[00:00:00] Speaker 01:
and 13 Cyber Genetics Corporation against the Institute of Environmental Science.

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Mr. Supko.

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Thank you, Your Honor.

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May it please the court, Mark Supko for cyber genetics.

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The invention in this case is a never before used combination of physical and analytical operations that dramatically improved on existing forensic DNA analysis technology.

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It made it possible for the first time

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to efficiently and accurately determine if a criminal suspect's DNA is in a physical specimen containing a mixture of DNA from multiple people.

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The invention is not abstract.

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It embodies a specific application of mathematics to provide a concrete solution to a technological problem.

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And it was far from well understood, routine, or conventional at the time of the invention.

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The record confirms that Dr. Perlin was the first to solve the DNA mixture problem in this way.

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My plan today is to focus on application of the Mayo-Alice test.

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Subject to questions from the court, we'll rest on our briefing with regard to the district court's misapplication of the Rule 12b6 standard and its erroneous approach to claim construction disputes.

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I will say that we believe either one of those issues should have led the district court to deny ESR's motion to dismiss.

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This is Judge Taranto.

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So as I read the district court's opinion and the red brief, the framing there is something like this.

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We have now repeatedly

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said that on ALICE step one, figuring out what the claim is directed to, you look at what the patents make clear is the focus of the claimed advance for what the improvement is that is asserted to be an advance.

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Here, there are the first four self-evidently physical steps.

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Right?

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Get the DNA mixture, amplify the relevant DNA, make signal observations, record them.

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All of that is, I think, under the patents, undisputedly old.

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That's what everybody was doing.

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What the patent does that says is, in fact, an advance is what

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is a new technique for analyzing the data, culminating in a once you get a certain result, you then compare it to unknown.

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Why isn't the only thing here that is in fact an advanced, entirely mathematical, and therefore abstract, and therefore there's nothing left?

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Your Honor, even if you were to take the position that the analysis of the genotypes and mixture weights is purely mathematical, there's still a very physical advance here with respect to quantification and accounting for the variance of the amplification process.

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I don't understand the term, the quantification and accounting as being physical.

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I thought you're starting with a pool of data, namely the signal representations, and you're trying to figure out what that data means.

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And what's new here is the mathematical analysis tools for figuring out what that data means.

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And that's it.

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Your Honor, I would submit that the limitations in the claim with respect to

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the variance of the amplification process is describing and then using something physical.

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Those four physical steps that you identified create a synthetic, a collection of synthetic copies of genetic material that's then used as a proxy for determining what the genotypes and mixture weights are in the physical sample.

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In claim one of the 021 patent, for example, element H

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requires deriving with a computer a data variance of the amplification process.

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And then when you're determining the genotypes and the mixture weights, you're doing that using a model that includes the data variance value.

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What that data variance value is is a comparison between the synthetic copies and what would have been expected from a perfect replication process.

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Nowhere in the prior art was anybody quantifying that difference between the result of the PCR amplification and what would have been expected and then accounting for that when determining what the genotypes in the physical sample are.

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And as a result of not quantifying and accounting for that variance of the amplification process, the results were inherently inaccurate.

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So in the context of criminal forensic science, those types of inaccuracies caused innocent people to be convicted and guilty people to go free.

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That was a specific physically-oriented technological advance that achieved significant improvements in the process compared to prior DNA analysis technology that didn't do that.

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That's a physical consideration we would submit, not a purely mathematical consideration.

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I think it's instructive to take a look at the aspects that you said were purely mathematical, Your Honor.

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And ESR makes much in their brief about the so-called standard linear equation.

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D equals G times W plus E that is discussed in the specification and then is employed for determining the genotypes and the mixture weight values for the contributors to that physical specimen.

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Well, first off, that's not a standard equation.

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There's nothing in this record that suggests that anyone before Dr. Perlin tried to describe the DNA mixture problem using that particular equation.

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However, that's a model.

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And what a model is, it's a mathematical way of describing something physical.

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It's not abstract.

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It's describing something physical.

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The D there is the quantitative genotyping data that was produced by the PCR amplification process, a laboratory process.

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The G represents the genotypes of the actual contributors

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to the physical sample, the physical DNA sample.

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The W is the relative contributions, the weight values, the relative amounts of DNA from each of the contributors to that physical sample.

