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 .
Status of Claims
Claims 9-14, 23, 26, and 19-119 have been cancelled; therefore, Claims 1-8, 15-22, 24-25, and 27-28 are currently pending in application 18/657,618.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 8/1/2024 (2), 10/18/2024, and 11/25/2025 are compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Rejections – 35 USC §101
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, 15-22, 24-25, and 27-28 are rejected under 35 U.S.C. § 101 because the claimed invention is directed to non-statutory subject matter, specifically an abstract idea.
Claims 1-8, 15-22, 24-25, and 27-28 are directed to a judicial exception (i.e., abstract idea), without providing a practical application, and without providing significantly more.
Under the 35 U.S.C. §101 subject matter eligibility two-part analysis, Step 1 addresses whether the claim is directed to one of the four statutory categories of invention, i.e., process, machine, manufacture, or composition of matter. See MPEP §2106.03. If the claim does fall within one of the statutory categories, it must then be determined in Step 2A [prong 1] whether the claim is directed to a judicial exception (i.e., law of nature, natural phenomenon, and abstract idea). See MPEP §2106.04. If the claim is directed toward a judicial exception, it must then be determined in Step 2A [prong 2] whether the judicial exception is integrated into a practical application. See MPEP §2106.04(d). Finally, if the judicial exception is not integrated into a practical application, it must additionally be determined in Step 2B whether the claim recites "significantly more" than the abstract idea. See MPEP §2106.05.
Examiner note: The Office’s 2019 Revised Patent Subject Matter Eligibility Guidance (2019 PEG) is currently found in the Ninth Edition, Revision 10.2019 (revised June 2020) of the Manual of Patent Examination Procedure (MPEP), specifically incorporated in MPEP §2106.03 through MPEP §2106.07(c).
Regarding Step 1,
Claims 1-8, 15-22, 24-25, and 27-28 are directed toward a process (method). Thus, all claims fall within one of the four statutory categories as required by Step 1.
Regarding Step 2A [prong 1],
Claims 1-8, 15-22, 24-25, and 27-28 are directed toward the judicial exception of an abstract idea. Independent claim 1 is directed specifically to the abstract idea of data analysis.
Regarding independent claim 1, the underlined limitations emphasized below correspond to the abstract ideas of the claimed invention:
A computer-implemented method for classifying analyte data into clusters, the method comprising, via a processor:
applying a regression model to determine a relationship between an initial set of analyte features and a cluster criterion; [Mathematical Concept (specifically, a mathematical algorithm or calculation) and a Mental Process (performing a regression analysis to determine relationships is fundamentally a calculation that can be performed in the human mind or with a pen and paper)]
generating a sparse set from at most a portion of the initial set of the analyte features based on the relationship; [Mathematical Concept and a Mental Process (educing data to a smaller subset based on math or a process a human could perform in their head)]
generating a classification model based on the sparse set; and [Mathematical Concept and a Mental Process (Constructing a classification model based on selected parameters is a process of organizing, manipulating, and applying mathematical relationships)]
applying the classification model to classify the analyte data into the clusters. [Mathematical Concept (Mathematical evaluation - using a learned model to group or classify data is purely an intellectual or mathematical act) and a Mental Process (Classifying information or sorting data; an activity traditionally performed by a human mind)]
As the underlined claim limitations above demonstrate, independent claim 1 are directed to the abstract idea of Mathematical concepts (mathematical relationships, mathematical formulas or equations, mathematical calculations); Mental processes (concepts performed in the human mind (including an observation, evaluation, judgment, or opinion)); and Certain methods of organizing human activity (fundamental economic principles or practices (including hedging, insurance, mitigating risk); commercial or legal interactions (including agreements in the form of contracts; legal obligations; advertising, marketing or sales activities or behaviors; business relations); managing personal behavior or relationships or interactions between people (including social activities, teaching, and following rules or instructions)).
