of aligned reads; and
This step reads on an abstract idea because it reads on data observation of the fifth class reads that can be achieved in human mind. Therefore step equates to an abstract idea of mental processes.
----This step in summary equates to data observation to the reads alignments, then make a decision (assign a number to the alignment class). Classifying of aligned reads into different classes is a judgement/decision-making activity that can be performed in human mind. Hence this step is an abstract idea of mental activities.
One or more encoding units, configured to encode said classified aligned reads as syntax elements comprising descriptors which univocally represent said classified and aligned reads by selecting said syntax elements according to said classes of aligned reads,
wherein the encoding of said classified aligned reads as a multiplicity of syntax elements is adapted according to the statistical properties of the data carried by the element,
This step reads on an abstract idea because it further limits “encoding” methods for the syntax elements is affected by the statistical properties of the data. Considering “encoding” is drawn to mathematical concepts, this step recites an abstract idea of mathematical concepts. Further, encoding and compression of genomic sequencing reads is achievable in the human mind. For example, when the human sees a lot “A” and only a few “C” in the sequence reads, he can encode “A” using a short bit (such as “1” and encode “C” using a long bit (such as “110”). This all can be achieved in the human mind, with perhaps the aid of a pen and paper. Computer can expedite this process with high accuracy, but that does not change the characteristics that encoding is an abstract idea.
Additionally, “encoding” is classified into abstract ideas by the Court. ("Adding one abstract idea (math) to another abstract idea (encoding and decoding) does not render the claim non-abstract"); Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016). Abstract ideas executed in the computer are still abstract ideas.
wherein the encoding of said classified aligned reads as a multiplicity of syntax elements associates a specific source model and a specific entropy coder to each element,
----This step reads on an abstract idea because it is interpreted as steps 205-2015 in Figure 20. Under a BRI, “entropy coder” refers to popular coding algorithms based on the Shannon’s entropy theory and the “entropy” refers to mathematical relationship among elements in a layer. As discussed in above “wherein” clauses, this is another step of “encoding” and “encoding” is drawn to mathematical concepts. Hence this step recites an abstract idea of mathematical concepts.
“Encoding” is classified into abstract ideas by the Court. ("Adding one abstract idea (math) to another abstract idea (encoding and decoding) does not render the claim non-abstract"); Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016). Abstract ideas executed in the computer are still abstract ideas.
wherein there is decomposition of the sequence read data and metadata into homogeneous syntax elements in order to obtain distinct information sources with reduced information entropy.
This step reads on an abstract idea because it is interpreted as data manipulation (“decomposition of the sequence read data and metadata into homogeneous syntax elements”) in order to draw some conclusions easily. This step reads on a judgement/decision-making activity following a data re-formatting and observation. The processes can be achieved in human mind. Therefore, this step equates to an abstract idea of mental processes.
----To summary this bid step, “to encode said classified aligned reads as syntax elements comprising descriptors” steps on mathematical operations according to algorithm. “Selecting said syntax elements according to said classes of aligned reads” reads on a decision-making process based on data observation. Hence this step is directed to abstract ideas of mathematical concepts and mental processes.
Step 2A Prong Two: Consideration of Practical Application
The claims result in a process of selectively encoding/decoding classified reads sequence data, which reads on mathematical concepts. The claims do not recite any additional elements that integrate the abstract idea/judicial exception into a practical application.
This judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
an additional element effects a transformation or reduction of a particular article to a different state or thing; and
an additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than
a drafting effort designed to monopolize the exception.
Step 2B: Consideration of Additional Elements and Significantly More
The claimed method also recites "additional elements" that are not limitations drawn to an abstract idea. The recited additional elements are drawn to:
A computer (claims 1, 5);
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because “a computer” is an additional element, but it is required for the program to execute. It is insignificant as it merely provides an environment to execute the abstract idea (MPEP §2106.06(f)).
The claims do not include additional elements that are sufficient to amount of significantly more than the judicial exception because it is routine and conventional to perform the acts of manipulating sequence data using a computer. A recitation of generic computer structure that serves to perform generic computer functions that are well-understood, routine, and conventional activities previously known to the pertinent industry. Viewed as a whole, these additional claim element(s) do not provide meaningful limitation(s) to transform the abstract idea recited in the instantly presented claims into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself. Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
Hence the JEs are not integrated into something significantly more in Step 2B.
Hence the 101 rejection is maintained.
Response to Applicant’s Argument
In the Remarks filed 4 June 2026, Applicant argued (page 8-9, the connection para) that “claims must be examined in their entirety in view of the specification, and should not be deconstructed or described at such a high level of abstraction that it ensures patent ineligibility”; and (page 10, 2nd para) “the Patent Office must find that the claims as a whole are directed to an abstract idea. It is not enough to find that a claim involves an abstract idea. Rather, the claim as a whole must directed to an abstract idea. As set forth in MPEP § 2106.04(II)(A)(1)”.