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And the E here in the context of this invention is that variance of the amplification process that I discussed a moment ago.

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That equation is describing something very, very physical.

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It's not an abstract mathematical concept, nor do these claims try to claim either that equation or any other specific mathematical concept.

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It's a series of steps, very specifically recited, that include physical operations at the beginning, analytical operations that determine what the genotypes and the weight values of the contributors are, and then

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not just a comparing step, but actually determining whether a particular suspect's DNA is in that original physical sample.

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So while we're applying mathematics, the claim isn't directed to any mathematical concepts.

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And cases like Diamond v. Deer, cases like Transova, cases like McRoe, they all tell us

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that it's OK to apply mathematics as long as you're not claiming any mathematical concepts.

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And we would submit that's the case here.

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This case is very much like Transova.

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In Transova, the invention was the application of very sophisticated mathematics to improve the operation of a particle separator.

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The invention, the advance, was the mathematics.

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There was no change to the particle separator itself.

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Just like in Transova, the mathematics here, the analytical operations, achieve an improved result, determining whether a suspect's DNA is in a physical sample, only when they're combined with the other steps of the claim.

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Achieving the same function, just in an analytical way, because it's not physically possible

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to separate out the DNA from multiple people from a DNA mixture.

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It can only be done analytically.

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And I'd like to turn briefly to the step two analysis as well.

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Even if this court were to conclude that the claims are directed to an abstract idea or a mathematical algorithm, which we don't agree is the case, there are at least two

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inventive concepts that are embodied in these claims.

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The first is the application of that linear model, the linear matrix analysis that I discussed a moment ago.

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The patents explain that approaching the DNA mixture problem as a linear matrix equation, which nobody had ever done before.

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There's nothing in the record to suggest that anyone did that before.

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It reduced the complexity of the DNA mixture problem

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to such an extent that a properly programmed personal computer could achieve something that the prior art processes couldn't do with even the most powerful computers.

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That comes right out of the specification.

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This is a technological improvement.

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It's expressly discussed in the specification.

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There's no contrary evidence in the record.

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Improve the performance of computer-based DNA analysis technology.

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ESR completely ignores those limitations in its step two analysis.

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But the cases that it cites don't say it's appropriate to ignore the mathematical limitations of the claims.

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The test there is whether or not the claims advance the innovation.

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It can't be just the novelty of the alleged abstract idea.

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But a performance improvement provided by the alleged abstract idea certainly can be your inventive concept.

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And is your view that there's something in TransOVA that there actually was no change in anything being done physically?

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There certainly was in McRoe, right?

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The physical thing that the human eye saw when watching these animations on the screen, that was actually different by the use of the mathematical or the technique for doing lip syncing.

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Change in something physical.

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You say that there was no such change in anything physical in TransOVA?

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In TransOVA, Your Honor, what was...

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May I finish the response, John?

[00:12:25] Speaker 03:
Yes, please respond.

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In TransOVA, the change was in the operation of the particle separator.

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The particle separator was able to more efficiently, more effectively separate the particles.

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But the only reason why it was able to do that was because the sophisticated mathematics that were used to program the particle separator.

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That sounds

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rather a lot like McRoe, namely, there was a change in the physical operation of something.

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Your Honor, and I guess what I understand the district court theory to have been and the red brief theory is that this case is different because there is no change in the physical operation of anything.

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The DNA collection, amplification, signal generation,

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produces data, that data was produced before this patent, what this patent does in a very useful way, I will assume, is to tell you what that data means.

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But it doesn't do anything else.

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Your Honor, I would submit that what the claimed invention achieves here is generating better information

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about something physical, better information with respect to the genotypes of the contributors to the physical DNA mixture, superior to what the prior art achieved.

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Similar to in McRoe, what was being achieved through the application of mathematics was improving information, visual information,

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that was presented to the user, more lifelike animation.

[00:14:15] Speaker 02:
No, no, no.

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What the eye detects is not information.

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It's detecting something physical, by definition.

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The eye is seeing something.

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The eye does not see information.

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Information is the abstract character that is taken away from something seen.

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In McRoe, what the

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I was seeing was actually different from what it would have seen without the change in animation techniques.

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I would agree with that, Your Honor.

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McRoe does say that there was nothing tangible about the invention, but I would agree that there was something physical in terms of what was displayed to the user.