Dependent claims 2-8, 15-22, 24-25, and 27-28 provide further details to the abstract idea of claim 1 regarding the received data, therefore, these claims include mathematical concepts, mental processes, and certain methods of organizing human activities for similar reasons provided above for claim 1.
After considering all claim elements, both individually and in combination and in ordered combination, it has been determined that the claims do not amount to significantly more than the abstract idea itself.
Regarding Step 2A [prong 2],
Claims 1-8, 15-22, 24-25, and 27-28 fail to integrate the recited judicial exception into any practical application. The claims recite additional limitations which are hardware or software elements or particular technological environment, such as a “computer” and a “processor. However, these limitations are not enough to qualify as “practical application” being recited in the claims along with the abstract idea since these limitations are merely invoked as a tool to perform instruction of an abstract idea in a particular technological environment and/or are generally linking the use of the abstract idea to a particular technological environment or field of use, and merely applying and abstract idea in a particular technological environment and merely limiting use of an abstract idea to a particular field or a technological environment do not provide practical application for an abstract idea (MPEP 2106.05 (f) & (h)). The claims do not amount to "practical application" for the abstract idea because they neither (1) recite any improvements to another technology or technical field; (2) recite any improvements to the functioning of the computer itself; (3) apply the judicial exception with, or by use of, a particular machine; (4) effect a transformation or reduction of a particular article to a different state or thing; (5) provide other meaningful limitations beyond generally linking the use of the judicial exception to a particular technological environment.
The relevant question under Step 2A [prong 2] is not whether the claimed invention itself is a practical application, instead, the question is whether the claimed invention includes additional elements beyond the judicial exception that integrate the judicial exception into a practical application by imposing a meaningful limit on the judicial exception. This is not the case with Applicant’s claimed invention. Automating the recited claimed features as a combination of computer instructions implemented by computer hardware and/or software elements as recited above does not qualify an otherwise unpatentable abstract idea as patent eligible. Examples where the Courts have found selecting a particular data source or type of data to be manipulated to be insignificant extra-solution activity include selecting information, based on types of information and availability of information in a power-grid environment, for collection, analysis and display, Electric Power Group, LLC v. Alstom S.A., 830 F.3d 1350, 1354-55, 119 USPQ2d 1739, 1742 (Fed. Cir. 2016); Applicant’s limitations as recited above do nothing more than supplement the abstract idea using additional hardware/software computer components as a tool to perform the abstract idea and generally link the use of the abstract idea to a technological environment, which is not sufficient to integrate the judicial exception into a practical application since they do not impose any meaningful limits. Dependent claims 2-8, 15-22, 24-25, and 27-28 merely incorporate the additional elements recited above, along with further embellishments of the abstract idea of independent claims respectively, but these features only serve to further limit the abstract idea of independent claims. Therefore, the additional elements recited in the claimed invention individually, and in combination fail to integrate the recited judicial exception into any practical application.
Regarding Step 2B,
Claims 1-8, 15-22, 24-25, and 27-28 fail to amount to “significantly more” than an abstract idea. The claims recite additional limitations which are hardware or software elements or particular technological environment, such as a “computer” and a “processor. However, these limitations are not enough to qualify as “significantly more” being recited in the claims along with the abstract idea since these limitations are merely invoked as a tool to perform instruction of Abstract idea in a particular technological environment and/or are generally linking the use of the abstract idea to a particular technological environment or field of use, and merely applying and abstract idea in a particular technological environment and merely limiting use of an abstract idea to a particular field or a technological environment do not provide significantly more to an abstract idea (MPEP 2106.05(f) & (h)). The claims do not amount to "significantly more" than the abstract idea because they neither (1) recite any improvements to another technology or technical field; (2) recite any improvements to the functioning of the computer itself; (3) apply the judicial exception with, or by use of, a particular machine; (4) effect a transformation or reduction of a particular article to a different state or thing; (5) add a specific limitation other than what is well-understood, routine and conventional in the field; (6) add unconventional steps that confine the claim to a particular useful application; nor (7) provide other meaningful limitations beyond generally linking the use of the judicial exception to a particular technological environment.
