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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 03 September 2025 has been entered.
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, 7, 9-11, 13, 16-19, 21-22, 24-27, 33-35, 64, and 70-72 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Regarding Claim 1,
Claim 1 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 1 is directed to a computer-implemented method of modeling a desired protein property, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The limitations:
“generating a …prediction of the desired protein property for a protein analyte based on a machine-readable representation of a primary amino acid sequence of the protein analyte, wherein the generated …prediction provides a continuous variable or value for the desired protein property.”
As drafted, under their broadest reasonable interpretations, cover mental processes, i.e., concepts performed in the human mind (including an observation, evaluation, judgement, opinion). The above limitations in the context of this claim correspond to mental processes, e.g., evaluation and judgement with assistance of pen and paper.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are mere instructions to apply an exception (See MPEP 2106.05(f)) and insignificant extra-solution activity (See MPEP 2106.05(g)).
The limitations:
“A computer-implemented method of modeling a desired protein property”
“providing a pretrained first system comprising a first machine-readable neural net embedder and a first machine-readable neural net predictor, the first machine-readable neural net predictor of the pretrained first system being configured to generate an output different from the desired protein property”
“by the second system including the part of the transferred first machine-readable neural net embedder, the second machine-readable neural net embedder of the second system, and the second machine-readable neural net predictor of the second system…”
“machine-informed”
As drafted, are additional elements that amount to no more than mere instructions to apply an exception for the abstract ideas. See MPEP 2106.05(f).
The limitations:
“transferring at least a part of the first machine-readable neural net embedder of the pretrained first system to a second system, the second system comprising a second machine-readable neural net embedder and a second machine-readable neural net predictor, the second machine-readable neural net predictor of the second system providing the desired protein property”
As drafted, are additional elements that amount to no more than insignificant extra-solution activity. See MPEP 2106.05(g).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements are “mere instructions to apply” and “insignificant extra-solution activity”. In addition, the transferring limitation recites the well-understood, routine, and conventional activity of receiving and transmitting data over a network. MPEP 2106.05(d)(II); OIP Techs., Inc., v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1093 (Fed. Cir. 2015) (sending messages over a network). Mere instructions to apply an exception and insignificant extra-solution activity cannot provide an inventive concept. The claim is not patent eligible.
Regarding Claim 7,
Claim 7 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 7 is directed to a computer-implemented method of modeling a desired protein property, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 1.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are additional details that do not apply the exception in a meaningful way (See MPEP 2106.05(e)).
The limitations:
“wherein the primary amino acid sequence includes annotations across at least one functional representation and wherein a functional representation of the at least one functional representation is based on a Gene Ontology (GO) functional representation, Pfam functional representation, keyword functional representation, Kegg Ontology functional representation, INTERPRO® functional representation, SUPFAM functional representation, OrthoDB functional representation, or a combination thereof”
As drafted, are additional elements that do not apply an exception for the abstract ideas in a meaningful way. See MPEP 2106.05(e).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements do not apply the exception in a meaningful way. The claim is not patent eligible.
Regarding Claim 9,
Claim 9 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 9 is directed to a computer-implemented method of modeling a desired protein property, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 1.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are additional details that do not apply the exception in a meaningful way (See MPEP 2106.05(e)).
The limitations:
“wherein the second system has an improved performance metric relative to a model trained without using the part of the transferred first machine-readable neural net embedder of the first system”
As drafted, are additional elements that do not apply an exception for the abstract ideas in a meaningful way. See MPEP 2106.05(e).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements do not apply the exception in a meaningful way. The claim is not patent eligible.
Regarding Claim 10,
Claim 10 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 10 is directed to a computer-implemented method of modeling a desired protein property, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 1.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are mere instructions to apply an exception (See MPEP 2106.05(f)).
The limitations:
“wherein at least one of the first system and the second systems are configured to be optimized by Adam, Root Mean Square Propagation (RMSprop), stochastic gradient descent (SGD) with momentum, SGD with momentum and Nestrov accelerated gradient, SGD without momentum, Adagrad, Adadelta, or NAdam”
As drafted, are additional elements that amount to no more than mere instructions to apply an exception for the abstract ideas. See MPEP 2106.05(f).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements are “mere instructions to apply. Mere instructions to apply cannot provide an inventive concept. The claim is not patent eligible.
