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` UNITED STATES DISTRICT COURT
` CENTRAL DISTRICT OF CALIFORNIA
`
` THE CALIFORNIA INSTITUTE OF
` TECHNOLOGY,
` Plaintiff and
` Counter-Defendants,
` vs. Case No.
` HUGHES COMMUNICATIONS, 2:13-cv-07245-MRP-JEM
` HUGHES NETWORK SYSTEMS LLC, DISH
` NETWORK L.L.C., and DISHNET
` SATELLITE BROADBAND, L.L.C.,
` Defendant and
` Counter-Plaintiffs.
`____________________________________/
`
` CONFIDENTIAL - OUTSIDE COUNSEL ONLY
`
` VIDEOTAPED DEPOSITION OF BRENDAN FREY, Ph.D.
` REDWOOD SHORES, CALIFORNIA
` TUESDAY, MARCH 10, 2015
`
` REPORTED BY:
` JANIS JENNINGS, CSR 3942, CLR, CCRR
` JOB NO. 90894
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` DEPOSITION OF BRENDAN FREY, Ph.D., taken
`on behalf of the Plaintiff and Counter-Defendants
`at Quinn Emanuel Urquhart & Sullivan, LLP, commencing
`at 9:03 a.m., Tuesday, March 10, 2015, before
`Janis Jennings, Certified Shorthand Reporter
`No. 3942, CLR, CCRR.
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`APPEARANCES OF COUNSEL:
`
` ON BEHALF OF PLAINTIFF AND COUNTER-DEFENDANTS:
` QUINN EMANUEL URQUHART & SULLIVAN
` 555 Twin Dolphin Drive
` Redwood Shores, California 94065
` BY: MARK TUNG, Ph.D., ESQ.
`
` ON BEHALF OF DEFENDANTS AND COUNTER-PLAINTIFFS:
` WILMERHALE
` 350 South Grand Avenue
` Los Angeles, California 90071
` BY: JAMES DOWD, ESQ.
` BRIAN SEEVE, ESQ.
`
` ALSO PRESENT:
` ALAN DIAS, Videographer
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` I N D E X
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`DEPOSITION OF
`BRENDAN FREY, Ph.D.
`
` EXAMINATION
` BY MR. TUNG 8
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` E X H I B I T S
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`Page 5
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`NUMBER DESCRIPTION PAGE
`Exhibit 1 Curriculum Vitae of Brendan J. Frey 39
`
`Exhibit 2 Expert Report of Dr. Brendan Frey 80
` Regarding Invalidity of Patents-In-
` Suit
`
`Exhibit 3 Paper "Irregular Turbocodes"; 82
` HUGHES00001821 - 1828
`
`Exhibit 4 Presentation "Irregular Turbo-Like 102
` Codes"; HUGHES00513989 - 514001
`
`Exhibit 5 Paper "Coding Theorems for 'Turbo-Like' 162
` Codes"; HUGHES00001916 - 1925
`
`Exhibit 6 United States Patent 7,116,710; 166
` CALTECH000001152 - 1162
`
`Exhibit 7 United States Patent 7,916,781; 187
` CALTECH000001918 - 1929
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` E X H I B I T S
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`NUMBER DESCRIPTION PAGE
`Exhibit 8 Low density parity check codes with 213
` semi-random parity check matrix;
` HUGHES00001706 - 1707
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`Exhibit 9 United States Patent 8,284,833; 220
` CALTECH000001930 - 1940
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`REDWOOD SHORES, CALIFORNIA; TUESDAY, MARCH 10, 2015;
` 9:03 A.M.
`
` THE VIDEOGRAPHER: Good morning. I am
`Alan Dias from TSG Reporting. This is a matter
`pending before the United States District Court,
`Central District of California, case number
`2:13-cv-07245-MRP-JEM.
` We are located today at 555 Twin Dolphin
`Drive in the city of Redwood Shores, California.
`Today is March 10th, 2015, and the time is 9:03 a.m.
` Here with me is Janis Jennings, also from
`TSG Reporting.
` Counsel, will you please identify yourself
`and your clients for the record.
` MR. TUNG: My name is Mark Tung from Quinn
`Emanuel for Caltech.