Dependent claims 2-8, 15-22, 24-25, and 27-28 merely recite further additional embellishments of the abstract idea of independent claim 1, but these features only serve to further limit the abstract idea of independent claim 1; however, none of the dependent claims recite an improvement to a technology or technical field or provide any meaningful limits. The addition of another abstract concept to the limitations of the claims does not render the claim other than abstract. Under the Interim Guidance on Patent Subject Matter Eligibility (PEG 2019), it specifically states that narrowing an abstract idea of claims do not resolve the claims of being "significantly more" than the abstract idea. Thus, the additional elements in the dependent claims only serve to further limit the abstract idea utilizing the computer components as a tool and/or generally link the use of the abstract idea to a particular technological environment.
Therefore, since there are no limitations in the claims 1-8, 15-22, 24-25, and 27-28 that transform the exception into a patent eligible application such that the claims amount to significantly more than the exception itself, and looking at the limitations as a combination and as an ordered combination adds nothing that is not already present when looking at the elements taken individually, claims 1-8, 15-22, 24-25, and 27-28 are rejected under 35 USC § 101 as being directed to non-statutory subject matter under 35 U.S.C. § 101.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-8, 15-22, 24-25, and 27-28 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Sugimoto (US 2021/0310053 A1).
As per independent Claim 1, Sugimoto discloses a computer-implemented method (See at least Para 0115, Fig.1) for classifying analyte data (See at least Para 0005, of “nucleic acid molecules”) into clusters (See at least Para 0099, “k-means clustering” may be performed), the method comprising, via a processor:
applying a regression model (See at least Para 0099, “k-means clustering”) to determine a relationship between an initial set of analyte features and a cluster criterion (See at least Para 0099, implicit for k-means clustering);
generating a sparse set from at most a portion of the initial set of the analyte features based on the relationship (See at least Para 0099, “principal components analysis” can also be applied);
generating a classification model (See at least Para 0098, “machine learning algorithm”) based on the sparse set; and
applying the classification model to classify the analyte data into the clusters (See at least Para 0098, “The machine learning algorithm may then be applied to test images to classify a cell within a population of cells as positive or negative for the one or more features of interest”).
As per Claim 2, Sugimoto discloses wherein the analyte data is flow cytometer data (See at least Para 0091, "the cell or population of cells may be flowing (such as through or in a flow channel or flow cell)).
As per Claim 3 (2), Sugimoto discloses wherein the cluster criterion is an association of the analyte data with a singlet (See at least Para 0143, the singlet being represented by the "unaggregated proteins"; See also Fig. 4F).
As per Claim 4 (3), Sugimoto discloses wherein the clusters comprise a singlet cluster and a non-singlet cluster (See at least Para 0143, showing "classification of cells with unaggregated proteins or aggregated proteins"; See also Fig. 4F).
As per Claim 5 (4), Sugimoto discloses wherein the non- singlet cluster comprises a doublet or an aggregate (See at least Para 0143, showing "classification of cells with unaggregated proteins or aggregated proteins"; See also Fig. 4F).
As per Claim 6 (2), Sugimoto discloses wherein the analyte features comprise a size feature, imaging feature, a scatter feature, or any combination thereof (See at least Para 0003, Imaging feature; Para 0010 and 0070, Size Feature).
As per Claim 7 (6), Sugimoto discloses wherein the analyte features comprise imaging features (See at least Para 0003).
As per Claim 8, Sugimoto discloses wherein the classification model comprises a mixture model, a density-based spatial clustering algorithm, a balanced iterative reducing and clustering using hierarchies (BIRCH) algorithm, a K-means clustering algorithm, or a spectral clustering algorithm (See at least Para 0099, “k-means clustering”).
