DETAILED ACTION
This action is in response to the Applicant Response filed 04 August 2023 for application 18/275,933 filed 04 August 2023.
Claim(s) 5-7, 10, 12, 14-17, 25-26 is/are currently amended.
Claim(s) 27 is/are new.
Claim(s) 18-24 is/are cancelled.
Claim(s) 1-17, 25-27 is/are pending.
Claim(s) 1-17, 25-27 is/are rejected.
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 .
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.
Claim(s) 1-17, 25-27 is/are rejected under 35 U.S.C. 101, because the claim(s) is/are directed to an abstract idea, and because the claim elements, whether considered individually or in combination, do not amount to significantly more than the abstract idea, see Alice Corporation Pty. Ltd. V. CLS Bank International et al., 573 US 208 (2014).
Regarding claim 1, the claim 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 method, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites a(n) method.
The limitation of determining a predicted amino acid sequence of the target protein based on the embedding of the target protein structure, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
The limitation of conditioning a generative neural network having a plurality of generative neural network parameters on the embedding of the target protein structure, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
The limitation of generating ... a representation of the predicted amino acid sequence of the target protein, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
The limitation of determining a structural similarity measure between: (i) the predicted protein structure of the protein having the predicted amino acid sequence, and (ii) the target protein structure, as drafted, is a process that, under its broadest reasonable interpretation, covers a mathematical concept. The limitation encompasses calculating a similarity value.
The limitation of determining gradients of the structural similarity measure with respect to the embedding neural network parameters and the generative neural network parameters, as drafted, is a process that, under its broadest reasonable interpretation, covers a mathematical concept. The limitation encompasses calculating gradients.
The limitation of adjusting current values of the embedding neural network parameters and the generative neural network parameters using the gradients of the structural similarity measure, as drafted, is a process that, under its broadest reasonable interpretation, covers a mathematical concept. The limitation encompasses calculating parameter values.
If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind, then it falls within the "Mental Processes" grouping. If a claim limitation, under its broadest reasonable interpretation, covers performance of mathematical concepts, then it falls within the "Mathematical Concepts" grouping. Accordingly, the claim recites an abstract idea.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated into a practical application.
The claim recites additional element(s) – one or more data processing apparatus. The additional element(s) is/are recited at a high-level of generality (i.e., as generic computer components performing generic computer functions of executing instructions on the computers) such that it amounts to no more than mere instructions to apply the exception using generic computer components (MPEP 2106.05(b)).
The claim recites additional element(s) – embedding neural network, generative neural network, protein folding neural network. The additional element(s) is/are recited at a high-level of generality such that it amounts to no more than indicating a field of use or technological environment in which to apply the judicial exception (MPEP 2106.05(h)).
The claim recites processing an input characterizing a target protein structure of a target protein using an embedding neural network having a plurality of embedding neural network parameters to generate an embedding of the target protein structure of the target protein; processing the representation of the predicted amino acid sequence using a protein folding neural network to generate a representation of a predicted protein structure of a protein having the predicted amino acid sequence which is simply applying the model recited at a high level of generality and amounts to the recitation of the words “apply it” (or an equivalent) or amounts to no more than mere instructions to implement an abstract idea or other exception on a computer (MPEP 2106.05(f)).
Accordingly, the additional element(s) do(es) not integrate the abstract idea into a practical application because the additional element(s) do(es) not impose any meaningful limits on practicing the abstract idea, and, therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the additional element(s) of:
one or more data processing apparatus amount(s) to no more than mere instructions to apply the exception using generic computer components (MPEP 2106.05(b))
applying the model amount(s) to no more than mere instructions to apply the exception (MPEP 2106.05(f))
embedding neural network, generative neural network, protein folding neural network amount(s) to no more than indicating a field of use or technological environment in which to apply the judicial exception (MPEP 2106.05(h))
The additional element(s) do(es) not provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 2, the claim 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 2 is directed to a method, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites a(n) method.