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Here, at the culmination of the process that's recited in the claims, we don't just have information that's

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displayed, contrary to ESR's argument, there was no display step in this claim.

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What's done is there is a determination of a genotype for a particular contributor to the DNA mixture and then using that to... Please complete the slide.

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Sure.

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Thank you, Your Honor.

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And then using that to make a determination, a real-world determination of whether a particular suspect's DNA was in that physical DNA mixture.

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In fact, since we're extending, let me ask you a question that's been on my mind from the beginning.

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These patents have expired.

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Is that right?

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So what sort of relief is being requested?

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Just damages for past infringement?

[00:16:01] Speaker 03:
Yes, Your Honor, that's correct.

[00:16:03] Speaker 01:
Okay.

[00:16:04] Speaker 01:
All right, let's hear from the other side.

[00:16:09] Speaker 01:
Mr. Vernyuk.

[00:16:10] Speaker 00:
Good morning.

[00:16:12] Speaker 00:
My name is Sergey Vernyuk on behalf of the Institute for Environmental Science and Research and Niche Vision Incorporated.

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May it please the court?

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This morning, I'd like to, in addition to answering any questions that the court may have, I'd like to discuss the main points of dispute under the

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Alice test, stage one, what the claim is directed to, and then stage two, the inventive concept.

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And if there's any time, perhaps a touch on the technological improvements argument.

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Under step one, as Judge Toronto correctly and briefly summarized, the question is, what is the focus of the claim?

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What is its claim to advance over the prior R's?

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It is just a mathematical algorithm to analyze the DNA data, just as it was in the two Stanford cases.

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Does the claim require any new data, data that had not previously been amassed?

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No, Your Honor.

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If we look at, for example, the 021 patent,

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The patents virtually share the same written description, so I will just focus on the 021 patent.

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In column one, for example, the paragraph that starts with line 30, it describes that oftentimes you may have a mixed DNA sample that needs to be analyzed, and previously it was done qualitatively, but then the subsequent paragraph says,

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Under appropriate data generation conditions, the peak data can be quantitatively analyzed.

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And it goes on to say such quantitative approaches have spawned heuristic and computer-based methods that can potentially resolve these complex data.

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These prior statistical computer programs are limited.

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And then it talks about, references three papers that talk about those prior art computer-based

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programs to resolve mixture data.

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So even the idea of using a computer to resolve or deconvolute a mixture, a DNA mixture, that was known.

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The only improvement here, alleged improvement, is the algorithm that is used to do this analysis.

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The front-end steps remain the same.

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The ultimate goal is the same.

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It's just

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the only difference is the algorithm that is used to get to that end goal.

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The specification spends maybe a couple of columns, columns three and four, just briefly mentioning the front-end steps, and then the rest of it talks about the algorithm.

[00:19:06] Speaker 02:
And if we compare the... Can I ask you the following question, and I will apologize in advance for any

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technical imprecision.

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So part of the mathematical structure here is putting into matrix form a bunch of information that could otherwise be written as a series of equations that would have to be solved simultaneously.

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Another part has to do with what is discussed mostly in column 14 about, and follow on columns, the more statistical side of things.

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And in particular, the discussion of, I'm just gonna call them several different kinds of variances.

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And I'm interested if you can

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in your explanation of the variances that are part of, there's a reference to variance in the claim, some slightly different references.

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And I wonder if you could explain what's going on there.

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Are these the variances in the usual pool of data, what's the spread, you know, square of the,

[00:20:35] Speaker 02:
well, just the spread, or is there something, are there other concepts of variance that work where you're trying to determine how the data compares to some other information?

[00:20:50] Speaker 00:
Certainly, Your Honor.

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So in column 14, around line 20, we have the reference to the variance of the data D. Then in line 44, we have the variance

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of the mixture weights W, and then at around line 57, we have the variance of the genotype estimate B. So from the basic, the core linear equation, D equals GW, the first variance around line 20, that's the variance of the D side on the left side of the equation.

[00:21:26] Speaker 02:
And that variance is just the usual spread measure?

[00:21:31] Speaker 00:
Correct.

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And that is the variance that is recited in the claims because, for example, element H, step H of claim one of the 021 patents is deriving with a computer a data variance.

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So this variance of the data, that's what is referred to in column 14, line 20.

