[ml] HMM workshop?

Mike Schachter mike at mindmech.com
Tue Aug 17 19:20:51 PDT 2010


I meant to say um, what you said :)



On Tue, Aug 17, 2010 at 6:30 PM, Glen Jarvis <glen at glenjarvis.com> wrote:

> OOH, I don't touch gene sequencing... We do protein MSA alignment HMMs --
> very different.
>
> But, I don't really know the theory (deep down) of what I'm doing anyhow...
> I'm coming with questions, not answers.
>
>
> Glen
>
>
> On Tue, Aug 17, 2010 at 5:17 PM, Mike Schachter <mike at mindmech.com> wrote:
>
>> Yep, should be a fairly forgiving audience :)  I'll also
>> try and brush up on HMMs in gene sequencing and see
>> if I can fill in any gaps.
>>
>>   mike
>>
>>
>>
>> On Tue, Aug 17, 2010 at 3:37 PM, Glen Jarvis <glen at glenjarvis.com> wrote:
>>
>>> I also intend to be there. I haven't had a chance to put together my
>>> presentation in a very polished way. However, our audience is fairly
>>> forgiving if it's succinct and clear, yes?
>>>
>>> Glen
>>>
>>>
>>> On Tue, Aug 17, 2010 at 12:19 AM, Mike Schachter <mike at mindmech.com>wrote:
>>>
>>>> Yep, just did last Thursday, did you see it? It was sent to
>>>> both noisebridge-discuss and ml. It's also on the official NB
>>>> calendar. Should be awesome, looking forward to it!!
>>>>
>>>>  mike
>>>>
>>>>
>>>>
>>>> On Mon, Aug 16, 2010 at 10:23 PM, Thomas Lotze <thomas.lotze at gmail.com>wrote:
>>>>
>>>>> Hey all,
>>>>>
>>>>> I just wanted to make sure everyone's still on for the HMM extravaganza
>>>>> Wednesday night.  Mike, do you want to send out an announcement to the main
>>>>> Noisebridge list?
>>>>>
>>>>> Cheers,
>>>>> Thomas
>>>>>
>>>>>
>>>>> On Thu, Aug 5, 2010 at 11:45 AM, Mike Schachter <mike at mindmech.com>wrote:
>>>>>
>>>>>> Glen - that sounds reasonable to me (short bio overview on DNA
>>>>>> sequences,
>>>>>> codons, amino acids, AA sequences, proteins), then how to use HMMs to
>>>>>> show
>>>>>> how sequences are similar to eachother and all that other good stuff
>>>>>> they're used
>>>>>> for that I don't know about.
>>>>>>
>>>>>> Erin - that sounds good. Sorry I misunderstood what you were saying.
>>>>>> We should
>>>>>> definitely work together on some of that stuff. Alternatively or in
>>>>>> addition you could
>>>>>> work with Tom on HMMs in R.
>>>>>>
>>>>>> I could start the workshop by giving a short presentation on markov
>>>>>> processes
>>>>>> and HMMs, so we won't have to worry about the mathematical background
>>>>>> when
>>>>>> talking about applications.
>>>>>>
>>>>>>   mike
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Thu, Aug 5, 2010 at 11:43 AM, erin <erin at j-fan.com> wrote:
>>>>>>
>>>>>>> Hey,
>>>>>>> To clarify, the speech recognition thing I was talking about was not
>>>>>>> HMMs.
>>>>>>> I used lda, qda and kmeans, which could possibly become a workshop
>>>>>>> later.
>>>>>>> Also the guy I was talking about is not a speech person, he does
>>>>>>> music.
>>>>>>>
>>>>>>> There is an NLP paper I've been meaning to read about Markov Chains,
>>>>>>> so maybe
>>>>>>> I could talk about that, or else I can work with Mike to assist in
>>>>>>> presenting
>>>>>>> one of his topics.
>>>>>>>
>>>>>>> -Erin
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Thu, Aug 5, 2010 at 11:10 AM, Mike Schachter <mike at mindmech.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>> > Hey guys (Erin, Tom, Glen, et. al),
>>>>>>> >
>>>>>>> > I think 9pm is too late to be meeting up. I suggest we forgo next
>>>>>>> > week's 9pm meeting and put our heads together to give a nice 2 hour
>>>>>>> > HMM workshop/lecture set on Wednesday, August 19th, at 7:30pm. We
>>>>>>> > can advertise it on the ML list and noisebridge-discuss, and
>>>>>>> encourage
>>>>>>> > donations to Noisebridge for attendance to help pay their rent.
>>>>>>> >
>>>>>>> > Here's the breakdown of what I think we could offer in that
>>>>>>> meeting:
>>>>>>> >
>>>>>>> > Me/Anyone Else: The basic math behind Markov Processes and HMMs
>>>>>>> >
>>>>>>> > Me/Erin/Erin's Speech Recognition Friend: Speech Recognition using
>>>>>>> HMMs
>>>>>>> >
>>>>>>> > Tom: HMMs using R
>>>>>>> >
>>>>>>> > Glen: HMMs in bioinformatics
>>>>>>> >
>>>>>>> > Anyone else: ?
>>>>>>> >
>>>>>>> > I feel like if we have two weeks to prepare something it'll give us
>>>>>>> time to
>>>>>>> > have good presentations and be worthwhile to everyone, what do you
>>>>>>> think?
>>>>>>> >
>>>>>>> >   mike
>>>>>>> >
>>>>>>> >
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Whatever you can do or imagine, begin it;
>>>>>>> boldness has beauty, magic, and power in it.
>>>>>>>
>>>>>>> -- Goethe
>>>>>>>
>>>>>>>
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>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _____________________________________________________________
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>>>>>>> http://j-fan.com
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>>>>>>>
>>>>>>
>>>>>>
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>>>>>>
>>>>>
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>>>
>>>
>>> --
>>> Whatever you can do or imagine, begin it;
>>> boldness has beauty, magic, and power in it.
>>>
>>> -- Goethe
>>>
>>
>>
>
>
> --
> Whatever you can do or imagine, begin it;
> boldness has beauty, magic, and power in it.
>
> -- Goethe
>
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