` MR. DOWD: Jim Dowd of Wilmer Cutler
`Pickering Hale and Dorr, and with me today is
`Brian Seeve, also of Wilmer Cutler Pickering Hale
`and Dorr. We represent the defendants and the
`witness, Dr. Frey.
` MR. TUNG: Good morning.
` THE WITNESS: Good morning.
` MR. DOWD: The swearing in.
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` THE VIDEOGRAPHER: This is the videotaped
`deposition of Brendan Frey. Will the court reporter
`please swear in the witness.
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`Page 8
`
` BRENDAN FREY, Ph.D.,
` the deponent herein, was sworn and
` testified as follows:
`
` EXAMINATION
`BY MR. TUNG:
` Q. Good morning.
` A. Good morning.
` Q. Can you state your full name for the record.
` A. Certainly. It's Brendan John Frey.
` Q. And what is your current address?
` A. My current address is Apartment 809,
`500 Sherbourne Street, Toronto, Ontario, Canada, and
`the postal code is M4X 1L1.
` Q. And what is your current position?
` A. I'm a professor at the University of
`Toronto, which is in Toronto, Canada.
` Q. In which department?
` A. I'm in electrical and computer engineering,
`and I also have appointments in computer science and
`also in the Center for Cellular and Biomolecular
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`Research.
` Q. How long have you been at the University of
`Toronto?
` A. I started there in 2001, so about 14 years.
` Q. And have you been with the same department
`at University of Toronto since 2001?
` A. I was first appointed in electrical and
`computer engineering, and then I received a
`cross-appointment to computer science two or three
`years later. And two or three years after that, I
`was appointed to the Center for Cellular and
`Biomolecular Research, which is in the faculty of
`medicine.
` Q. And what courses do you currently teach?
` A. I teach -- there's three different courses
`that I've taught over the last two or three years.
`One of them is a graduate course on machine
`learning, and by "machine learning" I mean
`techniques for training computers to learn from data
`sets of examples.
` That also includes within the course
`teaching them about graphical models, which is
`another important area in machine learning.
`Graphical models would include things like factor
`graphs, Bayesian networks, Markov random fields.
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` I also have taught a senior-level
`undergraduate course, which is called Probabilistic
`Inference and Machine Learning, and that course
`includes similar topics at a more junior level. For
`example, in that course I would teach factor graphs
`but spend more time talking about factor graphs. I
`spend more time giving examples -- for example,
`demonstrating how factor graphs are used in error
`correcting decoding.
` The third undergraduate course that I taught
`is a course on probability and statistics, so that
`would be introductory concepts of probability,
`things like what is probability, phase rule, a
`marginal probability, joint probability, conditional
`probability, other concepts of probability plus more
`advanced topics within the undergraduate curriculum,
`some more advanced topics like use of Markov chains
`and the Viterbi algorithm for error correcting and
`decoding and for other applications as well.
` Q. So none of these courses are focused on
`error correction codes; is that correct?
` MR. DOWD: Objection. Mischaracterizes.
` THE WITNESS: In two of the courses, we
`spend a significant amount of time talking about how
`these techniques can be used for error correcting
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`and decoding; and in particular, some of the
`examples we use are state-of-the-art examples such
`as low-density parity-check codes and turbocodes.
`BY MR. TUNG:
` Q. So which courses do you use low-density
`parity-check codes and turbocodes?
` A. For example, ECE521 would be a course where
`we would -- we -- well, I'm the only person who's
`taught the course. So ECE521 would be an example of
`a course where I would teach factor graphs and the
`sum-product algorithm and the min-sum algorithm. We
`would then look at chains, Markov-chain-type
`structures for the factor graphs. We would look at
`the Viterbi algorithm and the forward-backward
`algorithm, also known as the BCJR algorithm, and
`applications then to convolutional codes and then to
`other codes, most popular ones, of course, being low
`density parity check codes and turbocodes.
` Q. And so in these classes are students
`expected to create new codes, error correcting
`codes?
` A. No. These undergraduate courses, students
`are mainly expected to understand the body of the
`material, and they would be expected to have some
`level of creativity, I suppose. But mainly it's
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`Page 12
`very restricted to understanding how something works
`and being able to vary things. Like for a typical
`example of an assignment -- I can tell you about a
`typical example of an assignment.