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And when we look at that equation that appears around line 29, it says that this variance

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It really is the difference between the data that we've quantified from the sample subtracted from that matrix, G times W, which is the calculated or what we would have expected to see under our assumed contributor genotypes that are in G and under our assumed or our set mixture weight, which is in vector W. So that just says

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What's the data that we've gotten from the actual DNA mixture?

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And how far away is it?

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What's its difference from what we would have expected to get from our calculation based on our assumed genotypes and assumed contributor proportions?

[00:22:47] Speaker 02:
Okay, thank you.

[00:22:49] Speaker 00:
Sure.

[00:22:50] Speaker 00:
And, yeah, cybergenetics makes much of these physical laboratory steps and

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Perhaps one may say those might be the only differences between our case and Stanford because Stanford, both Stanford opinions, the claims there started with either receiving genotype data or receiving allele data.

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But those first steps necessarily assumed that certain laboratory steps were done to convert a human's DNA to such data.

[00:23:25] Speaker 00:
We humans, we have biological tissues or cells.

[00:23:31] Speaker 00:
They need to somehow be converted to the data.

[00:23:33] Speaker 00:
So in Stanford, those steps weren't expressly recited, but they were necessary in order to get the data to do the analysis.

[00:23:43] Speaker 00:
And so if the result in Stanford, would it really have been any different if the claims expressly recited such steps?

[00:23:52] Speaker 00:
The Perkin-Elmer decision cited in our brief and NRA BRCA1 decisions, they say no, because both of those cases had claims directed to abstract ideas, even though they had physical data gathering steps at the beginning, like for example, PCR, Amplific,

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amplification at the front end.

[00:24:15] Speaker 00:
And the same goes for the claims in Mayo.

[00:24:18] Speaker 00:
Those front-end steps, if we allow the claims here to be eligible, find them to be eligible, then really the results would be just based on draftsman's art.

[00:24:29] Speaker 00:
If you could take Stanford's claims, add some routine, conventional, well-known steps at the front end that cyber genetics claims it didn't invent, that would really turn the results

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on just draftsman's art.

[00:24:45] Speaker 01:
But are you saying that these are all routine, conventional steps?

[00:24:51] Speaker 00:
The front-end data gathering steps, yes, Your Honor.

[00:24:54] Speaker 00:
Those are all routine and conventional, and cyber genetics admits that those were well-known.

[00:25:00] Speaker 00:
That's in Appendix 401.

[00:25:02] Speaker 01:
Not just the front-end.

[00:25:03] Speaker 01:
All of the steps.

[00:25:06] Speaker 00:
Well, all of the steps include the mathematical algorithm.

[00:25:09] Speaker 00:
And that mathematical algorithm, that is what, at step one, is the claimed advance.

[00:25:18] Speaker 00:
And if we were to look at the novelty or the unconventionality of all of the steps, that would be conflating a 102 inquiry with a 101 inquiry, which are separate inquiries.

[00:25:34] Speaker 00:
Turning to step two of the ALICE test,

[00:25:38] Speaker 00:
We look at what else is there in the claims that could save them.

[00:25:42] Speaker 00:
Unlike my friend on the other side, the claims don't, I'm sorry, we don't ignore the algorithm steps.

[00:25:54] Speaker 00:
We just note that those steps are directed to the abstract idea that cannot provide the inventive concept.

[00:26:03] Speaker 00:
The generic computer and the memory that are recited

[00:26:06] Speaker 00:
Alice says that that is also insufficient to provide an inventive concept.

[00:26:11] Speaker 00:
And then lastly, those data gathering steps at the front end, those physical steps, CyberGenetics admits that it didn't invent them and that they are well known, so they also cannot provide an inventive concept.

[00:26:25] Speaker 00:
And as I've just mentioned, CyberGenetics says, well, the inventive concept is the entire combination.

[00:26:31] Speaker 00:
All of the claims taken together, they are unconventional.

[00:26:35] Speaker 00:
But again, that misunderstands and confuses a Section 101 inquiry with a Section 102 inquiry.

[00:26:44] Speaker 01:
And then lastly... A concern here is that, at least in my mind, is certainly marginal as far as Section 101 is concerned.

[00:26:54] Speaker 01:
How deeply did the presentations go into Sections 102 and 103?

