DETAILED ACTION
Applicant’s response, filed Nov 7 2025, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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 .
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 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.
Claim Status
Claims 1-16 are pending.
Claims 13-16 are newly added.
Claim 10 is objected to.
Claims 1-16 are rejected.
Priority
Applicant's claim for the benefit of a prior-filed application, PCT/JP2020/030151, filed Aug 6 2020, is acknowledged.
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d) to App. No. JP2019-152592, filed Aug 23 2019. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55. Should the applicant desire to obtain the benefit of foreign priority under 35 U.S.C. 119(a)-(d), a certified English translation of the foreign priority application must be submitted. Failure to provide a certified translation may result in no benefit being accorded for the non-English application.
Accordingly, each of claims 1-16 are afforded the effective filing date of Aug 23 2019.
Specification
The amendments to the specification submitted Nov 7 2025 are accepted.
Claim Objections
The outstanding objections to the claims are withdrawn in view of the amendments submitted herein.
The claims are objected to because of the following informalities. The instant objection is newly stated and is necessitated by claim amendment.
Claim 10 recites “A storage device storing a program that, when executed by a computed…”, which should be amended to recite “computer”.
Claim Interpretation
The previous interpretation of a “calculation unit” recited in claim 2 under 35 USC 112(f) as discussed in the previous Office Action is applied to the recitation of a calculation as now recited in amended claim 1 for the same reasons.
Claim Rejections- 35 USC § 112
The outstanding rejections to the claims are withdrawn in view of the amendments submitted herein.
Claim Rejections - 35 USC § 101
The outstanding rejection of claim 10 as being directed to non-statutory subject matter from the previous Office Action are withdrawn in view of the amendments submitted herein.
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 1-16 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more. The rejection is newly stated and is based on claim amendment.
MPEP 2106 organizes judicial exception analysis into Steps 1, 2A (Prongs One and Two) and 2B as follows below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Framework with which to Evaluate Subject Matter Eligibility:
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter;
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1
With respect to Step 1: yes, claims 1-16 are directed to a device, a method, and a system i.e., a process, machine, or manufacture within the above 101 categories; [Step 1: YES for claims 1-16; See MPEP § 2106.03].
Step 2A, Prong One
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims are found to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) and mathematical concepts (in particular mathematical relationships and formulas) are as follows:
Independent claims 1 and 9-11: determining… a correspondence relationship between: a gate obtained by gate analysis of an analysis target having a plurality of attributes based on the plurality of attributes, and a cluster obtained by cluster analysis of the analysis target based on the plurality of attributes; and
displaying… the gate and the correspondence relationship between the gate and the cluster.
Dependent claims 2-8 and 13-16 recite further steps that limit the judicial exceptions in dependent claim 2 and, as such, also are directed to those abstract ideas. For example, claim 2 further limits determining and displaying the correspondence relationship; claim 3 further limits the data being analyzing to being from a plurality of cells and calculating the matching degree to using a confusion matrix; claim 4 further limits the data being analyzed to intensities corresponding to a plurality of fluorescent dyes detected from the plurality of cells labeled with the plurality of fluorescent dyes; claims 5-7 further limits calculating a matching degree with a cluster received by the reception unit for all the gates and displaying that information; claim 8 further limits calculating a matching degree for combinations of all the clusters and all the gates and displaying that information; and claims 13-16 further limits the displaying the gate.
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined to each cover performance either in the mind and/or by mathematical operation because the method only requires a user to manually calculate a matching degree and display that information. Without further detail as to the methodology involved in “determining”, “calculating”, and “displaying”, under the BRI, one may simply, for example, use pen and paper to determine a correspondence relationship between a gate and a cluster of cells by calculating a matching degree between the gate and the cluster of cells based on their fluorescent intensities and then displaying the corresponding relationship between the gate and the cluster. The display of an abstract idea (i.e., the corresponding relationship between a gate and a cluster) is considered to recite that same abstract idea (see Interval Licensing LLC v AOL, Inc., 896 F.3d 1335, 1344-45 (Fed. Cir. 2018), which recognized that information “is an intangible” and that “the collection, organization, and display of two sets of information on a generic display device is abstract absent a specific improvement to the way computers operate”).