The limitation of backpropagating gradients of the structural similarity measure through the protein folding neural network into the generative neural network and the embedding neural network, as drafted, is a process that, under its broadest reasonable interpretation, covers a mathematical concept. The limitation encompasses calculating gradients.
If a claim limitation, under its broadest reasonable interpretation, covers performance of mathematical concepts, then it falls within the "Mathematical Concepts" grouping. Accordingly, the claim recites an abstract idea.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated
into a practical application. The claim does not recite any additional elements which integrate the
abstract idea into a practical application and, therefore, does not impose any meaningful limits on
practicing the abstract idea. Therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the claim does not recite any additional elements which
provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 3, the claim 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 3 is directed to a method, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites a(n) method.
The limitation of determining gradients of the realism score with respect to the embedding neural network parameters and the generative neural network parameters, as drafted, is a process that, under its broadest reasonable interpretation, covers a mathematical concept. The limitation encompasses calculating gradients.
The limitation of adjusting current values of the embedding neural network parameters and the generative neural network parameters using the gradients of the realism score, as drafted, is a process that, under its broadest reasonable interpretation, covers a mathematical concept. The limitation encompasses calculating parameter values.
If a claim limitation, under its broadest reasonable interpretation, covers performance of mathematical concepts, then it falls within the "Mathematical Concepts" grouping. Accordingly, the claim recites an abstract idea.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated into a practical application.
The claim recites additional element(s) – discriminator neural network. The additional element(s) is/are recited at a high-level of generality such that it amounts to no more than indicating a field of use or technological environment in which to apply the judicial exception (MPEP 2106.05(h)).
The claim recites processing the representation of the predicted protein structure of the protein having the predicted amino acid sequence using a discriminator neural network to generate a realism score that defines a likelihood that the predicted amino acid sequence was generated using the generative neural network which is simply applying the model recited at a high level of generality and amounts to the recitation of the words “apply it” (or an equivalent) or amounts to no more than mere instructions to implement an abstract idea or other exception on a computer (MPEP 2106.05(f)).
Accordingly, the additional element(s) do(es) not integrate the abstract idea into a practical application because the additional element(s) do(es) not impose any meaningful limits on practicing the abstract idea, and, therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the additional element(s) of:
applying the model amount(s) to no more than mere instructions to apply the exception (MPEP 2106.05(f))
discriminator neural network amount(s) to no more than indicating a field of use or technological environment in which to apply the judicial exception (MPEP 2106.05(h))
The additional element(s) do(es) not provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 4, the claim 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 4 is directed to a method, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites a(n) method.
The limitation of backpropagating gradients of the realism score through the discriminator neural network and the protein folding neural network into the generative neural network and the embedding neural network, as drafted, is a process that, under its broadest reasonable interpretation, covers a mathematical concept. The limitation encompasses calculating gradients.
If a claim limitation, under its broadest reasonable interpretation, covers performance of mathematical concepts, then it falls within the "Mathematical Concepts" grouping. Accordingly, the claim recites an abstract idea.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated
into a practical application. The claim does not recite any additional elements which integrate the
abstract idea into a practical application and, therefore, does not impose any meaningful limits on
practicing the abstract idea. Therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the claim does not recite any additional elements which
provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 5, the claim 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 5 is directed to a method, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites a(n) method. The Step 2A Prong One Analysis for claim 3 is applicable here since claim 5 carries out the method of claim 3 but for the recitation of additional element(s) of wherein generating the realism score comprises processing an input that includes both: (i) the representation of the predicted protein structure having the predicted amino acid sequence, and (ii) the representation of the predicted amino acid sequence, using the discriminator neural network.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated into a practical application. In particular, the claim recites additional information regarding the model and the element(s) do(es) not apply the exception in a meaningful way (MPEP 2106.05(e)). Accordingly, the additional element(s) do(es) not integrate the abstract idea into a practical application because the additional element(s) do(es) not impose any meaningful limits on practicing the abstract idea, and, therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the additional element(s) of additional information regarding the model do(es) not apply the exception in a meaningful way (MPEP 2106.05(e)). Not applying the exception in a meaningful way does not provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 6, the claim 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 6 is directed to a method, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites a(n) method.