Regarding Claim 11,
Claim 11 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 11 is directed to a computer-implemented method of modeling a desired protein property, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 1.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are mere instructions to apply an exception (See MPEP 2106.05(f)).
The limitations:
“wherein the first system and the second system are configured to be optimized using any of the following activation functions: softmax, Exponential Linear Unit (ELU), Scaled Exponential Linear Unit (SeLU), softplus, softsign, Rectified Linear Unit (ReLU), tanh, sigmoid, hard_sigmoid, exponential function, Parametric Rectified Linear Unit (PReLU), and Leaky ReLU, or linear function”
As drafted, are additional elements that amount to no more than mere instructions to apply an exception for the abstract ideas. See MPEP 2106.05(f).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements are “mere instructions to apply. Mere instructions to apply cannot provide an inventive concept. The claim is not patent eligible.
Regarding Claim 13,
Claim 13 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 13 is directed to a computer-implemented method of modeling a desired protein property, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 1.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are mere instructions to apply an exception (See MPEP 2106.05(f)).
The limitations:
“wherein at least one of the first system and the second system utilizes a regularization selected from: early stopping, L1-L2 regularization, skip connections, or a combination thereof, and wherein the regularization is performed on 1 or more layers”
As drafted, are additional elements that amount to no more than mere instructions to apply an exception for the abstract ideas. See MPEP 2106.05(f).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements are “mere instructions to apply”. Mere instructions to apply cannot provide an inventive concept. The claim is not patent eligible.
Regarding Claim 16,
Claim 16 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 16 is directed to a method of modeling a desired protein property, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 1.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are additional details that do not apply the exception in a meaningful way (See MPEP 2106.05(e)).
The limitations:
“wherein a second model of the second system comprises a first model of the first system in which a last layer of the first model is removed”
As drafted, are additional elements that do not apply an exception for the abstract ideas in a meaningful way. See MPEP 2106.05(e).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements do not apply the exception in a meaningful way. The claim is not patent eligible.
Regarding Claim 17,
Claim 17 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 17 is directed to a method of modeling a desired protein property, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The limitations:
“wherein 2 or more layers of the first model are removed in a transfer to the second model”
As drafted, under their broadest reasonable interpretations, cover mental processes, i.e., concepts performed in the human mind (including an observation, evaluation, judgement, opinion). The above limitations in the context of this claim correspond to mental processes, e.g., evaluation and judgement with assistance of pen and paper.
Step 2A Prong Two Analysis: See corresponding analysis of claim 16.
Step 2B Analysis: See corresponding analysis of claim 16.
Regarding Claim 18,
Claim 18 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 18 is directed to a method of modeling a desired protein property, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 17.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are additional details that do not apply the exception in a meaningful way (See MPEP 2106.05(e)).
The limitations:
“wherein transferred layers from the first model are frozen during training of the second model”
As drafted, are additional elements that do not apply an exception for the abstract ideas in a meaningful way. See MPEP 2106.05(e).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements do not apply the exception in a meaningful way. The claim is not patent eligible.
Regarding Claim 19,
Claim 19 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 19 is directed to a method of modeling a desired protein property, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 17.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are additional details that do not apply the exception in a meaningful way (See MPEP 2106.05(e)).
The limitations:
“wherein transferred layers from the first model are unfrozen during training of the second model”
As drafted, are additional elements that do not apply an exception for the abstract ideas in a meaningful way. See MPEP 2106.05(e).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements do not apply the exception in a meaningful way. The claim is not patent eligible.
Regarding Claim 21,
Claim 21 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 21 is directed to a method of modeling a desired protein property, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 1.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are additional details that do not apply the exception in a meaningful way (See MPEP 2106.05(e)).
