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 .
Applicant’s Response
Applicant’s response, filed 10/17/2025, has been fully considered.
Claims Status
Claim 3 was previously canceled.
Claims 1 , 2, and 4-23 are pending.
Claims 1, 2, and 4-23 are examined.
Withdrawn Objections/Rejections
The rejection of claims 1, 2, 4, 5, and 12-22 under 35 USC 103 over Meng et al. in view of DeGregorio et al. is withdrawn in view of the amendments submitted
The rejection of claims 6-11 and 23 under 35 USC 103 over Meng et al. in view of DeGregorio et al. and further in view of Dolgov et al. is withdrawn in view of amendments submitted
Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn.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.
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, 2, and 4-23 are rejected under 35 U.S.C. 101 because the claimed inventions are directed to an abstract idea of mental steps, mathematic concepts, or a natural law without significantly more. Any newly recited portion is necessitated by claim amendment.
The MPEP at MPEP 2106.03 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of
matter?
(2A)(1) Are the claims directed to a judicially recognized exception, i.e. a law of nature,
a natural phenomenon, or an abstract idea?
(2A)(2) If the claims are directed to a judicial exception under Prong One, then is the
judicial exception integrated into a practical application?
(2B) If the claims are directed to a judicial exception and do not integrate the judicial
exception, do the claims provide an inventive concept?
With respect to step (1): Yes, claims 1, 2, 4-20, and 23 recite a method, claim 21 recites a system, and claim 22 recites a non-transitory computer-readable media.
With respect to step (2A)(1): The claims recite an abstract idea of mental processes and mathematic concepts. “Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection” (MPEP 2106.04). Abstract ideas include mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (procedures for observing, evaluating, analyzing/judging and organizing information (MPEP 2106.04(a)(2)). Laws of nature or natural phenomena include naturally occurring principles/relations that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature (MPEP 2106(b)).
Mathematic concepts recited in claims 1 and 21-22:
each molecular degree of freedom is characterized by a gridding of allowable values, and wherein the set of inputs comprises a molecular electric force-field function
approximating a partition function of the non-lattice system using a tensor network and based at least in part on the set of inputs, wherein approximating a partition function of the non-lattice system comprises, at each of a plurality of iterations
adaptively updating, using a molecular configuration sample to vary over the one or more molecular degrees of freedom with respect to the gridding of allowable values, the gridding of allowable values for one or more molecular degrees of freedom based on an approximation error of the partition function wherein adaptively updating the gridding of allowable values comprises
determining the approximation error of the partition function at a particular molecular degree of freedom configuration using the molecular electric force-field function
modifying a number of gridpoints of the gridding of allowable values for the one or more molecular degrees of freedom based on the approximation error of the partition function at the particular molecular degree of freedom configuration
determining a plurality of system characterization entities from the partition function for a corresponding plurality of conformations that are each specified by a respective configuration of molecular degrees of freedom, wherein the system characterization entities comprise corresponding respective measures of free energy for each of the plurality of conformations
generating a free energy landscape using the respective measures of free energy for each of the plurality conformations
using the free energy landscape to determine one or more metrics of the non-lattice system, wherein the one or more metrics comprise at least one of a free energy of solvation, or observation likelihood of a respective conformation, or a combination
Dependent claims 5-20, and 23 recite additional steps that either are directed to abstract ideas or further limit the judicial exceptions in independent claim 1 and as such, are further directed to abstract ideas. Hence, the claims explicitly recite numerous elements that individually and in combination constitute abstract ideas. The relevant recitations are:
Claim 5: “conformational sampling comprising varying over angular and dihedral rotational degrees of free of the non-lattice system”
Claim 6: “a tensor-train cross approximation to determine an approximated partition function”, “initializing a high-dimensional probability function tensor network comprising generating a low-rank decomposition of matrix product states based at least in part on the set of inputs, wherein the high-dimensional probability function tensor network is associated with a plurality of dimensions, corresponding with each molecular degree of freedom, and wherein each dimension is traversable with a respective index along the gridding of allowable values”, “determining a plurality of pivot indices using rook pivoting, each pivot index comprising a set of index values for each dimension of the tensor network”, “evaluating the partition function at the pivot indices”, “approximating the high-dimensional probability function at a plurality of unevaluated indices by interpolating between one or more evaluated values of the high dimensional probability function at pivot indices”, and “integrating the approximated high-dimensional probability function to determine the approximated partition function of the system”
Claim 7: “performing a regression to minimize an objective to a target function comprising the one or more evaluated values of the high-dimensional probability function at pivot indices”
Claim 8: “constructing splines between the one or more evaluated values of the high-dimensional probability function at pivot indices and the plurality of unevaluated indices on the grid”