The step of calculating a matching degree recited in the dependent claims requires a mathematical technique as the only supported embodiments, as the “calculation unit” doing the calculation invokes interpretation under 35 USC 112(f), and the specification provides a formula of precision=TP/(FP*TP) and recall=TP/(FN+TP) as the corresponding structure of the calculation unit at [0071-0072].
Therefore, claims 1 and 9-11 and those claims dependent therefrom recite an abstract idea [Step 2A, Prong 1: YES; See MPEP § 2106.04].
Step 2A, Prong Two
Because the claims do recite judicial exceptions, direction under Step 2A, Prong Two, provides that the claims must be examined further to determine whether they integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d).III).
Additional elements, Step 2A, Prong Two
With respect to the instant recitations, the claims recite the following additional elements:
Dependent claim 5: receives selection of a cluster.
The claims also include non-abstract computing and data gathering elements. For example, independent claim 1 includes an information processing device comprising a calculation unit and a display control unit that displays information on a display; dependent claim 5 includes a reception unit; independent claim 9 includes a processor and a display device; independent claim 10 includes a storage device storing a program that, when executed by a computed, is configured to cause the computer to function as a calculation unit and a display control unit that causes a display to display information; and independent claim 11 includes an information processing system comprising a measurement device including a measurement unit that irradiates a measurement target with light; detects fluorescence emitted from the measurement target; and measures a fluorescence intensity; and an information processing device including a calculation unit and a display control unit that causes a display device to display information. Dependent claim 12 further limits the measurement device to a flow cytometer.
Considerations under Step 2A, Prong Two
With respect to Step 2A, Prong Two, the additional elements of the claims do not integrate the judicial exceptions into a practical application for the following reasons. Those steps and non-directed to data gathering elements, such as “receiving” a selection as in claim 5 and the measurement device in claims 11-12, perform functions of collecting the data needed to carry out the judicial exceptions. Data gathering does not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. Data gathering steps are not sufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(g)).
Further steps directed to additional non-abstract computing elements do not describe any specific computational steps by which the “computer parts” perform or carry out the judicial exceptions, nor do they provide any details of how specific structures of the computer, such as the computer-readable recording media, are used to implement these functions. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, and therefore the claim does not integrate that judicial exceptions into a practical application. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc.… are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (MPEP 2106.05(f)). Further, the computer system contains the recited calculation unit and reception unit (i.e., software) that are used for receiving a selection of a cluster (which is a data gathering element that does not integrate the judicial exceptions), and calculating a matching degree between the gate and the cluster (which is nothing but mathematical operations). Thus, the limitations only generically link the use of the judicial exceptions to the technological environment of a computer.
The specification discloses that the technical problem addressed by the invention is that it is difficult for a user to cause two analysis results to correspond to each other at [0005], but does not provide a clear explanation for how the additional elements provide any improvements. Therefore, the additional elements do not clearly improve the functioning of a computer, or comprise an improvement to any other technical field. Further, the additional elements do not clearly affect a particular treatment; they do not clearly require or set forth a particular machine; they do not clearly effect a transformation of matter; nor do they clearly provide a nonconventional or unconventional step (MPEP2106.04(d)).
Thus, none of the claims recite additional elements which would integrate a judicial exception into a practical application, and the claims are directed to one or more judicial exceptions [Step 2A, Prong 2: NO; See MPEP § 2106.04(d)].
Step 2B (MPEP 2106.05.A i-vi)
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims, the specification as published discloses that samples may be labeled with a fluorescent dye by a known method and is not limited beyond what is known [0041; 0043], that known photodetectors may be used [0049]. The prior art review to Adan et al. (Critical Reviews in Biotechnology, 37(2):163-176; newly cited) discloses that flow cytometers are measurement devices for measuring fluorescence intensity of cells, as in claims 11-12, which are well known in the art. The entire review is relevant. Further, the courts have found that receiving and outputting data are well-understood, routine, and conventional functions of a computer when claimed in a merely generic manner or as insignificant extra-solution activity (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network), Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015), and OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, as discussed in MPEP 2106.05(d)(II)(i)). As such, the claims simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception (MPEP2106.05(d)). The data gathering steps as recited in the instant claims constitute a general link to a technological environment which is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)).