` A typical example of an assignment might be
`to randomly generate a permutor, and so then the
`student would be expected to figure out to randomly
`generate a permutor. Another example of an
`assignment would be try changing the polynomials
`that are used in the convolutional code in a
`turbocode, so, you know, use a simple turbocode, try
`changing the way the turbo code is built, that kind
`of thing.
` But it would be -- they would be told --
`kind of told what to do, and really the assignment
`or the final exam would be testing whether they have
`understood the material and whether they can make
`minor variations to demonstrate that they understand
`the material.
` Q. Do you cover published -- published
`technical papers in the courses?
` A. Not in the undergraduate course. In the
`graduate course we do. The graduate course is a
`mixture of my lecture notes, a mixture -- combined
`with sometimes a textbook, although quite often for
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`the graduate course the textbooks are not a perfect
`fit, so maybe chapters from a textbook. And quite
`often Wikipedia nowadays is a good resource, and
`also papers. Yes, for the graduate course we
`usually cover -- not many papers. The papers -- I
`don't overload the students with papers; maybe just
`one paper or two papers.
` Q. And what are examples of papers you've used
`in your graduate course?
` A. The graduate course that I taught -- last
`year I was on sabbatical. The year before, the
`paper -- one of the papers that we covered was a
`paper describing -- a paper describing how -- it's a
`bit of a technical topic, but essentially a paper
`describing a generalization of belief propagation or
`a generalization of the sum-product algorithm. It's
`a technique that -- that's being used. It was
`invented -- one of the authors of the paper --
`co-authors of the paper was from Mitsubishi, and it
`was a technique describing an algorithm that
`supposedly works better, and so we were
`investigating that algorithm.
` The algorithm has been used -- it mainly
`came out of the coding community, the error
`correcting coding community where there has been a
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`lot of interest in algorithms that perform better.
`It's been used in the coding community, and other
`communities have also tried to use it as well.
` Q. And who is the co-author you are thinking
`of?
` A. Jonathan Yedidia.
` Q. And what's the title of the paper?
` A. I don't recall.
` Q. Do you know just the journal or publication?
` A. I think it was the Proceedings of the
`Conference on Uncertainty and Artificial
`Intelligence.
` Q. And is that something that you're referring
`to in the coding community?
` A. That's a good question. Coding researchers
`often publish in journals that are on topics of
`computer science and artificial intelligence. In
`the last 15 years, we have seen this occur quite a
`bit, so -- so coding theorists will publish papers
`at artificial intelligence conferences, and other
`artificial intelligence researchers will publish
`papers at coding conferences. There is really no
`distinction between the researchers.
` It is interesting, for example, this
`Conference on -- Conference on Uncertainty and
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`Artificial Intelligence, I think it was -- I think
`it was 1997 Bob McEliece gave a keynote talk at that
`conference on coding.
` Q. So this artificial intelligence proceedings,
`have you published in this journal?
` A. Yes.
` Q. And have you read papers by Bob McEliece in
`this journal?
` A. Yes. I should clarify. It's the
`proceedings of the conference that are published,
`but it's not a journal. We wouldn't refer to it as
`a journal.
` Q. Okay. When was the conference started?
` A. I can't -- I can't say for certain. It's at
`least -- well, I know the first time I attended it
`was in 1990- -- I believe -- I'm not certain, but I
`would have attended it maybe in 1996 or 1995,
`something like that. So it's at least that old. At
`least 20 years or 19 years.
` Q. In your graduate course you also mentioned
`the use of textbooks. What are examples of
`textbooks that you've used in your course?
` A. The textbook that I used most often was the
`textbook by David MacKay of the University of
`Cambridge, England.
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` Q. And what was the name of the textbook?
` A. I don't remember. The textbook, it was
`something along the lines of coding theory, neural
`networks and probability, something like that.
` Q. Have you authored any textbooks?
` A. I've authored one book, which has been used
`for teaching -- that has been used for teaching
`courses. It's called Graphical Models For Machine
`Learning and Digital Communication.
