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 .
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Claims 9-11 are withdrawn;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 directed to a process, here “a computer-implemented method” for compression of genome sequence data, with process steps like “aligning…”, “classifying …”, and “encoding …”.
Claims 5, 7-8, 13, 15, 17 and 19-20 are directed to another process, here “a computer-implemented method” for decompression of a genomic stream, with process steps "parsing …”, “expanding …”, and “decoding …”.
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 particular physical structure such as a machine (A machine is a "concrete thing, consisting of parts, or of certain devices and combination of devices." MPEP $2106.03) or 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).
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. 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.
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. 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. “Entropy coders” are drawn to mathematical concepts. Hence this step recites an abstract idea of mathematical concepts.
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. Therefore this step recites abstract ideas of mathematical concepts.
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.
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. 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.
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 21 October 2025, Applicant argued (page 10, penultimate para through page 11, 2nd para) that claims 1, 5, and 6 do not recite abstract ideas of mental process or mathematical concepts. Applicant’s argument refers to Step 2A/Prong One in the 101 analysis, the argument is not persuasive. Even the genomic sequence data is generated by sequencing machine, it is readable, align-able, and comparable by human mind. For example, human mind is equipped to align one read sequence to a reference sequence; classifying the reads into five different classes based on the alignment situations is a classic human decision-making activity. Computer do speed up such a process but an abstract idea executed in the computer is still an abstract idea. The claims as whole, or considered individually, recite data analysis/data manipulation that are achievable in human mind and is hence directed to abstract ideas of mental processes.
In the Remarks, Applicant argued (page 11, 3rd para through page 12, 2nd para) ) that claims 1, 5, and 6 recite improvements to the method of encoding and decoding of genomic sequence data.
In response, Applicants argue that the instant claims are directed to an improvement to the encoding and decoding of genomic sequence data. However, encoding and decoding of genomic sequence data are directed to abstract ideas. An abstract idea may be improved however, an improved abstract idea is not deemed an improvement to technology unless it is applied to an additional element or improves the functioning of a computer. Here however, the computer is used as tool to transform one form of data into another form of data through math. This process is an abstract idea. The function of the computer is not changed. Furthermore, Applicant’s argument refers to Step 2A/Prong Two in the 101 analysis, relating to whether claims are integrated into a practical application due to a technological improvement or not. The argument is not persuasive. At Step 2A/Prong Two, Additional elements are searched because adding one abstract idea (a mental process) to another abstract idea (encoding and decoding) does not render the claim non-abstract. Instead, a technical improvement is furnished by an additional element or combination of additional elements that is recited in the claims in addition to (beyond) the judicial exception. In the instant claims, what achieved is perhaps a better data encoding/decoding, which is drawn to abstract ideas, because encoding and decoding of genomic sequence data rely on mathematical algorithms (such as the Entropy coder/decoder). The only additional element identified is “a computer”. “A computer” does not capture or reflect any potential technical improvement in a meaningful way, because using generic computer for data analysis is well-known and routine extra-solution activity (MPEP §2106.06(f-g)).
In the Remarks, Applicant argued (page 12, 3rd para through page 15, 1st para) that claims 1, 5, and 6 recite improvements to the method of encoding and decoding of genomic sequence data. Applicant’s argument refers to Step 2A/Prong Two or Step 2B in the 101 analysis, and the argument is not persuasive. At Step 2A/Prong Two or Step 2B in the 101 analysis, the focus is whether the claims as a whole, integrated into a practical application or the claims are significantly more than judicial exceptions. Detailed analysis of elements in Step 2A/Prong One is for better reference to Applicant. The instant claims do recite improvements, but the improvements (“without substantial redundancy improves system operating efficiency and reduce storage costs”) are not used by, captured by, or reflected in additional elements. The alleged improvement is perhaps a better data encoding/decoding of genomic data, which is drawn to abstract ideas, because encoding and decoding of genomic sequence data rely on mathematical algorithms (such as the Entropy coder/decoder). Computing is the conventional and well-known way to speed up data analysis and data manipulations. To qualify as “a patent- eligible improvement,” the invention must be directed to a specific improvement in the computer’s functionality, not simply to use of the computer “as a tool” to implement an abstract idea. Customedia Techs., LLC v. Dish Network Corp., 951 F.3d 1359, 1363-1364 (Fed. Cir. 2020). Here, the invention falls into the latter category. It focuses on using a general purpose computer to carry out the abstract ideas. Consequently, we do not discern an inventive concept in how the computer system operates.
The emphasized parts regarding paragraphs [011, 014-018] (page 13) tries to justify a case of technical improvement, but is not persuasive. There are “layers of syntax elements” (claims 1 and 6) but a data structure is not clearly claimed.
The alleged improvement over digital data compression (MPEP §2106.05(a)(II)(iv)) is not persuasive. There is simplify no improvement to any additional elements. The comparison to Berkheimer is not a good comparison as the claimed technical improvement is not realized in any additional elements in the instant claims.
Applicants argue (page 14, par. 3) that the claims are similar to those in the
Berkheimer memo and relate to improvements to computer speed, efficiency, and
resource usage for storing representation of genome sequence data. Applicants argue
that a data structure that improves performance as disclosed herein in concert with the claimed embodiments is patent eligible.
To response, Applicant’s argument is not persuasive. Again, this argument refers to Step 2A/Prong two in the 101 analysis. A data structure is not clearly claimed. “Improvements to computer speed, efficiency, and resource usage” is not claimed either. The “layers of syntax elements” (claims 1 and 6) and the associated classifying or encoding/decoding operations, render the claimed element to be classified into abstract ideas of mental processes or mathematical concepts. Therefore the alleged improvements are not captured and reflected in an additional element, and hence there is integration into a practical application.
Applicants argue (page 15, par. 1) that Examiner “fails to account for the numerous additional structural elements recited in each of the claims which allow the claims to achieve the technological benefits in decoding specific data types described hereinabove. For example, independent claim 1 recites various entropy coders, such that "each of the layers of the multiplicity of layers of syntax elements" are associated with a specific entropy coder. The entropy coders recited in independent claim 1 are similarly recited in independent claims 5 and 6, and enable the compression benefits
described hereinabove.”
To response, Applicant’s argument refers to Step 2A/Prong one in the 101 analysis. This argument is not persuasive. “Entropy encoders” are not additional elements. Instead, it is directed to abstract ideas of mathematical concepts. “Additional structural elements” is a misunderstanding to “additional elements” in the 101 analysis. “Additional elements” don’t need be structural. They are the opposite of “abstract ideas”.
In the Remarks, Applicant argued (page 15, 2nd~3rd paras) over the recently released guidance (Ex parte Desjardins, Director Squires emphasized "that §§ 102, 103 and 112 are the traditional and appropriate tools to limit patent protection to its proper scope"), the argument is not specific to be persuasive. Even if the 101 rejection is not stressed in the list, 101 analysis is still required by the MPEP guidance.
Therefore, the 101 rejection is maintained.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/GL/
Patent Examiner
Art Unit 1686
/Anna Skibinsky/
Primary Examiner, AU 1635