The limitations:
“wherein the second machine-readable neural net predictor of the second system predicts one or more of protein binding activity, nucleic acid binding activity, protein solubility, protein stability, or a combination thereof”
As drafted, are additional elements that do not apply an exception for the abstract ideas in a meaningful way. See MPEP 2106.05(e).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements do not apply the exception in a meaningful way. The claim is not patent eligible.
Regarding Claim 22,
Claim 22 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 22 is directed to a method of modeling a desired protein property, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 1.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are additional details that do not apply the exception in a meaningful way (See MPEP 2106.05(e)).
The limitations:
“wherein the second machine-readable neural net predictor of the second system predicts at least one of protein fluorescence and enzymatic activity”
As drafted, are additional elements that do not apply an exception for the abstract ideas in a meaningful way. See MPEP 2106.05(e).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements do not apply the exception in a meaningful way. The claim is not patent eligible.
Regarding Claim 24,
Claim 24 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 24 is directed to a computer-implemented method for identifying a previously unknown association between an amino acid sequence and a protein function, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The limitations:
“generating… a first machine-readable model of a plurality of associations between a plurality of protein properties and a plurality of amino acid sequences”
“generating… a second machine-readable model comprising at least a portion of the first machine-readable model”
“perform a …identification of the previously unknown association between the amino acid sequence and the protein function”
As drafted, under their broadest reasonable interpretations, cover mental processes, i.e., concepts performed in the human mind (including an observation, evaluation, judgement, opinion). The above limitations in the context of this claim correspond to mental processes, e.g., evaluation and judgement with assistance of pen and paper.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are mere instructions to apply an exception (See MPEP 2106.05(f)) and insignificant extra-solution activity (See MPEP 2106.05(g)).
The limitations:
“A computer-implemented method for identifying a previously unknown association between an amino acid sequence and a protein function”
“with a first machine-readable machine learning software module”
“by the second machine-readable machine learning software module”
“employing the second machine-readable model to…”
“machine-informed”
As drafted, are additional elements that amount to no more than mere instructions to apply an exception for the abstract ideas. See MPEP 2106.05(f).
The limitations:
“transferring the first machine-readable model or a portion thereof to a second machine-readable machine learning software module”
As drafted, are additional elements that amount to no more than insignificant extra-solution activity. See MPEP 2106.05(g).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements are “mere instructions to apply” and “insignificant extra-solution activity”. In addition, the transferring limitation recites the well-understood, routine, and conventional activity of receiving and transmitting data over a network. MPEP 2106.05(d)(II); OIP Techs., Inc., v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1093 (Fed. Cir. 2015) (sending messages over a network). Mere instructions to apply an exception and insignificant extra-solution activity cannot provide an inventive concept. The claim is not patent eligible.
Regarding Claim 25,
Claim 25 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 25 is directed to a computer implemented method for identifying a previously unknown association between an amino acid sequence and a protein function, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 24.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are additional details that do not apply the exception in a meaningful way (See MPEP 2106.05(e)).
The limitations:
“wherein the amino acid sequence comprises a primary protein structure”
As drafted, are additional elements that do not apply an exception for the abstract ideas in a meaningful way. See MPEP 2106.05(e).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements do not apply the exception in a meaningful way. The claim is not patent eligible.
Regarding Claim 26,
Claim 26 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 26 is directed to a computer implemented method for identifying a previously unknown association between an amino acid sequence and a protein function, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 24.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are additional details that do not apply the exception in a meaningful way (See MPEP 2106.05(e)).
The limitations:
“wherein the amino acid sequence causes a protein configuration that results in the protein function”
As drafted, are additional elements that do not apply an exception for the abstract ideas in a meaningful way. See MPEP 2106.05(e).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements do not apply the exception in a meaningful way. The claim is not patent eligible.
Regarding Claim 27,
Claim 27 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 27 is directed to a computer implemented method for identifying a previously unknown association between an amino acid sequence and a protein function, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 24.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are additional details that do not apply the exception in a meaningful way (See MPEP 2106.05(e)).
The limitations:
“wherein the protein function comprises at least one of fluorescence, enzymatic activity, nuclease activity, and protein stability”
As drafted, are additional elements that do not apply an exception for the abstract ideas in a meaningful way. See MPEP 2106.05(e).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements do not apply the exception in a meaningful way. The claim is not patent eligible.