[00:27:03] Speaker 00:
Your Honor, at this stage, procedural posture of the case, they did not because the motion to dismiss was based solely on Section 101, just like it was in Parker versus Luke, for example.

[00:27:19] Speaker 02:
And lastly, we have to assume that the mathematics here might well be new.

[00:27:30] Speaker 02:
But your point is that doesn't matter because it's the wrong type of thing for purposes of 101, which I think you said before.

[00:27:43] Speaker 00:
Yes, Your Honor, that's exactly correct.

[00:27:46] Speaker 00:
In SAT America, for example, an improved mathematical

[00:27:51] Speaker 00:
algorithm is still an abstract idea, same as in the Stanford cases, you know, an enhancement to a mathematical algorithm that... I got it.

[00:28:00] Speaker 02:
You keep referring to the Stanford cases and I don't know what you're referring to.

[00:28:06] Speaker 00:
Well, I'm sorry, Your Honor.

[00:28:06] Speaker 00:
We submitted a notice of Supplemental Authority citing the... Oh, Supplemental Authority, okay.

[00:28:12] Speaker 00:
Sorry.

[00:28:12] Speaker 00:
Yes, there are two recent decisions in Ray, Board of Trustees, Stanford,

[00:28:18] Speaker 00:
We cited those in our letter of supplemental authority.

[00:28:23] Speaker 02:
Those are our decisions or some other court?

[00:28:25] Speaker 00:
Yes, Your Honor, this court.

[00:28:29] Speaker 00:
Sure.

[00:28:31] Speaker 00:
And lastly, I'd like to just briefly touch on this technological improvement argument.

[00:28:39] Speaker 00:
Cybergenetics argues that it can analyze in perhaps seconds trillion, trillion, trillion, trillion possibilities that previously were intractable.

[00:28:49] Speaker 00:
One point right away is that that argument is untethered from the actual claims.

[00:28:57] Speaker 00:
If we read the specification column nine from lines 41 to 57, for example, that is a passage that has that trillion, trillion,

[00:29:09] Speaker 00:
trillion, trillion phrase, that says that that's only the case if the analysis is of 15 loci.

[00:29:17] Speaker 00:
But the representative claims here they only require an analysis of one locus, which does not result in that many possibilities.

[00:29:27] Speaker 00:
In fact, column 22 of the specification, line 49, says that with just one locus,

[00:29:36] Speaker 00:
with the alleles of either three or four, only six possibilities are there.

[00:29:41] Speaker 00:
So the representative claims, they don't invoke that dramatic improvement that allegedly was previously intractable, just like in ChargePoint, for example, where the specification full of additional details just ended in broad claims that did not recite those details.

[00:30:00] Speaker 00:
The computer itself is not improved.

[00:30:03] Speaker 00:
It's just an off-the-shelf PC that remains an off-the-shelf computer.

[00:30:07] Speaker 00:
Any improved accuracy is similar to the claim made in the Stanford decisions that they improved the accuracy in their predictions, which was viewed as insufficient.

[00:30:20] Speaker 00:
And, of course, it's not surprising that cyber genetics would try to fit its case within the framework of the others that were found patent-eligible, but all those other claims

[00:30:31] Speaker 00:
like Transover that it cited, they recited specific concrete limitations that were unconventional versus just broad result-oriented, purely functional language, and they actually resulted in an improved laboratory or industrial process.

[00:30:47] Speaker 00:
In the software-related claims, they specifically improved basic computer capabilities.

[00:30:53] Speaker 00:
But here, as I mentioned, the basic capabilities of a computer remain as they were

[00:30:58] Speaker 00:
No physical results occur, unlike TransOVO, which actually physically separated the particles.

[00:31:05] Speaker 00:
Here, we just have an improved analysis, like Stanford or SAP America, and the language used in the claim steps is purely functional.

[00:31:15] Speaker 00:
For example, amplifying the DNA mixture.

[00:31:18] Speaker 00:
PCR is just one way of amplifying, but this doesn't say use PCR.

[00:31:22] Speaker 00:
It doesn't use any amplification methods.

[00:31:24] Speaker 00:
also producing from the amplification product a signal with signal peaks.

[00:31:30] Speaker 00:
There's more than one way of viewing that.

[00:31:34] Speaker 01:
Please finish your thought.