The computer-related elements or the general purpose computer recited in the claims do not rise to the level of significantly more than the judicial exception. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, which the courts have found to not provide significantly more when recited in a claim with a judicial exception (Alice Corp., 573 U.S. at 225-26, 110 USPQ2d at 1984; see MPEP 2106.05(A)). The specification as published also notes that computer processors and systems, as example, are commercially available or widely used at [0121-0128]. The additional elements are set forth at such a high level of generality that they can be met by a general purpose computer. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the judicial exceptions (see MPEP 2106.05(b)I-III).
Taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself [Step 2B: NO; See MPEP § 2106.05].
Therefore, instant claims 1-16 are not drawn to eligible subject matter as they are directed to one or more judicial exceptions without significantly more. For additional guidance, applicant is directed generally to the MPEP § 2106.
Response to Applicant Arguments
At p. 11, Applicant submits that claims 2-9 have been amended to provide significantly more than the judicial exception.
It is respectfully submitted that this is not persuasive. As set forth in the above rejection, the additional elements of the claims do not recite significantly more than the judicial exception.
Claim Rejections - 35 USC § 102
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 1-2 and 9-12 are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by Chen et al. (US 2017/0371886; newly cited). Any newly cited portions are necessitated by claim amendment.
The prior art to Chen discloses a method for identifying clusters in a dataset (abstract) by analyzing cytometry data with the aid of a computer (title). Chen teaches the instant features as follows. Instantly claimed elements which are considered to be equivalent to the prior art teachings are described in bold for all claims.
Claim 1 discloses an information processing device comprising a calculation unit and a display control unit. Claim 9 discloses a display method comprising a processor. Claim 10 discloses a storage device storing a program that, when executed by a computer, is configured to cause the computer to function as a calculation unit and a display control unit. Claim 11 discloses an information processing system comprising: a measurement device including a measurement unit that irradiates a measurement target with light, detects fluorescence emitted from the measurement target, and measures a fluorescence intensity; and an information processing device including a calculation unit and a display control unit. Claim 12, which depends on claim 11, discloses that the measurement device is a flow cytometer. Claim 9 and the calculation unit of claims 1 and 10-11 determines a correspondence relationship between a gate obtained by gate analysis of an analysis target having a plurality of attributes based on the plurality of attributes and a cluster obtained by cluster analysis of the analysis target based on the plurality of attributes. Claim 9 and the display control unit of claims 1 and 10-11 displays, on a display device, the gate and the correspondence relationship between the gate and the cluster.
Chen teaches a computer system (i.e., an information processing device, as in claims 1 and 11) configured to perform the disclosed method (i.e., a display method, as in claim 9), where the computer system includes a processor (as in claim 9), an output interface [0076] which may include a display for display the visualization of the clusters (i.e., a display control unit, as in claims 1 and 10-11) [0079], and processes implemented as modules that are executable on the computer system (i.e., a program for causing a computer to function as a display control unit, as in claim 10) [0031; 0077]. As Chen teaches flow cytometry, it is considered that Chen fairly teaches “a measurement device including a measurement unit that irradiates a measurement target with light, detects fluorescence emitted from the measurement target, and measures a fluorescence intensity” as recited in claim 11, because claim 12 limits such a device to a flow cytometer. It is therefore considered that a flow cytometer inherently that irradiates a measurement target with light, detects fluorescence emitted from the measurement target, and measures a fluorescence intensity.
Chen teaches calculating the precision, recall, and F-measures of the various clustering algorithms and the manually determined gates in FIG. 13 (i.e., displaying the gate such that the gate corresponds to the cluster on a basis of a matching degree) [0066], which is considered to read on the claimed calculation unit under the interpretation of 35 USC 112(f) as described in the previous Office Action. Chen also teaches overlaying manually determined gates [0065-0066] and clusters [0057] onto dimension reduction visualizations of the cytometry data by mapping. Chen also teaches a user interface of a web application for visualization of results (i.e., a display control unit) in FIG. 8-9 [0018-0019] on a display (i.e., a display device) [0079]. Chen teaches the analysis of cytometry data from flow cytometry instruments (i.e., a measurement device including a measurement unit as in claims 11-12) [0033].