The limitation of determining a sequence similarity measure between: (i) the predicted amino acid sequence of the target protein, and (ii) a target amino acid sequence of the target protein, as drafted, is a process that, under its broadest reasonable interpretation, covers a mathematical concept. The limitation encompasses calculating a similarity value.
The limitation of determining gradients of the sequence similarity measure with respect to the embedding neural network parameters and the generative neural network parameters, as drafted, is a process that, under its broadest reasonable interpretation, covers a mathematical concept. The limitation encompasses calculating gradients.
The limitation of adjusting current values of the embedding neural network parameters and the generative neural network parameters using the gradients of the sequence similarity measure, as drafted, is a process that, under its broadest reasonable interpretation, covers a mathematical concept. The limitation encompasses calculating parameter values.
If a claim limitation, under its broadest reasonable interpretation, covers performance of mathematical concepts, then it falls within the "Mathematical Concepts" grouping. Accordingly, the claim recites an abstract idea.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated
into a practical application. The claim does not recite any additional elements which integrate the
abstract idea into a practical application and, therefore, does not impose any meaningful limits on
practicing the abstract idea. Therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the claim does not recite any additional elements which
provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 7, the claim 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 method, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites a(n) method. The Step 2A Prong One Analysis for claim 1 is applicable here since claim 7 carries out the method of claim 1 but for the recitation of additional element(s) of wherein the embedding neural network input characterizing the target protein structure comprises: (i) a respective initial pair embedding corresponding to each pair of amino acids in the target protein that characterizes a distance between the pair of amino acids in the target protein structure, and (ii) a respective initial single embedding corresponding to each amino acid in the target protein.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated into a practical application. In particular, the claim recites additional information regarding the data and the element(s) do(es) not apply the exception in a meaningful way (MPEP 2106.05(e)). Accordingly, the additional element(s) do(es) not integrate the abstract idea into a practical application because the additional element(s) do(es) not impose any meaningful limits on practicing the abstract idea, and, therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the additional element(s) of additional information regarding the data do(es) not apply the exception in a meaningful way (MPEP 2106.05(e)). Not applying the exception in a meaningful way does not provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 8, the claim 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 8 is directed to a method, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites a(n) method.
The limitation of updating the current single embeddings, in accordance with values of the update block parameters of the update block, based on the current pair embeddings, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
The limitation of updating the current pair embeddings, in accordance with the values of the update block parameters of the update block, based on the updated single embeddings, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind, then it falls within the "Mental Processes" grouping. Accordingly, the claim recites an abstract idea.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated into a practical application.
The claim recites wherein a first update block in the sequence of update blocks receives the initial pair embeddings and the initial single embeddings; wherein a final update block in the sequence of update blocks generates final pair embeddings and final single embeddings which is simply applying the model recited at a high level of generality and amounts to the recitation of the words “apply it” (or an equivalent) or amounts to no more than mere instructions to implement an abstract idea or other exception on a computer (MPEP 2106.05(f)).
The claim recites receiving current pair embeddings and current single embeddings, which is simply receiving data recited at a high level of generality. This is nothing more than insignificant extra-solution activity (MPEP 2106.05(g)).
The claim recites wherein the embedding neural network comprises a sequence of update blocks, wherein each update block has a respective set of update block parameters ... which is simply additional information regarding the model, and the element(s) do(es) not apply the exception in a meaningful way (MPEP 2106.05(e)).