` Q. So would you characterize that your area of
`research relates to machine learning?
` A. Yes.
` Q. And that was the description that you
`provided for your graduate course as well; right?
` A. Machine learning -- the description is
`machine learning and inference algorithms. In fact,
`I think that it's inference algorithms and machine
`learning, is the name -- the other way around. It's
`inference algorithms and machine learning.
` Q. You said you have a joint appointment with
`the Center For Cellular and Biomolecular Research in
`the medical department; is that right?
` A. That's correct.
` Q. So how is this research related to the
`medical community?
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` A. What we're doing is, because of my
`background in analyzing sequences of bits -- that
`was what we did in the field of error correcting
`coding -- I learned a lot of tools having to do with
`how to analyze sequences of symbols, how to analyze
`noisy sequences of symbols, such as what you see at
`the output of an error correcting coding channel,
`and also analyze long sequences and blocks of
`symbols. So that was experience that I gained
`working in the field of error correcting codes.
` The genome -- the human genome was sequenced
`around 2001. That was when the rough draft came
`out. 2004 was when -- 2004 is usually the date that
`people think of as being the date when the final,
`near -- nearly complete version of the human genome
`was prepared. And the human genome is 6 billion
`letters long. It's made up of the letters A, C, G
`and T, and so it's a very long sequence of symbols,
`and I recognize it as being kind of similar to the
`output of an error correcting code.
` In the case of the genome, there is some
`sort of redundancy built into the system in order to
`protect against mutations and errors that accumulate
`over time, much like an error correcting code. When
`the code word is transmitted across the channel,
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`Page 18
`different kinds of sources of noise can corrupt the
`code word and introduce errors, which would be the
`same kind of thing as a mutation in the DNA.
` There can be other kind of errors as well,
`much like it's widely known in the error correcting
`coding community that there are errors that can
`cause bits to be deleted or inserted or erased.
`Similarly, in the case of DNA, you can have pieces
`of short segments of DNA that might be deleted. You
`can have other kinds of noise introduced into the
`DNA.
` And so when I saw the parallel between error
`correcting decoding and the human genome, the DNA
`sequence and how noise is introduced into DNA and
`that kind of thing, I realized that it would be --
`it would be interesting if I could apply some of
`those tools that I had learned about and introduced
`and invented myself in the field of genomics, and so
`that's the connection.
` Now, the genome is important for medicine
`because many medical issues are caused by errors in
`the DNA. It is caused by mutations and that kind of
`thing. And so the connection, then, between my
`interest in understanding the genome and
`understanding how DNA works, essentially, the phrase
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`Page 19
`that's been used is "decoding the genome." And my
`interest in decoding the genome led to research
`results that are useful for medicine, so that's the
`connection to medicine.
` Q. So you work also in the field of genomics;
`is that right?
` A. That's the field, yeah.
` Q. And you're working on the decoding aspect of
`the genome. There is no encoding of the genome that
`you work on; right?
` MR. DOWD: Objection. Vague. Compound.
` THE WITNESS: Could you clarify the
`question?
`BY MR. TUNG:
` Q. Yeah. So I believe you drew some analogies
`to error correcting coding in terms of the decoding
`aspects. We talked about introduction of errors.
`What I'm trying to get at is: Is there an analog to
`the encoding aspect of, you know, error correcting
`codes to the work you're doing in genomes?
` MR. DOWD: Objection. Vague.
` THE WITNESS: I still don't understand
`exactly what your question is.
`BY MR. TUNG:
` Q. So you understand what encoding is in error
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`correcting codes; right?
` A. Yes.
` Q. And you understand what decoding is in the
`field of error correcting codes; right?
` A. Yes.
` Q. And in your current research on genomics,
`you drew some analogies with the decoding aspect of
`error correcting codes?
` A. Yes.
` Q. I'm asking if there are any analogies that
`you can draw on the encoding aspects of error
`correcting codes.
` A. An analogy would be that the DNA in the
`genome is encoded by a process of evolution, so the
`ultimate goal of the biology, the cellular biology,
`is to take information and convert it to a useable
`form. And the information is essentially the
`information that specifies the organism, and
`mutations in the DNA can lead to changes in the
`organism, and that's the process of evolution.