Chen teaches manually gating different cell populations according to 8 different markers (i.e., analysis target having a plurality of attributes) in two datasets and also applying several dimensionality reduction methods, including t-SNE, on the two datasets [0061]. Chen teaches overlaying the gated cell populations onto the plots of the three dimensionality reduction methods in FIG. 10-11 [0062-0063]. Chen teaches comparing clustering performed by various clustering algorithms mapped on the t-SNE plot in FIG. 12-13, where the clusters are manually mapped to the gated populations using FlowJo (i.e., a correspondence relationship between a gate obtained by gate analysis and a cluster obtained by cluster analysis) [0065-0066]. Chen teaches that FIG. 13 shows a table showing the clustering results as compared to the manually gated population of the first dataset, where the clusters identified by each method are identified in relation to the gated population [0023]. Chen teach displaying the gate and the correspondence in the table of FIG. 13 which shows the gated population, the clusters, and the F-measures.
Regarding claim 2, Chen teaches the information processing device of claim 1 as described above. Claim 2 further adds that the calculation unit determines the correspondence relationship by calculating a matching degree between the gate and the cluster, and that the display control unit displays the correspondence relationship by displaying the gate such that the gate corresponds to the cluster on a basis of a matching degree calculated by the calculation unit.
Chen teaches calculating the precision, recall, and F-measures (i.e., a matching degree) of the various clustering algorithms and the manually determined gates in FIG. 13 (i.e., displaying the gate such that the gate corresponds to the cluster on a basis of a matching degree) [0066], which is considered to read on the claimed calculation unit under the interpretation of 35 USC 112(f) as described in the previous Office Action. Chen also teaches overlaying manually determined gates [0065-0066] and clusters [0057] onto dimension reduction visualizations of the cytometry data by mapping. Chen teaches displaying the gate such that the gate corresponds to the cluster on a basis of a matching degree calculated by the calculation unit in the table of FIG. 13 which shows the gated population, the clusters, and the F-measure.
Response to Applicant Arguments
At p. 9-10, par. 1, Applicant submits that Chen fails to describe “"a display control unit that displays, on a display device, the gate and the correspondence relationship between the gate and the cluster” because Chen teaches only visualization of the clusters. At p. 10, par. 2-3, Applicant submits that Chen fails to describe a gate because the cell populations taught by Chen are not gates. At p. 10-11, section II, Applicant reiterates that the amended claim language applies to claims 9-11 as well as claim 1, as described above.
It is respectfully submitted that this is not persuasive. While Chen may not display a figure with the gates, clusters, and correspondence as claimed, the table in FIG. 13 clearly displays the information as claimed. Therefore, the rejection is maintained.
Further, Chen clearly obtaining manually gated cell populations (see at least FIG. 13), which is considered to read on a gate as instantly claimed.
Claim Rejections - 35 USC § 103
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
A. Claims 3-6, 8, and 13-16 are rejected under 35 U.S.C. 103 as being unpatentable over Chen, as applied to claims 1-2 in the above 35 USC 102 rejection, in view of Aghaeepour et al. (Nature Methods, 2013, 10(3):228-243; previously cited). The instant rejection is newly stated and is necessitated by claim amendment.
Regarding claim 3, Chen in view of Aghaeepour teaches the information processing device of claims 1-2 as described above. Claim 3 further adds that the analysis target is a plurality of cells, and the calculation unit calculates the matching degree using a confusion matrix based on a number of cells included in the gate and the number of cells included in the cluster.
Chen teaches methods of detecting cell sub-populations in a plurality of cells [0002]. Chen teaches calculating an F-measure (i.e., a matching degree) as described above [0066], but does not teach using a confusion matrix as instantly claimed.