Accordingly, the additional element(s) do(es) not integrate the abstract idea into a practical application because the additional element(s) do(es) not impose any meaningful limits on practicing the abstract idea, and, therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the additional element(s) of:
applying the model amount(s) to no more than mere instructions to apply the exception (MPEP 2106.05(f))
receiving data amount(s) to no more than insignificant extra-solution activity (MPEP 2106.05(g)), wherein the insignificant extra-solution activity is the well-understood routine and conventional activit(y/ies) of receiving or transmitting data over a network and/or storing and retrieving information in memory (MPEP 2016.05(d))
additional information regarding the model do(es) not apply the exception in a meaningful way (MPEP 2106.05(e))
The additional element(s) do(es) not provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 9, the claim 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 method, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites a(n) method. The Step 2A Prong One Analysis for claim 8 is applicable here since claim 9 carries out the method of claim 8 but for the recitation of additional element(s) of wherein generating the embedding of the target protein structure of the target protein comprises: generating the embedding of the target protein structure of the target protein based on the final pair embeddings, the final single embeddings, or both.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated into a practical application. In particular, the claim recites additional information regarding the data and the element(s) do(es) not apply the exception in a meaningful way (MPEP 2106.05(e)). Accordingly, the additional element(s) do(es) not integrate the abstract idea into a practical application because the additional element(s) do(es) not impose any meaningful limits on practicing the abstract idea, and, therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the additional element(s) of additional information regarding the data do(es) not apply the exception in a meaningful way (MPEP 2106.05(e)). Not applying the exception in a meaningful way does not provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 10, the claim 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 method, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites a(n) method. The Step 2A Prong One Analysis for claim 8 is applicable here since claim 10 carries out the method of claim 8 but for the recitation of additional element(s) of wherein updating the current single embeddings based on the current pair embeddings comprises: updating the current single embeddings using attention over the current single embeddings, wherein the attention is conditioned on the current pair embeddings.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated into a practical application. In particular, the claim recites additional information regarding the model and the element(s) do(es) not apply the exception in a meaningful way (MPEP 2106.05(e)). Accordingly, the additional element(s) do(es) not integrate the abstract idea into a practical application because the additional element(s) do(es) not impose any meaningful limits on practicing the abstract idea, and, therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the additional element(s) of additional information regarding the model do(es) not apply the exception in a meaningful way (MPEP 2106.05(e)). Not applying the exception in a meaningful way does not provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 11, the claim 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 method, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites a(n) method.
The limitation of generating, based on the current single embeddings, a plurality of attention weights, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
The limitation of generating, based on the current pair embeddings, a respective attention bias corresponding to each of the attention weights, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
The limitation of generating a plurality of biased attention weights based on the attention weights and the attention biases, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
The limitation of updating the current single embeddings using attention of the current single embeddings based on the biased attention weights, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind, then it falls within the "Mental Processes" grouping. Accordingly, the claim recites an abstract idea.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated
into a practical application. The claim does not recite any additional elements which integrate the
abstract idea into a practical application and, therefore, does not impose any meaningful limits on
practicing the abstract idea. Therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the claim does not recite any additional elements which
provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 12, the claim 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 12 is directed to a method, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites a(n) method.
The limitation of applying a transformation operation to the updated single embeddings, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
The limitation of updating the current pair embeddings by adding a result of the transformation operation to the current pair embeddings, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind, then it falls within the "Mental Processes" grouping. Accordingly, the claim recites an abstract idea.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated
into a practical application. The claim does not recite any additional elements which integrate the
abstract idea into a practical application and, therefore, does not impose any meaningful limits on
practicing the abstract idea. Therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the claim does not recite any additional elements which
provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 13, the claim 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 method, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites a(n) method. The Step 2A Prong One Analysis for claim 12 is applicable here since claim 13 carries out the method of claim 12 but for the recitation of additional element(s) of wherein the transformation operation comprises an outer product operation.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated into a practical application. In particular, the claim recites additional information regarding the model and the element(s) do(es) not apply the exception in a meaningful way (MPEP 2106.05(e)). Accordingly, the additional element(s) do(es) not integrate the abstract idea into a practical application because the additional element(s) do(es) not impose any meaningful limits on practicing the abstract idea, and, therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the additional element(s) of additional information regarding the model do(es) not apply the exception in a meaningful way (MPEP 2106.05(e)). Not applying the exception in a meaningful way does not provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 14, the claim 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 14 is directed to a method, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites a(n) method.
