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 .
Specification
The specification incorporates essential term “Eilers’ estimation” in claims 5 and 24 by reference to a non-patent literature Boelens et al. (see Spec. para. [0048]). The incorporation of essential material in the specification by reference to an unpublished U.S. application, foreign application or patent, or to a publication is improper. Applicant is required to amend the disclosure to include the material incorporated by reference, if the material is relied upon to overcome any objection, rejection, or other requirement imposed by the Office. The amendment must be accompanied by a statement executed by the applicant, or a practitioner representing the applicant, stating that the material being inserted is the material previously incorporated by reference and that the amendment contains no new matter. 37 CFR 1.57(g).
The disclosure is objected to because of the following informalities:
Para. [0039]: “Depp MALDI” should be “DEEP MALDI”
Appropriate correction is required.
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 1-28 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea (i.e., mental processes and mathematical steps for collecting information from a mass spectrum and then performing mathematical processing), and the claims do not recite additional elements that integrate the abstract idea into a practical application or amount to significantly more than the judicial exception.
Step 2A, Prong One – Judicial exception (Abstract Idea)
The courts consider a mental process (thinking) that “can be performed in the human mind, or by a human using a pen and paper” to be an abstract idea. CyberSource Corp. v. Retail Decisions, Inc., 654 F.3d 1366, 1372, 99 USPQ2d 1690, 1695 (Fed. Cir. 2011). As the Federal Circuit explained, “methods which can be performed mentally, or which are the equivalent of human mental work, are unpatentable abstract ideas the ‘basic tools of scientific and technological work’ that are open to all.’” 654 F.3d at 1371, 99 USPQ2d at 1694 (citing Gottschalk v. Benson, 409 U.S. 63, 175 USPQ 673 (1972)). See also Mayo Collaborative Servs. v. Prometheus Labs. Inc., 566 U.S. 66, 71, 101 USPQ2d 1961, 1965 ("‘[M]ental processes[] and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work’" (quoting Benson, 409 U.S. at 67, 175 USPQ at 675)); Parker v. Flook, 437 U.S. 584, 589, 198 USPQ 193, 197 (1978) (same). Further, the courts do not distinguish between claims that recite mental processes performed by humans and claims that recite mental processes performed on a computer. As the Federal Circuit has explained, "[c]ourts have examined claims that required the use of a computer and still found that the underlying, patent-ineligible invention could be performed via pen and paper or in a person’s mind." Versata Dev. Group v. SAP Am., Inc., 793 F.3d 1306, 1335, 115 USPQ2d 1681, 1702 (Fed. Cir. 2015). See also Intellectual Ventures I LLC v. Symantec Corp., 838 F.3d 1307, 1318, 120 USPQ2d 1353, 1360 (Fed. Cir. 2016) (‘‘[W]ith the exception of generic computer-implemented steps, there is nothing in the claims themselves that foreclose them from being performed by a human, mentally or with pen and paper.’’); Mortgage Grader, Inc. v. First Choice Loan Servs. Inc., 811 F.3d 1314, 1324, 117 USPQ2d 1693, 1699 (Fed. Cir. 2016) (holding that computer-implemented method for "anonymous loan shopping" was an abstract idea because it could be "performed by humans without a computer").
In the instant case, the independent claims recite limitations that, when considered in their broadest reasonable interpretation, fall within the abstract idea of (i) mental process (concepts formed in the human mind such as observation, evaluation, and judgment) and/or (ii) mathematical concepts (relationships, comparisons, subtracting, and mathematical operations such as computing convolution). For instance, the independent claim 1 recites (independent claims 25-28, recites similar limitations):
reading a mass spectrum of a sample originating from a matrix-assisted laser desorption/ionization (MALDI) mass spectrometer;
reading a peak shape function of the mass spectrometer;
determining a fine structure component for a first range of the mass spectrum, wherein determining the fine structure component comprises estimating a first background of the mass spectrum,
subtracting the first background from the mass spectrum;
determining a bump structure for the first range of the mass spectrum, wherein determining the bump structure component comprises
estimating a second background of the mass spectrum, the second background being stiffer than the first background;
subtracting the second background from the first background;
computing a convolution of the fine structure component for the first range of the mass spectrum with the peak shape function;
determining a first plurality of peaks in the first range of the mass spectrum from the
convolution;
determining a feature value indicative of an abundance associated with each of the first plurality of peaks, wherein determining the feature value comprises combining the first plurality of peaks with the bump structure.