` And so the encoding of information in terms
`of DNA, if you think of DNA being the code word, is
`critical for encoding this information about the
`organism and different kinds of organisms and
`changes in organisms in a robust way so that then it
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`can be decoded in living cells and used to do things
`like construct cell walls and that kind of thing,
`much in the same way as in a digital communication
`system the user who comes up with a message has an
`intention to convey some useful information.
` If nothing changes, then there is no useful
`information. The user would come up with some
`useful information, and then the goal would be to
`encode it in such a way that it's protected against
`errors and then can be decoded to recover the useful
`information. That's the analogy.
` Q. And so by that analogy you don't create
`genomes? You don't do the encoding process. That's
`done by nature; right?
` MR. DOWD: Objection. Vague. Incomplete
`hypothetical.
` THE WITNESS: There's a lot of -- in fact,
`what I gave you is an example. There is a wide
`range of things that can be done. For example, a
`group led by Craig Venter recently designed the
`genome. Recently, for example, last year a
`technique called CRISPR/Cas9 was introduced that
`enables us to edit genomes. So an important area of
`research is currently redesigning genomes, modifying
`them, and this is literally done by editing the
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`genome, making massive changes or making small
`changes, and we are pretty much quite in control of
`now editing the genome and making changes.
`BY MR. TUNG:
` Q. Is that the focus of your group's research?
` A. Currently, that is.
` Q. And what tools do you use to edit the
`genome?
` A. So there are different kind of tools. One
`tool that's used is called a mutagenesis experiment.
`It's a tool where a piece of DNA, if you like, is
`copied into a -- what's called a minigenome reporter
`in a bacteria, and then we study how that results --
`how that edited DNA behaves differently within that
`cell.
` Another tool that we use is CRISPR/Cas9
`where we can make edits to DNA in human cells,
`change the DNA in the human cell, and then see what
`the consequences are in the human cell.
` Q. And when you say "see what the consequences
`are," is that done by experiment?
` A. That's right. Nowadays labs can usually
`conduct these kinds of experiments.
` Q. Have you been deposed before?
` A. No.
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` Q. Have you ever testified before?
` A. No.
` Q. Have you ever served as an expert in
`litigation before?
` A. No.
` Q. How did you decide to serve as an expert in
`this particular case?
` MR. DOWD: Objection. I will just caution
`you. To the extent that that would -- that question
`will call for you to reveal any communications that
`you had with attorneys or any attorney-client
`privileged material, I will instruct you not to get
`into that. If you can answer outside of discussions
`with attorneys, things done at the direction of
`attorneys, you may do so.
` THE WITNESS: For that reason, I decline to
`answer.
`BY MR. TUNG:
` Q. So, just to be clear, my question is not
`about what you said to your attorneys, what your
`attorneys said to you. I'm asking how you made the
`decision to serve as an expert in this case.
` MR. DOWD: And I will just object on the
`same basis. I will give you the same caution. If
`you're able to answer without getting into any
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`discussions with attorneys or back-and-forth with
`attorneys, you may do so. If answering will require
`you to reveal any discussions with attorneys, then I
`would instruct you not to do so.
` THE WITNESS: I decline to answer.
`BY MR. TUNG:
` Q. And is the reason that you decline to answer
`is because you cannot answer the question without
`getting into attorney-client discussions?
` A. That's correct.
` Q. Did you have any views on the opinions
`expressed in your expert report prior to your
`contact with attorneys in this case?
` MR. DOWD: Objection. Vague.
` THE WITNESS: Could you clarify?
`BY MR. TUNG:
` Q. For the opinions that are expressed in your
`expert report, did you form any of those opinions
`prior to your contact with attorneys in this case?
` MR. DOWD: Objection. Vague. Assumes
`facts.
` THE WITNESS: I'm still unclear.
`BY MR. TUNG:
` Q. Which part are you unclear about?
` A. The -- the question is unclear. It's hard
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`for me to -- to be certain what you're asking.
` Q. Which part of the question?
` MR. DOWD: Objection.
` THE WITNESS: The second part.
`BY MR. TUNG:
` Q. Prior to your contact with attorneys in this
`case?