The limitation of wherein updating the current pair embeddings based on the updated single embeddings further comprises, after adding the result of the transformation operation to the current pair embeddings: updating the current pair embeddings using attention over the current pair embeddings, wherein the attention is conditioned on the current pair embeddings, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind, then it falls within the "Mental Processes" grouping. Accordingly, the claim recites an abstract idea.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated
into a practical application. The claim does not recite any additional elements which integrate the
abstract idea into a practical application and, therefore, does not impose any meaningful limits on
practicing the abstract idea. Therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the claim does not recite any additional elements which
provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 15, the claim 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 15 is directed to a method, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites a(n) method.
The limitation of processing the embedding of the target protein structure to generate data defining parameters of a probability distribution over a latent space, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
The limitation of sampling a latent variable from the latent space in accordance with the probability distribution over the latent space, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
The limitation of processing the latent variable sampled from the latent space to generate the representation of the predicted amino acid sequence, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind, then it falls within the "Mental Processes" grouping. Accordingly, the claim recites an abstract idea.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated
into a practical application. The claim does not recite any additional elements which integrate the
abstract idea into a practical application and, therefore, does not impose any meaningful limits on
practicing the abstract idea. Therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the claim does not recite any additional elements which
provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 16, the claim 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, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites a(n) method.
The limitation of for each position in the predicted amino acid sequence: processing: (i) the embedding of the target protein structure, and (ii) data defining amino acids at any preceding positions in the predicted amino acid sequence, to generate a probability distribution over a set of possible amino acids, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
The limitation of for each position in the predicted amino acid sequence: ... sampling an amino acid for the position in the predicted amino acid sequence from the set of possible amino acids in accordance with the probability distribution over the set of possible amino acids, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind, then it falls within the "Mental Processes" grouping. Accordingly, the claim recites an abstract idea.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated
into a practical application. The claim does not recite any additional elements which integrate the
abstract idea into a practical application and, therefore, does not impose any meaningful limits on
practicing the abstract idea. Therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the claim does not recite any additional elements which
provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 17, the claim 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, which is directed to a process, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites a(n) method. The Step 2A Prong One Analysis for claim 1 is applicable here since claim 17 carries out the method of claim 1 but for the recitation of additional element(s) of obtaining a representation of a three-dimensional shape and size of a surface portion of a target body, and obtaining the target protein structure as a structure including a portion which has a shape and size complementary to the shape and size of the surface portion of the target body.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated into a practical application.
The claim recites obtaining a representation of a three-dimensional shape and size of a surface portion of a target body, and obtaining the target protein structure as a structure including a portion which has a shape and size complementary to the shape and size of the surface portion of the target body, which is simply receiving data recited at a high level of generality. This is nothing more than insignificant extra-solution activity (MPEP 2106.05(g)).
Accordingly, the additional element(s) do(es) not integrate the abstract idea into a practical application because the additional element(s) do(es) not impose any meaningful limits on practicing the abstract idea, and, therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the additional element(s) of:
receiving data amount(s) to no more than insignificant extra-solution activity (MPEP 2106.05(g)), wherein the insignificant extra-solution activity is the well-understood routine and conventional activit(y/ies) of receiving or transmitting data over a network and/or storing and retrieving information in memory (MPEP 2016.05(d))
The additional element(s) do(es) not provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 25, the claim 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 system with a computer, which is directed to a machine, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites a(n) system.