Regarding Claim 33,
Claim 33 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 33 is directed to a computer implemented method for identifying a previously unknown association between an amino acid sequence and a protein function, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 24.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are additional details that do not apply the exception in a meaningful way (See MPEP 2106.05(e)).
The limitations:
“wherein the plurality of amino acid sequences forms a primary protein structure, a secondary protein structure, and a tertiary protein structure for a plurality of proteins”
As drafted, are additional elements that do not apply an exception for the abstract ideas in a meaningful way. See MPEP 2106.05(e).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements do not apply the exception in a meaningful way. The claim is not patent eligible.
Regarding Claim 34,
Claim 34 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 34 is directed to a computer implemented method for identifying a previously unknown association between an amino acid sequence and a protein function, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 24.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are mere instructions to apply an exception (See MPEP 2106.05(f)).
The limitations:
“wherein the first machine-readable model is trained on input data comprising a multidimensional tensor, a representation of 3-dimensional atomic positions, an adjacency matrix of pairwise interactions, a character embedding, or a combination thereof”
As drafted, are additional elements that amount to no more than mere instructions to apply an exception for the abstract ideas. See MPEP 2106.05(f).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements are “mere instructions to apply”. Mere instructions to apply cannot provide an inventive concept. The claim is not patent eligible.
Regarding Claim 35,
Claim 35 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 35 is directed to a computer implemented method for identifying a previously unknown association between an amino acid sequence and a protein function, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 24.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are mere instructions to apply an exception (See MPEP 2106.05(f)).
The limitations:
“inputting to the second machine-readable machine learning software module, at least one of data related to a mutation of a primary amino acid sequence, a contact map of an amino acid interaction, a tertiary protein structure, and a predicted isoform from alternatively spliced transcripts”
As drafted, are additional elements that amount to no more than mere instructions to apply an exception for the abstract ideas. See MPEP 2106.05(f).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements are “mere instructions to apply”. Mere instructions to apply cannot provide an inventive concept. The claim is not patent eligible.
Regarding Claim 64,
Claim 64 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 64 is directed to a computer implemented method modeling a desired protein property, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The limitations:
“generating …a…prediction of the desired protein property for a protein analyte based on a machine-readable representation of a primary amino acid sequence of the protein analyte, wherein the generated machine-informed prediction provides a continuous variable or value for the desired protein property”
As drafted, under their broadest reasonable interpretations, cover mental processes, i.e., concepts performed in the human mind (including an observation, evaluation, judgement, opinion). The above limitations in the context of this claim correspond to mental processes, e.g., evaluation and judgement with assistance of pen and paper
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are mere instructions to apply an exception (See MPEP 2106.05(f)) and insignificant extra-solution activity (See MPEP 2106.05(g)).
The limitations:
“training a first machine-readable system with a first set of data, the first machine-readable system comprising a first transformer encoder and a first decoder, the first decoder being configured to generate an output different from the desired protein property”
“training the second machine-readable system with a second set of data, the second set of data comprising a set of proteins representing a smaller number of classes of proteins than the first set of data, wherein the classes of proteins are: (a) classes of proteins within the first set of data, (b) classes of proteins excluded from the first set of data, or a combination of (a) and (b)”
“by the second machine-readable system”
“machine-informed”
As drafted, are additional elements that amount to no more than mere instructions to apply an exception for the abstract ideas. See MPEP 2106.05(f).
The limitations:
“transferring at least a part of the first transformer encoder of the first machine-readable system to a second machine-readable system, the second machine-readable system comprising a second transformer encoder and a second decoder”
As drafted, are additional elements that amount to no more than insignificant extra-solution activity. See MPEP 2106.05(g).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements are “mere instructions to apply” and “insignificant extra-solution activity”. In addition, the transferring limitation recites the well-understood, routine, and conventional activity of receiving and transmitting data over a network. MPEP 2106.05(d)(II); OIP Techs., Inc., v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1093 (Fed. Cir. 2015) (sending messages over a network). Mere instructions to apply an exception and insignificant extra-solution activity cannot provide an inventive concept. The claim is not patent eligible.