In response, Applicant’s arguments are not persuasive. Claims did receive examinations in their entirety in view of the specification. The MPEP protocol ensures that claims are examined “as a whole” with consideration under Step 2A/Prong two and Step 2B. As a whole, claim reads on data manipulations (compression and decompression) without being applied in an additional element so that the additional element captures and reflects any technical merits resulted from the data manipulation, or the claims recite data manipulations (compression and decompression) without significantly more. The claims hence, as a whole, not eligible under 35 U.S.C. 101.
In the Remarks, Applicant argues (page 10, last para through page 12, 1st para) that “the human mind cannot comprise or mimic an entropy encoder (or an entropy decoder). A mental process is one that can be practically performed in the human mind. Here, the steps of ‘encoding said classified and aligned reads as a multiplicity of layers of syntax elements comprising descriptors which univocally represent said classified and aligned reads’".
In response, Applicant’s argument is not persuasive. An entropy encoder reads on an abstract idea because the conditional part (classification into five different layers based on the alignment results when “where said aligned reads” match one of the five conditions) reads on the human judgement or decision-making (to go into one of the five layers), which is a mental process; while the entropy encoding (or decoding) part reads on mathematical algorithms hence this part is classified into mathematical concepts. As a whole, an entropy encoder reads on an abstract idea. Applicant ignored the mathematical part and mixed the mathematical part with the human mental activity part when arguing “the human mind does not encode and compress genomic sequencing reads into multiplicity of layers of syntax elements” and “the human mind is not an entropy encoder or decoder”. Further, encoding and compression of genomic sequencing reads is achievable in the human mind. For example, when the human sees a lot “A” and only a few “C” in the sequence reads, he can encode “A” using a short bit (such as “1” and encode “C” using a long bit (such as “110”). This all can be achieved in the human mind, with perhaps the aid of a pen and paper. Computer can expedite this process with high accuracy, but that does not change the characteristics that encoding is an abstract idea.
Additionally, “Encoding/Decoding” is classified into abstract ideas by the Court. ("Adding one abstract idea (math) to another abstract idea (encoding and decoding) does not render the claim non-abstract"); Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016). Abstract ideas executed in the computer are still abstract ideas.
In the Remarks, Applicant argues (page 12, 2nd para through page 12, 1st para) that “human information compression does occur, but it is fundamentally semantic rather than entropic”; “human cognition relies on heuristics, contextual judgment, and approximation rather than exact probability calculation”; and “the computational demands of entropy encoding also exceed the limits of human cognitive architecture.”
In response, Applicant’s arguments are not persuasive. The first two arguments are falling far away from the claim limitations. The application of computers in entropy encoding does not change the fact that entropy encoding reads on abstract ideas.
Entropy Coding (EC) encompasses a whole series of coding techniques that exploit the statistical redundancy in data with the ultimate goal of finding, without losing information, a more compact representation. EC is related to the definition of entropy in the context of the Information Theory In this field, the entropy quantifies the average amount of information represented by a data set, so that the higher the entropy, the better the efficiency of such representation.
The entropy of the source, denoted H, is defined as:
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(hence “entropy” is defined and measured by math).
“Encoding” is classified into abstract ideas by the Court. ("Adding one abstract idea (math) to another abstract idea (encoding and decoding) does not render the claim non-abstract"); Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016). Abstract ideas executed in the computer are still abstract ideas.
The singular purpose of computers and computer networks, is to perform large numbers of calculations, via algorithms, rapidly, and without error (assuming no error in user input). Although a general purpose computer can perform calculations at a rate and accuracy that can far outstrip the mental performance of a skilled artisan, the nature of the activity is essentially the same, and constitutes an abstract idea. See Bancorp Serves., L.L. C. v. Sun Life Assur. Co. of Canada (U.S.), 687 F.3d 1266,1278 (Fed. Cir. 2012) (holding that “the fact that the required calculations could be performed more efficiently via a computer does not materially alter the patent eligibility of the claimed subject matter”); see also See SiRF Tech., Inc. v. Int’l Trade Comm ’n, 601 F.3d 1319,1333 (Fed. Cir. 2010) (holding that: In order for the addition of a machine to impose a meaningful limit on the scope of a claim, it must play a significant part in permitting the claimed method to be performed, rather than function solely as an obvious mechanism for permitting a solution to be achieved more quickly, i.e., through the utilization of a computer for performing calculations).
In the Remarks, Applicant argues (page 12, last para through page 17, 2nd para) that “the claims as a whole are not directed to a mathematical concept”. Further, Applicant compared examples 38, 39 and 41 in details to the current claims, with the following request (page 16, 3rd para):
“Notably, these Examples have not been withdrawn or revised by the Patent Office, and thus still serve as Examples upon which Applicants can rely when interpreting 35 U.S.C. § 101 and MPEP § 2106.04(a)(2). These Examples must therefore be harmonized with the guidance set forth in MPEP § 2106.04(a)(2), and must be considered when analyzing the present claims.
In response, Applicant’s argument is not persuasive. Regarding Examples 38/39, the claims are not reciting a judicial exception. The reasoning was that the claims may involve mathematical concepts, but they do not themselves set forth a mathematical formula, calculation, or mental process in the claim. A claim that merely involves a judicial exception may be eligible without further eligible analysis.