The limitation of determining a predicted amino acid sequence of the target protein based on the embedding of the target protein structure, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
The limitation of conditioning a generative neural network having a plurality of generative neural network parameters on the embedding of the target protein structure, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
The limitation of generating ... a representation of the predicted amino acid sequence of the target protein, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
The limitation of determining a structural similarity measure between: (i) the predicted protein structure of the protein having the predicted amino acid sequence, and (ii) the target protein structure, as drafted, is a process that, under its broadest reasonable interpretation, covers a mathematical concept. The limitation encompasses calculating a similarity value.
The limitation of determining gradients of the structural similarity measure with respect to the embedding neural network parameters and the generative neural network parameters, as drafted, is a process that, under its broadest reasonable interpretation, covers a mathematical concept. The limitation encompasses calculating gradients.
The limitation of adjusting current values of the embedding neural network parameters and the generative neural network parameters using the gradients of the structural similarity measure, as drafted, is a process that, under its broadest reasonable interpretation, covers a mathematical concept. The limitation encompasses calculating parameter values.
If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind, then it falls within the "Mental Processes" grouping. If a claim limitation, under its broadest reasonable interpretation, covers performance of mathematical concepts, then it falls within the "Mathematical Concepts" grouping. Accordingly, the claim recites an abstract idea.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated into a practical application.
The claim recites additional element(s) – system, one or more computers, one or more storage devices, instructions. The additional element(s) is/are recited at a high-level of generality (i.e., as generic computer components performing generic computer functions of executing instructions on the computers) such that it amounts to no more than mere instructions to apply the exception using generic computer components (MPEP 2106.05(b)).
The claim recites additional element(s) – embedding neural network, generative neural network, protein folding neural network. The additional element(s) is/are recited at a high-level of generality such that it amounts to no more than indicating a field of use or technological environment in which to apply the judicial exception (MPEP 2106.05(h)).
The claim recites processing an input characterizing a target protein structure of a target protein using an embedding neural network having a plurality of embedding neural network parameters to generate an embedding of the target protein structure of the target protein; processing the representation of the predicted amino acid sequence using a protein folding neural network to generate a representation of a predicted protein structure of a protein having the predicted amino acid sequence which is simply applying the model recited at a high level of generality and amounts to the recitation of the words “apply it” (or an equivalent) or amounts to no more than mere instructions to implement an abstract idea or other exception on a computer (MPEP 2106.05(f)).
Accordingly, the additional element(s) do(es) not integrate the abstract idea into a practical application because the additional element(s) do(es) not impose any meaningful limits on practicing the abstract idea, and, therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the additional element(s) of:
system, one or more computers, one or more storage devices, instructions amount(s) to no more than mere instructions to apply the exception using generic computer components (MPEP 2106.05(b))
applying the model amount(s) to no more than mere instructions to apply the exception (MPEP 2106.05(f))
embedding neural network, generative neural network, protein folding neural network amount(s) to no more than indicating a field of use or technological environment in which to apply the judicial exception (MPEP 2106.05(h))
The additional element(s) do(es) not provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 26, the claim 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 computer storage media, which is directed to an article of manufacture, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites computer storage media.
The limitation of determining a predicted amino acid sequence of the target protein based on the embedding of the target protein structure, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
The limitation of conditioning a generative neural network having a plurality of generative neural network parameters on the embedding of the target protein structure, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
The limitation of generating ... a representation of the predicted amino acid sequence of the target protein, as drafted, is a process that, under its broadest reasonable interpretation, covers a mental process. The limitation is directed to observation, evaluation, judgment and opinion and is a process capable of being performed by a human mentally or using pen and paper.
The limitation of determining a structural similarity measure between: (i) the predicted protein structure of the protein having the predicted amino acid sequence, and (ii) the target protein structure, as drafted, is a process that, under its broadest reasonable interpretation, covers a mathematical concept. The limitation encompasses calculating a similarity value.
The limitation of determining gradients of the structural similarity measure with respect to the embedding neural network parameters and the generative neural network parameters, as drafted, is a process that, under its broadest reasonable interpretation, covers a mathematical concept. The limitation encompasses calculating gradients.