As per Claim 15, Sugimoto discloses wherein the initial set of analyte features comprises from 5 to 20 analyte features (See at least Para 0099; and Para 0116, implicit at least for the case that "display adapters" are used).
As per Claim 16 (15), Sugimoto discloses wherein the initial set of analyte features comprises from 7 to 15 analyte features (See at least Para 0099 and Para 0116).
As per Claim 17 (16), Sugimoto discloses wherein the initial set of analyte features comprises from 9 to 11 analyte features (See at least Para 0099 and Para 0116).
As per Claim 18, Sugimoto discloses wherein the initial set of analyte features comprises 10% or more of possible analyte features (See at least Para 0099 and Para 0116).
As per Claim 19 (18), Sugimoto discloses wherein the initial set of analyte features comprises 15% or more of possible analyte features (See at least Para 0099 and Para 0116).
As per Claim 20 (19), Sugimoto discloses wherein the initial set of analyte features comprises 20% or more of possible analyte features (See at least Para 0099 and Para 0116).
As per Claim 21, Sugimoto discloses wherein the sparse set of analyte features comprises from 2 to 10 analyte features (See at least Para 0098-0099 and Para 0116).
As per Claim 22 (21), Sugimoto discloses wherein the sparse set of analyte features comprises from 2 to 5 analyte features (See at least Para 0098-0099 and Para 0116).
As per Claim 24, Sugimoto discloses wherein classifying the analyte data comprises including 90% or more of analyte data associated with the cluster criterion in a cluster associated with the cluster criterion (See at least Para 0100, implicit at least for an “accuracy of at least … 99%”).
As per Claim 25 (24), Sugimoto discloses wherein classifying the analyte data comprises including 95% or more of the analyte data associated with the cluster criterion in the cluster associated with the cluster criterion (See at least Para 0099-0100).
As per Claim 27, Sugimoto discloses wherein classifying the analyte data comprises excluding 85% or more of analyte data not associated with the cluster criterion from a cluster associated with the cluster criterion (See at least Para 0099-0100).
As per Claim 28 (27), Sugimoto discloses wherein classifying the analyte data comprises excluding 90% or more of the analyte data not associated with the cluster criterion from the cluster associated with the cluster criterion (See at least Para 0099-0100).
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 15-28 are also rejected under 35 U.S.C. 103(a) as being unpatentable over Sugimoto.
As per Claims 15-28, the claimed limitations are design choices that are known in biotechnology, bioinformatics, and biomedical Sciences (biological research, medical diagnoses and assessments of overall health and wellness of a patient); and to modify Sugimoto to incorporate the limitations would have been obvious, before the effective filing date of the claimed invention, to one of ordinary skill in the art to produce a desired result.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure can be found in the PTO-892 Notice of References Cited. The Examiner suggests the applicant review all of these documents before submitting any amendments.
TANG et al. (US 2018/0032665 A1) – Tang discloses a computer-implemented (on the "computer or programmable processor", See at least Para 0154) method for classifying analyte data into clusters, the method comprising, via a processor: applying a regression model (e.g., "DBSCAN", See at least Para 0120) to determine a relationship between an initial set of analyte features and a cluster criterion; generating a sparse set (the "reduced data set representation of the matrix", See at least Para 0007; See also Para 0197) from at most a portion of the initial set of the analyte features based on the relationship; generating a classification model (using the "one or more linear modeling analysis algorithms", See at least Para 0010) based on the sparse set; and applying the classification model to classify the analyte data into the clusters (since "determining the presence or absence of a genetic variation for the sample based on the classification", See at least Para 0010, takes place).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JONATHAN P OUELLETTE whose telephone number is (571)272-6807. The examiner can normally be reached on M-F 8am-6pm.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Lynda C Jasmin, can be reached at telephone number (571) 272-6782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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June 25, 2026
/JONATHAN P OUELLETTE/Primary Examiner, Art Unit 3629
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