The instant claims 1, 5 and 6 are different from the data types in Examples 38/39. In Example 38, the data is binary data about analog audio signals. The datatype is not for the human to read, and to think upon. In Example 39, the datatype is binary image file, again a datatype not for the human to read and to think upon. As to the instant claims, the datatype is genomic sequence and sequence alignments, a datatype that is traditionally readable and thinkable, judgeable.
In Examples 38/39, the claims are short, the two claims merely involve judicial exceptions and hence are eligible without further eligible analysis. However, instant claims 1, 5 and 6 are long. Words like “aligning said reads to one or more reference sequences”, “statistical properties of the data”, “entropy coder”, “encoding data in each of the layers”, “decomposition of the sequence read data and metadata into homogeneous syntax elements”, “reduced information entropy” are dispersed everywhere in the claims. “Entropy” refers to mathematical relationship among elements in a layer. Limitation like “reduce a source entropy of each layer” and “reduce information entropy”, are interpreted as mathematical operations to compare the mathematical calculation results (of entropy) from different status (of compression).
It is important to note that a mathematical concept need not be expressed in mathematical symbols, because "[w]ords used in a claim operating on data to solve a problem can serve the same purpose as a formula." In re Grams, 888 F.2d 835, 837 and n.1, 12 USPQ2d 1824, 1826 and n.1 (Fed. Cir. 1989). See, e.g., SAP America, Inc. v. InvestPic, LLC, 898 F.3d 1161, 1163, 127 USPQ2d 1597, 1599 (Fed. Cir. 2018) (holding that claims to a ‘‘series of mathematical calculations based on selected information’’ are directed to abstract ideas); Digitech Image Techs., LLC v. Elecs. for Imaging, Inc., 758 F.3d 1344, 1350, 111 USPQ2d 1717, 1721 (Fed. Cir. 2014) (holding that claims to a ‘‘process of organizing information through mathematical correlations’’ are directed to an abstract idea); and Bancorp Servs., LLC v. Sun Life Assurance Co. of Can. (U.S.), 687 F.3d 1266, 1280, 103 USPQ2d 1425, 1434 (Fed. Cir. 2012) (identifying the concept of ‘‘managing a stable value protected life insurance policy by performing calculations and manipulating the results’’ as an abstract idea).
Instant claims 1, 5 and 6 hence are not merely involving a judicial exception, they recite judicial exceptions, in both the mental process grouping and the mathematical concept grouping, as discussed above in the 101 analysis.
In a summary, Examples 38/39 are just short exemplary claims, they are not analogous to the current claims. Claims 1, 5 and 6 do recite judicial exceptions at Step 2A/Prong one.
In the Remarks, Applicant argues (page 17, paras 3-4) that “applicant affirms the conclusion above that the claims are not directed to a judicial exception, and respectfully asserts that the claims do indeed incorporate any judicial exception into a practical application. Even assuming, arguendo, that the claims are directed to an abstract idea, the elements of the independent claims integrate the exception into a practical application.”
In response, Applicant’s argument refers to Step 2A/Prong two, relating to whether claims are integrated into a practical application or not. To integrated into a practical application, additional elements are needed that apply, capture and reflect the JEs. However, Applicant does not provide additional elements. Therefore, Applicant’s argument is not persuasive.
In the Remarks, Applicant argues (page 17, last para through page 19, 2nd para) that “applicant submits that claims 1, 5, and 6 recite additional elements (wherein the claims are to be analyzed individually and as a whole) that amount to ‘significantly more’ than the alleged judicial exception as indicative of an inventive concept that involves more than performance of well-understood, routine, and conventional activities.”
In response, Applicant’s argument is not persuasive. Applicant seems arguing over Step 2B in the 101 analysis, but uses evidence of “improvement” (page 18, 1st para through page 19, 3rd para). (Technological) improvement is an evidence weighted at Step 2A/Prong two.
In the Remarks, Applicant argues (page 19, last para through page 20, 1st para) that “such an allegation is an oversimplification of the recitations of claims 1, 5, and 6, and fails to account for the numerous additional structural elements recited in each of the claims”.
In response, Applicant’s argument is not persuasive. The listed additional elements, such as (page 20, 1st para) “various entropy coders, such that ‘each of the layers of the multiplicity of layers of syntax elements’ are associated with a specific entropy coder” are not additional elements. “Entropy coders” read on functional software units, and “layers of syntax elements” reads on data. There is nothing significantly more than the JEs at Step 2B.
Therefore, the 101 rejection is maintained.
Conclusion
No claims are allowed.
All claims are identical to, patentably indistinct from, or have unity of invention with the claims in the application prior to the entry of the submission under 37 CFR 1.114 (that is, restriction (including a lack of unity of invention) would not be proper) and all claims could have been finally rejected on the grounds and art of record in the next Office action if they had been entered in the application prior to entry under 37 CFR 1.114. Accordingly, THIS ACTION IS MADE FINAL even though it is a first action after the filing of a request for continued examination and the submission under 37 CFR 1.114. See MPEP § 706.07(b). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
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/GL/
Patent Examiner
Art Unit 1686
/Anna Skibinsky/
Primary Examiner, AU 1635
Prosecution Insights