The limitation of adjusting current values of the embedding neural network parameters and the generative neural network parameters using the gradients of the structural similarity measure, as drafted, is a process that, under its broadest reasonable interpretation, covers a mathematical concept. The limitation encompasses calculating parameter values.
If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind, then it falls within the "Mental Processes" grouping. If a claim limitation, under its broadest reasonable interpretation, covers performance of mathematical concepts, then it falls within the "Mathematical Concepts" grouping. Accordingly, the claim recites an abstract idea.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated into a practical application.
The claim recites additional element(s) – one or more ... computer storage media, instructions, one or more computers. The additional element(s) is/are recited at a high-level of generality (i.e., as generic computer components performing generic computer functions of executing instructions on the computers) such that it amounts to no more than mere instructions to apply the exception using generic computer components (MPEP 2106.05(b)).
The claim recites additional element(s) – embedding neural network, generative neural network, protein folding neural network. The additional element(s) is/are recited at a high-level of generality such that it amounts to no more than indicating a field of use or technological environment in which to apply the judicial exception (MPEP 2106.05(h)).
The claim recites processing an input characterizing a target protein structure of a target protein using an embedding neural network having a plurality of embedding neural network parameters to generate an embedding of the target protein structure of the target protein; processing the representation of the predicted amino acid sequence using a protein folding neural network to generate a representation of a predicted protein structure of a protein having the predicted amino acid sequence which is simply applying the model recited at a high level of generality and amounts to the recitation of the words “apply it” (or an equivalent) or amounts to no more than mere instructions to implement an abstract idea or other exception on a computer (MPEP 2106.05(f)).
Accordingly, the additional element(s) do(es) not integrate the abstract idea into a practical application because the additional element(s) do(es) not impose any meaningful limits on practicing the abstract idea, and, therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the additional element(s) of:
one or more ... computer storage media, instructions, one or more computers amount(s) to no more than mere instructions to apply the exception using generic computer components (MPEP 2106.05(b))
applying the model amount(s) to no more than mere instructions to apply the exception (MPEP 2106.05(f))
embedding neural network, generative neural network, protein folding neural network amount(s) to no more than indicating a field of use or technological environment in which to apply the judicial exception (MPEP 2106.05(h))
The additional element(s) do(es) not provide an inventive concept, and, therefore, the claim is not patent eligible.
Regarding claim 27, the claim 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 computer storage media, which is directed to an article of manufacture, one of the statutory categories.
Step 2A Prong One Analysis: The claim recites computer storage media.
The limitation of backpropagating gradients of the structural similarity measure through the protein folding neural network into the generative neural network and the embedding neural network, as drafted, is a process that, under its broadest reasonable interpretation, covers a mathematical concept. The limitation encompasses calculating gradients.
If a claim limitation, under its broadest reasonable interpretation, covers performance of mathematical concepts, then it falls within the "Mathematical Concepts" grouping. Accordingly, the claim recites an abstract idea.
Step 2A Prong Two Analysis: With respect to the abstract idea, the judicial exception is not integrated
into a practical application. The claim does not recite any additional elements which integrate the
abstract idea into a practical application and, therefore, does not impose any meaningful limits on
practicing the abstract idea. Therefore, the claim is directed to an abstract idea.
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 idea into a practical application, the claim does not recite any additional elements which
provide an inventive concept, and, therefore, the claim is not patent eligible.
Conclusion
Any inquiry concerning this communication or earlier communication from the examiner should be directed to MARSHALL WERNER whose telephone number is (469) 295-9143. The examiner can normally be reached on Monday – Thursday 7:30 AM – 4:30 PM ET.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Kamran Afshar, can be reached at (571) 272-7796. The fax number for the organization where this application or proceeding is assigned is (571) 273-8300.
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/MARSHALL L WERNER/ Primary Examiner, Art Unit 2125