Claim 9: “identifying a tensor bipartition by selecting a first and second variable dimension for index traversal; alternatingly evaluating a random set of samples along the first and second variable dimension within the tensor bipartition for each sample within the random set of samples, wherein evaluating comprises: generating a first evaluation of the high-dimensional probability function at a respective set of index values specified by the sample; comparing the first evaluation to a second interpolated evaluation at the respective set of index values comprising interpolating between one or more evaluated values of the high-dimensional probability function at pivot indices at the respective set of index values; updating the gridding of allowable values for a second sample in the random set of samples in accordance with the approximation error between the first evaluation and the second interpolated evaluation; identifying the respective set of index values with a largest approximation error between the first evaluation and second evaluation”, “adding the first evaluation at the set of index values with the largest approximation error to the tensor network”
Claim 10: “determining a sequence of pivot indices in accordance with maximizing a measure of volume of a submatrix”
Claim 11: “calculating a volume metric for an intersection matrix determined by a pivot index, wherein calculating the volume metric comprises, for each pivot index in the sequence of pivot indices: evaluation the intersection matrix represented by the pivot index comprising a value of a determinant of the intersection matrix determined by the pivot index; alternately updating the first and second variable dimension of the pivot index; and choosing the pivot index associated with a maximal volume intersection matrix”
Claim 12: “determining a system characterization derivative function or system characterization quantity from the partition function”
Claim 13: “determining one or more of marginal and moment distributions over possible degrees of freedom of the partition function”
Claim 14: “determining the corresponding respective measures of free energy for each of the plurality of conformations”
Claim 15: “a binding of free energy describing a binding free energy for an interaction between a protein and a small molecule”, “using the binding free energy to determine a distribution of possible docking configurations as a binding free energy landscape”, “for each possible docking configuration in the binding free energy landscape, determining a docking score comprising a probability of the interaction between the protein and small molecule resulting in the docking configuration”
Claim 16: “identifying a candidate small molecule for inclusion in a drug based at least on the docking score of the candidate small molecule”
Claim 17: “a solubility metric, crystal structure metric, and polymer conformation metric for the small molecule”
Claim 18: “using the one or more metrics to assess at least one of a measure of manufacturability of a pill that includes the small molecule and a measure of toxicity of administering the pill to a subject”
Claim 19: “designing an active material based at least on the one or more metrics”
Claim 20: “the active material is a catalyst”
Claim 23: “refining an interval between allowable values of the gridding based on the approximation error; or maintaining a current gridding discretization of the gridding of allowable values”
The abstract ideas recited in the claims are evaluated under Broadest Reasonable Interpretation (BRI) and determined herein to each cover mathematical concepts and mental processes because the claims simply involve performing calculations to characterize a molecular system.
Because the claims do recite judicial exceptions, direction under (2A)(2) provides that the claims must be examined further to determine whether they integrate the abstract ideas 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 abstract idea is integrated into a practical application (MPEP 2106.04(d).I; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim is said to fail to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
With respect to the instant recitations, claim 1 recites the following additional elements:
receiving a set of inputs characterizing thermodynamic entities of a non-lattice system with one or more molecular degrees of freedom
Claim 21-22 recites the following additional elements:
one or more computers and one or more non-transitory storage devices on which are stored instructions that are operable, when executed by the one or more computers, to cause the one or more computer to perform operations
receiving a set of inputs characterizing thermodynamic entities of a non-lattice system with one or more molecular degrees of freedom
The elements of --receiving a set of inputs characterizing thermodynamic entities is directed to data gathering as it gathers the data on which the judicial exceptions are performed. Data gathering does not impose any meaningful limitation on the abstract idea, or how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application (MPEP 2106.05(g)). The additional non-abstract elements of a computer readable program, and a computer do not describe any specific computation steps by which the computer parts perform or carry out the abstract idea, nor do they provide any details of how specific structures of the computer are used to implements these functions. The claims state nothing more than a generic computer which performs the functions that constitute the abstract idea. Hence, these are mere instructions to apply the abstract idea using a computer, and therefore the claim does not integrate that abstract idea 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 (see MPEP 2106.05(f)).
Dependent claims 2 and 4 are directed to data gathering as they provide limitations on the inputs that characterize the thermodynamic entities of a non-lattice system.
None of these dependent claims recite additional elements, alone or in combination, which would integrate a judicial exception into a practical application.
With respect to step (2B): Because the claims recite an abstract idea, and do no integrate that abstract idea into a practical application, the claims lack a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception (MPEP 2106.05.A i-vi).