Regarding Claim 70,
Claim 70 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 70 is directed to a computer-implemented method of modeling a desired protein property, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 1.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are additional details that do not apply the exception in a meaningful way (See MPEP 2106.05(e)).
The limitations:
“wherein the continuous variable or value represents an intensity of auto-fluorescence of the protein analyte, stability of the protein analyte, a targeted specificity of a matrix metalloprotease for a particular substrate extracellular matrix component, a target molecule binding affinity, target reaction rate of an enzyme, or a target thermostability”
As drafted, are additional elements that do not apply an exception for the abstract ideas in a meaningful way. See MPEP 2106.05(e).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements do not apply the exception in a meaningful way. The claim is not patent eligible.
Regarding Claim 71,
Claim 71 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 71 is directed to a computer implemented method modeling a desired protein property, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 64.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are additional details that do not apply the exception in a meaningful way (See MPEP 2106.05(e)).
The limitations:
“wherein the continuous variable or value represents an intensity of auto-fluorescence of the protein analyte, stability of the protein analyte, a targeted specificity of a matrix metalloprotease for a particular substrate extracellular matrix component, a target molecule binding affinity, target reaction rate of an enzyme, or a target thermostability”
As drafted, are additional elements that do not apply an exception for the abstract ideas in a meaningful way. See MPEP 2106.05(e).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements do not apply the exception in a meaningful way. The claim is not patent eligible.
Regarding Claim 72,
Claim 72 is rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1 Analysis: Claim 72 is directed to a computer-implemented method for identifying a previously unknown association between an amino acid sequence and a protein function, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: See corresponding analysis of claim 24.
Step 2A Prong Two Analysis: The judicial exceptions are not integrated into a practical application. In particular, the claim recited additional elements that are mere instructions to apply an exception (See MPEP 2106.05(f)).
The limitations:
“training, by the first machine-readable machine learning software module, the first machine-readable model using a first training data set and training, by the second machine-readable machine learning software module, the second machine-readable model using a second training data set”
As drafted, are additional elements that amount to no more than mere instructions to apply an exception for the abstract ideas. See MPEP 2106.05(f).
Therefore, the additional elements do not integrate the abstract ideas into a practical application.
Step 2B Analysis: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to the integration of the abstract ideas into a practical application, all of the additional elements are “mere instructions to apply”. Mere instructions to apply cannot provide an inventive concept. The claim is not patent eligible.
Response to Arguments
Regarding the objection to the specification previously set forth in the Final Rejected, dated 03 June 2025, Applicant’s amendments to the specification overcome the objection.
Regarding the rejection applied under 35 U.S.C. 101, Applicant firstly asserts that the amended elements of “machine-readable” and “machine-informed” are rooted in computer technology and therefore, the limitations of the amended independent claims are not mentally performable (“Remarks”, Page 12).
However, as discussed above in the 35 U.S.C. 101 rejection of claim 1 above, and in accordance with MPEP 2106.05(f), the “machine-informed” element is mere instructions to apply, as it pertains to a generic recitation of hardware or use of a computer to perform abstract ideas. Further, a “machine-readable” element does not necessarily require a machine. For example, programming languages are “machine-readable”, but the program code itself is produced by a human programmer and can therefore be mentally produced and mentally readable using evaluation and judgement. Therefore a “machine-readable” element does not necessarily require the use of computer technology. Further, as discussed above in the 35 U.S.C. 101 rejection of claim 1 above, the amended independent claims each contain at least an abstract idea, and the additional elements do not integrate the abstract ideas into a practical application. Therefore, the claims remain rejected under 35 U.S.C. 101.
Regarding the rejection applied under 35 U.S.C. 103, Applicant’s amendments overcome the rejection.
Conclusion
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/KURT NICHOLAS PRESSLY/Examiner, Art Unit 2125
/KAMRAN AFSHAR/Supervisory Patent Examiner, Art Unit 2125