` A. The attorneys in this case.
` Q. Have you -- and I'm not asking you the
`substance. But have you communicated with attorneys
`in this case?
` A. Yes.
` Q. Who have you communicated with in this case
`that's an attorney? And, again, I don't want you to
`get into the substance. I'm just asking who you
`communicated with.
` MR. DOWD: So if you recall a name, you can
`say the name.
` THE WITNESS: David Marcus.
`BY MR. TUNG:
` Q. When was the first time you communicated
`with David Marcus with respect to this case?
` A. I believe it was December -- middle of
`December.
` Q. And you mean December 2014?
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` A. That's correct.
` Q. Have you communicated with other attorneys
`in this case prior to your communication -- your
`first communication with David Marcus?
` A. Are you -- yes.
` Q. And who have you communicated with -- which
`attorneys have you communicated with with respect to
`this case prior to your first communication with
`David Marcus?
` A. Brian Seeve.
` Q. When was the first time you communicated
`with Brian Seeve about this case?
` A. I believe it was the end of October 2014.
`That would be 2014.
` Q. Did you communicate with any other attorneys
`in this case prior to your first communication with
`Brian Seeve?
` A. A clarification I need is that when you
`refer to "this case," can you -- which aspects of
`this case?
` Q. By "this case," at the beginning of this
`transcript, the videographer read a case number.
`I'm referring to this case, you know, the one that's
`referenced by that case number.
` MR. DOWD: Objection. Objection. Vague.
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` THE WITNESS: Could you clarify?
`BY MR. TUNG:
` Q. Do you remember that the videographer read a
`case number and the caption of this case at the
`beginning of this deposition?
` A. Yes.
` Q. That is what I'm referring to.
` MR. DOWD: I will just object. That is
`vague. For a nonlawyer that doesn't make any sense.
` THE WITNESS: Yeah. I don't know how to map
`the case number to a description of the case. If
`you can present me with a document, perhaps, or
`describe it...
`BY MR. TUNG:
` Q. Okay. You understand that there is a
`current patent litigation pending in the Central
`District of California?
` A. Yes.
` Q. And that Caltech has asserted certain
`patents against the defendants in this case?
` A. Yes.
` Q. And that you're being deposed as an expert
`pursuant to that case?
` A. I guess that's the part I need clarification
`on. I understand there's an infringement aspect and
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`an invalidity aspect. Are you referring to those as
`one, as one case?
` Q. Correct.
` A. I see. Thank you.
` Q. So regardless of the subject matter, I mean,
`the entire case deals with patent infringement, and
`you have provided an opinion on the invalidity of
`the patents in the case; correct?
` A. Yes, that is correct.
` Q. But when I'm referring to "this case," I'm
`talking about the entire case. It involves all of
`the issues involving the patents that are being
`asserted.
` A. I understand now.
` Q. Okay. Let me re-ask my question, then.
`Prior to your communication with Brian Seeve, did
`you communicate with any other attorneys in this
`case?
` A. Yes.
` Q. And who did you communicate with prior to
`your first communication with Brian Seeve?
` A. Jeff Hantson.
` Q. And when was the first time you communicated
`with Jeff Hantson about this case?
` A. I believe it was early October or mid
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`October. It's going a bit far back. It's hard for
`me to remember exactly when, but it would be
`sometime around then. Possibly -- possibly even
`September, but I'm not certain. And that would be
`in 2014.
` Q. Did you communicate with any other attorneys
`in this case prior to your first communication with
`Jeff Hantson?
` A. I may have. There were two attorneys that I
`spoke to at that time. Jeff was one of them, and
`the other one's name is eluding my memory at the
`moment. And I don't remember exactly the order in
`which I spoke to the two of them. I believe I spoke
`to Jeff Hantson -- I recall having a telephone call
`with Jeff Hantson. As for the other attorney, I may
`have had a telephone call with him as well. And I
`do not remember the order in which those calls took
`place, so -- they were fairly close together in
`time, though.
` Q. "Fairly close together" meaning within --
` A. Days. Within days.
` Q. Did you communicate with any attorneys in
`this case prior to your first communication with
`Jeff Hantson and this other attorney whose name you
`don't remember?
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