The additional elements of data gathering described above do not rise to the level of significantly more than the judicial exception. As set forth in the MPEP at 2106.05(d)(I), determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either 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 claim 1: The additional element of receiving a set of inputs characterizing thermodynamic entities of a non-lattice system with one or more molecular degrees of freedom does not rise to the level of significantly more than the judicial exception. The prior art Meng et al. (“Molecular Docking: A powerful approach for structure-based drug discovery”, IDS reference) discloses the Monte Carlo algorithm as a typical algorithm that generates poses of a ligand through bond rotation, rigid-body translation or rotation and it is tested with an energy-based criterion (page 3, paragraphs 5 and 6). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 2: The additional element of one or more of molecular degrees of freedom, an electric force-field function, particle masses, and a temperature of the system does not rise to the level of significantly more than the judicial exception. The prior art Meng et al. discloses the Monte Carlo algorithm as a typical algorithm that generates poses of a ligand through bond rotation, rigid-body translation or rotation and it is tested with an energy-based criterion (page 3, paragraphs 5 and 6). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 4: The additional element of a classical molecular system of one or more molecules does not rise to the level of significantly more than the judicial exception. The prior art Meng et al. discloses the Monte Carlo algorithm as a typical algorithm that generates poses of a ligand through bond rotation, rigid-body translation or rotation and it is tested with an energy-based criterion (page 3, paragraphs 5 and 6). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 21 and 22: The additional elements of one or more computers and one or more storage devices on which are stored instructions that are operable, when executed by the one or more computers, to cause the one or more computer to perform operations and receiving a set of inputs characterizing thermodynamic entities of a non-lattice system with one or more molecular degrees of freedom do not rise to the level of significantly more than the judicial exception. The prior art Meng et al. discloses the Monte Carlo algorithm as a typical algorithm that generates poses of a ligand through bond rotation, rigid-body translation or rotation and it is tested with an energy-based criterion (page 3, paragraphs 5 and 6). With respect to the one or more computers and one or more storage devices, as exemplified in the MPEP at 2106.05(f) with reference to Alice Corp. 573 US at 223, 110 USPQ2d at 1983 “claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible”. 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 abstract idea (see MPEP 2105(b)I-III). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
In combination, the collection or generation of the data, acted upon by the judicial exception, fail to rise to the level of significantly more. The data gathering steps provide the data for the judicial exception. No non-routine step or element has clearly been identified.
The claims have all been examined to identify the presence of one or more judicial exceptions. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether the additional limitations integrate the judicial exception into a practical application. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether those additional limitations provide an inventive concept which provides significantly more than those exceptions. Individually, the limitations of the claims and the claims as a whole have been found to not meet the eligibility requirements.
Response to Arguments
Applicant states that the claims are patent eligible because the judicial exceptions are integrated into a practical application through the improvement to the technical field of computational modeling of non-lattice systems under the reasoning of Ex parte Desjardins, Enfish, and Example 3 of the USPTO Subject Matter Eligibility Examples, because the claimed invention provides an improvement through the reduced consumption of computation resources, for example by “in storing the tensor network as a number of matrix products states” and “in determining the approximation of the partition function of a non-lattice system relative to a ‘computationally intensive molecular dynamics of Monte Carlo simulation’” Applicant states that the claimed invention “provides a technical improvement in computer technology by providing a computationally efficient technique for ‘approximating [the] partition function of [a] non-lattice system’” and that the claims are patent eligible due to the reasonings outlines in Ex parte Desjardins, Enfish, and Example 3.
It is respectfully submitted that this is not persuasive. Firstly, Applicant the features described in the Specification that demonstrate an improvement to technology. With specific regard to the element of reduced consumption of computation resources by storing the tensor network as a number of matrix product states, the claims do not sufficiently reflect this improvement, especially with regard to the storing of the tensor network in a different state. Furthermore, Although it can be argued that the reasoning of Ex parte Desjardins applies to the instant claims with regard to the approximating of a partition function using a tensor network, wherein the steps of adaptively updating improve the tensor network and thus improve computational efficiency, this improvement does not integrate all of the judicial exceptions. Beyond the steps of determining approximation error and modifying a number of gridpoints of the gridding of allowable values, which Applicant argues provides an improvement, the independent claims also recite steps of “determining a plurality of system characterization entities from the partition function…” and “using the free energy landscape to determine one or more metrics of the non-lattice system…”. Thus, although the machine learning aspect may be an improvement, there are further abstract ideas performed that use this information, and thus the improved machine learning does not integrate these steps of determining system characterization entities and determining metrics of the non-lattice system. The instant claims are directed to a method and system for improved mathematical concepts which are thus used to perform other mathematical steps of determination, which are not interpreted as being performed by the tensor network. Thus, the instant claims do not reflect an improvement to technology in the manner that Ex parte Desjardins, Enfish, and Example 3 do. Therefore, the rejection under 35 USC 101 is maintained.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Emilie A Smith whose telephone number is (571)272-7543. The examiner can normally be reached 9am - 5pm.
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/E.A.S./Examiner, Art Unit 1686
/LARRY D RIGGS II/Supervisory Patent Examiner, Art Unit 1686