However, the prior art to Aghaeepour discloses an analysis of flow cytometry data processing challenges to examine whether automated algorithms can reproduce expert manual gating (abstract). Aghaeepour teaches performing manual gating by experts for comparison against cell population membership defined by each automated algorithm (p. 229, col. 2, par. 2). Aghaeepour teaches calculating an F-measure between the results of each cell population program and the reference method of manual gating by the subject matter expert (i.e., matching degree) using a 2x2 contingency table to calculate F = (2 × Pr × Re)/(Pr + Re), with the true positive (TP) defined as the situation in which the positive assignment of the prediction algorithm matches a positive assignment of manual gating, false positive (FP) when the positive assignment of the prediction algorithm matches a negative assignment of manual gating, and false negative (FN) when the negative assignment of the prediction algorithm matches a positive assignment of manual gating (p. 239, col. 2, par. 2). As the instant specification as published discloses that “In the confusion matrix, the number of cells belonging to the gate for which the matching degree is calculated and belonging to the cluster for which the matching degree is calculated is represented by True Positive (TP). In addition, the number of cells belonging to the gate for which the matching degree is calculated and belonging to a cluster other than the cluster for which the matching degree is calculated is represented by False Negative (FN). In addition, the number of cells belonging to a gate other than the gate for which the matching degree is calculated and belonging to the cluster for which the matching degree is calculated is represented by False Positive (FP).” at [0071], it is considered that the contingency table of Aghaeepour reads on the confusion matrix as instantly claimed. Aghaeepour further teaches comparing manual-gate consensus and ensemble clustering results by displaying the manual gates and results of the clustering algorithms on the same graph (Figure 3a and c).
Regarding claim 4, Chen teaches the information processing device of claims 1-2, and, in view of Aghaeepour, of claim 3, as described above. Claim 4 further adds that the plurality of attributes is intensities corresponding to a plurality of fluorescent dyes detected from the plurality of cells labeled with the plurality of fluorescent dyes.
Chen teaches analyzing cytometry data (title) of flow cytometry experiments [0033], where data are positive or negative for different biomarker signals like CD4, CD8, CD3, etc. [0061], but does not explicitly teach that the attributes is intensities corresponding to a plurality of fluorescent dyes detected from the plurality of cells labeled with the plurality of fluorescent dyes.
However, Aghaeepour teaches that flow cytometers provide high-dimensional quantitative measurement of light scatter and fluorescence emission properties of hundreds of thousands of individual cells in each analyzed sample (p. 228, col. 1, par. 1), which is considered to teach the instant limitation, or, alternatively, to provide evidence that the cytometry data of Chen fairly teaches the instant limitation.
Regarding claims 5-6, Chen teaches the information processing device of claims 1-2 as described above. Claim 5 further adds a reception unit that receives selection of a cluster, wherein the calculation unit calculates a matching degree with a cluster received by the reception unit for all gates, and the display control unit displays a gate having a highest matching degree with the cluster received by the reception unit by a display method different from display methods of gates not having the highest matching degree. Claim 6 further adds the different display method is a different color.
Chen teaches that the software package may include a Graphical User Interface (GUI) that allows a user to customize their analysis to choose the preferred merging method, cluster method and visualization method [0059], which is considered to read on a reception unit that receives selection of a cluster as instantly claimed. Chen teaches plotting cells using the first two dimensions of the dimensionality-transformed data and color coding by gated populations [0062-0063]. Chen also teaches that each cluster identified by the subset detection module may be represented with a different color, that each cluster may represent one cell type, and that the color map may also display different shapes for points on the map belong to different input data files [0056], which is considered to read on a display method different from display methods of the other gates as instantly claimed. Chen teaches calculating and then displaying in a table the precision, recall, and F-measures (i.e., a matching degree) of the various clustering algorithms and the manually determined gates in FIG. 13, where only the clusters and the manually determined gates with the highest F-measures are displayed (i.e., displaying a gate having a highest matching degree with the cluster received by the reception unit) [0066]. It is noted that the data displayed on the display control unit has no patentable weight (see the above claim interpretation section). Chen does not teach displaying the gate and the correspondence using a display method different from display methods of gates not having the highest matching degree.