These limitations collectively recite collecting information from a mass spectrum and processing mass spectral data to extract feature values. Such collection, observation, selection and computation of data are fundamentally a form of data analysis and mathematical evaluation, activities that have long been performed by humans mentally or with pen and paper, and therefore can be characterized as an abstract idea.
Step 2A, Prong Two – Integration into a Practical Application
The claims are not integrated into a practical application because in practice, executing all of the steps is indistinguishable from: (i) mere data acquisition from a conventional instrument environment, and (ii) generic computer implementation of the abstract analysis. That is to say that integration into a practical application is lacking where, as here, the abstract idea has no effect on the material world or the execution of the process.
Although the claims include additional elements (e.g., “mass spectrometer”, “classifier,” “computer node,” “computer program product”), these additional elements do not integrate the abstract idea into a practical application. For example, the claims use a MALDI mass spectrometer as input data and produce feature values, classifier results, or trained classifier. However, the claims do not require an improvement to the operation of the MALDI mass spectrometer itself, do not control the mass spectrometer, do not change how a sample is prepared or measured, and do not require any treatment or other action based on the result. In addition, each of the “classifier,” “computer node,” and “computer program product” is merely recited as software-implemented generic computer processing modules providing a technological environment for carrying out the mathematical analysis.
Therefore, the claims as a whole are directed to an abstract idea.
Step 2B– Significant More (Inventive Concept)
The claims do not include additional elements, either individually or as an ordered combination, that amount to significant more than the abstract idea. The additional elements, such as reading a mass spectrum, reading a peak shape function, reading a reference peak list, using a trained classifier, and implementing the steps on a processor/computer node/computer readable medium, amount to data gathering, generic computer implementation, and outputting analytical results. Independent claims 25 and 26 additionally recite disease detection or classifier training, but the claims only use the calculated feature values as input to a classifier and receive an indication of disease or train the classifier. They do not require any particular treatment diagnostic device improvement, or transformation of the biological samples. Independent claims 27 and 28 additionally recite a system of computer program product for performing the method if claim 1. The mass spectrometer, computer node, processor, and computer-readable storage medium are generic components used to execute the same abstract data-processing steps and do not provide significant more. Thus, these elements do not add an inventive concept beyond the mental process and/or mathematical concept itself.
Dependent claims 2-19 and 21-24 merely add further mathematical/data processing details, such as aligning peaks, fitting peak shape functions, asymmetric least square/Eilers background estimation, amplitude/area calculation, asymmetric Gaussian coefficients, clustering peak candidates, thresholding, SNR filtering, MAD filtering, MALDI-TOF context, and baseline correction. These limitations further define the abstract mathematical analysis and do not integrate the exception into a practical application or add significantly more.
Taken alone or as ordered combination, claims 1-19 and 21-28 fail to recite patent eligible subject matter.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 5 and 24 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 5 and 24 each recites “Eilers' estimation,” which is not adequately described in the specification. The specification merely identifies this term by name and generally describes it as asymmetric least square fitting, does not provide the required algorithm or implementation details. Because this term is essential to the claimed limitation, the missing details cannot be incorporated by referencing a non-patent literature.
Claims 5, 15, 20, and 24 rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 5 and 24 each recites “Eilers' estimation” which is unclear in scope. The specification does not define the term with sufficient detail to determine what specific background estimation procedure is required, or how it differs from other asymmetric least square/background fitting method. As a result, one of ordinary skilled in the art would not be reasonably apprised of what specific background estimation procedure is required by the claim.
Claim 15 recites the limitation “the threshold amplitude.” There is insufficient antecedent basis for this limitation in the claim.
Claim 20 recites the limitation “performing Deep MALDI.” Neither the claims nor the specification adequately explains how one is to determine when “Deep MALDI” has been performed. Further, the term appears to be a trademarked term. The claim is indefinite because it is unclear whether one must perform the MALDI technique protected by the trademark, a MALDI technique equivalent to that of the trademarked technique, or simply a technique with an arbitrary number of shots.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JING WANG whose telephone number is (571)272-2504. The examiner can normally be reached M-F 7:30-17:00.
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/JING WANG/Examiner, Art Unit 2881
/WYATT A STOFFA/Primary Examiner, Art Unit 2881
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