[00:31:36] Speaker 00:
Thank you, Your Honor.

[00:31:37] Speaker 00:
I was just going to point out that, for example, in the column three, line 66, it mentions capillary electrophoresis and gel electrophoresis as ways of detecting, producing from the amplification product the signal with peaks.

[00:31:52] Speaker 00:
But the claim doesn't recite it.

[00:31:54] Speaker 00:
It just says in a functional way, just get those signal peaks however way you can do it.

[00:32:00] Speaker 00:
And the last, and so for those reasons, we think that the technological improvement argument is insufficient to render the claims patent eligible.

[00:32:11] Speaker 00:
And we ask the court to affirm the district court's decision.

[00:32:14] Speaker 00:
Thank you for your time.

[00:32:16] Speaker 01:
Okay.

[00:32:16] Speaker 01:
Thank you.

[00:32:17] Speaker 01:
Any more questions for counsel?

[00:32:19] Speaker 01:
Nope.

[00:32:20] Speaker 01:
All right.

[00:32:20] Speaker 01:
Mr. Sepko, you have three minutes.

[00:32:24] Speaker 03:
Thank you, your honor.

[00:32:25] Speaker 03:
I'd like to go back to a question that Judge Toronto asked.

[00:32:29] Speaker 03:
Is there any new data that's reflected in these claims?

[00:32:34] Speaker 03:
And I would submit that there absolutely is, with reference to claim one, element H of the 021 patent, deriving with the computer a data variance of the amplification process from a model that includes both the quantitative genotyping data and the linear combination.

[00:32:53] Speaker 03:
There is nothing in this record to suggest that anyone before Dr. Perlin generated that data variance of the amplification process.

[00:33:02] Speaker 03:
Yes, it was recognized that the PCR amplification wasn't a perfect process, but nobody before Dr. Perlin quantified that variance of the amplification process by comparing the actual output of the PCR amplification process

[00:33:22] Speaker 03:
to what was expected from a perfect replication.

[00:33:28] Speaker 03:
And that quantification and then using that in determining the genotypes that were contained in the DNA mixture was entirely new.

[00:33:38] Speaker 03:
ESR's counsel referred to the Stanford case a couple of times, the two cases there.

[00:33:46] Speaker 03:
The problem with the genetic analysis invention in those cases, what

[00:33:52] Speaker 03:
there was no practical application.

[00:33:54] Speaker 03:
That's what the court said in both of those cases.

[00:33:57] Speaker 03:
It was patent ineligible because there was no practical application.

[00:34:01] Speaker 03:
Here, even if you assume that there's a lot of math in this claim, the practical application is determining whether a criminal suspect's DNA is in a physical mixture of DNA.

[00:34:15] Speaker 03:
There was also some discussion, I think Judge Tarana was asking about different forms of variance.

[00:34:23] Speaker 03:
When we're talking about the variance of the amplification process, we're not just talking about the spread of data.

[00:34:29] Speaker 03:
We're talking about the imperfections in the amplification process.

[00:34:35] Speaker 03:
And those are discussed to some extent in the specification.

[00:34:39] Speaker 03:
Those are discussed in great detail in our amended complaint.

[00:34:43] Speaker 03:
The allegations in the amended complaint talk about the problem with the prior art with respect to data variance, the solution that the invention provided, and the technological improvements that the invention provided.

[00:34:56] Speaker 03:
None of those allegations were credited by the district court.

[00:35:00] Speaker 03:
So at a very minimum, the district court should not have granted the motion to dismiss because of disputed issues of fact.

[00:35:08] Speaker 03:
The inventive concept issue, whether or not the use of the variance of the amplification process and the linear matrix analysis, whether or not they were known, routine, conventional, that's an issue of fact.

[00:35:25] Speaker 03:
And the district court resolved that issue of fact against us at the 12b6 stage, which was improper.

[00:35:34] Speaker 03:
Subject to any other questions from the court, my time is up.

[00:35:38] Speaker 01:
Any more questions for Mr. Suffco?

[00:35:40] Speaker 01:
No.

[00:35:42] Speaker 01:
Thank you.

[00:35:42] Speaker 01:
All right.

[00:35:43] Speaker 01:
Thanks to both counsel.

[00:35:45] Speaker 01:
The case is taken under submission.