However, Aghaeepour displays the manual gates and results of the clustering algorithms on the same graph colored by the F-measure (Figure 3a and c), where the different colors read on different display methods as instantly claimed.
Regarding claim 8, Chen teaches the information processing device of claims 1-2 as described above. Claim 8 further adds that the calculation unit calculates a matching degree for combinations of all clusters and all gates, and the display control unit displays the gates by using a display color of a cluster having a highest matching degree.
Chen teaches calculating the precision, recall and F-measure of each clustering method using the manually gated populations of cells [0065-0066], which is considered to read on calculating a matching degree for combinations of the clusters and the gates as instantly claimed. Chen teaches displaying the results with the highest F-measure for each cluster and gated population combination in FIG. 13. Chen does not teach a display color of a cluster having a highest matching degree.
However, Aghaeepour teaches a display color of a cluster having a highest matching degree in Figure 3a and c where the gates and clusters are colored by F-measure.
Regarding claims 13-16, Chen teaches the information processing device according to claim 1, the display method of claim 9, the storage device of claim 10, and the information processing system of claim 11 as described in the above 35 USC 102 rejection. Claims 13-16 further add displaying one or more lines constituting the gate or displaying a name of the gate, which Chen does not teach.
However, Aghaeepour displays the gates defined by lines (Figure 3a and c).
Regarding claims 3-6, 8, and 13-16, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Chen and Aghaeepour because both references disclose methods for analyzing cytometry data by comparing manual and automated gating methods. The prior art to Chen and Aghaeepour each teach methods for calculating the same type of F-measure to determine the performance of various methods in comparison to a ground truth dataset. Therefore, it would have been obvious to one of ordinary skill in the art to substitute the methods of calculating the F-measures. The substitution of the method of calculating the F-measure using the confusion matrix/contingency table, as taught by Aghaeepour, for the method of calculating the F-measure as taught by Chen in the method and system of Chen thus is no more than the simple substitution of one known element for another. Further, the motivation to display the gates, the clusters, and their correspondence according to the method of Aghaeepour would have been to demonstrate the practical utility of ensemble clustering of automated algorithm results through a visual example, as taught by Aghaeepour (p. 232, col. 2, par. 3).
B. Claim 7 is rejected under 35 U.S.C. 103 as being unpatentable over Chen, as applied to claims 1-2 in the above 35 USC 102 rejection, in view of Aghaeepour, as applied to claims 5-6 above, and in further view of Gondois-Rey et al. (Cytometry, 2016, 89A:480-490; newly cited). The instant rejection is newly stated and is necessitated by claim amendment.
Regarding claim 7, Chen teaches the information processing device of claims 1-2 and 5-6 as described above. Claim 7 further adds that the display control unit displays a parent gate of the gate having the highest matching degree in a color different from a color of the gate having the highest matching degree.
Chen teaches that each cluster identified by the subset detection module may be represented with a different color, that each cluster may represent one cell type, and that the color map may also display different shapes for points on the map belong to different input data files [0056]. Chen does not teach displaying a parent gate.
However, the prior art to Gondois-Rey discloses a comparison of unsupervised computation tools of multi-stained samples to manual gating (abstract). Gondois-Rey teaches hierarchical gating strategies of different populations of cells, where the gates on the left of the figures are considered parent gates and those further to the right are subpopulations (Figure 1A, C, and D). Gondois-Rey displays the parent gate and subpopulation gates with different colors (red and black).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Chen in view of Aghaeepour with Gondois-Rey because both references disclose methods for analyzing cytometry data by comparing manual and automated gating methods. The motivation to display parent gates and gates of subpopulations would have been to visualize either fluorochrome intercontaminations or targeted population characteristics, as taught by Gondois-Rey (p. 484, col. 1, par. 1).
Double Patenting
The outstanding rejections over copending Application No. 17/291,700, U.S. Patent No. 11,727,612, copending Application No. 17/636,013, U.S. Patent No. 12,298,220, copending Application No. 18/016,286, copending Application No. 18/570,354, copending Application No. 19/013,463, and copending Application No. 19/029,448 from the previous Office Action are withdrawn in view of the amendments submitted herein.
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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/J.N.S./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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