[ml] HMM workshop?

Glen Jarvis glen at glenjarvis.com
Tue Aug 17 18:30:51 PDT 2010


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
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> ml mailing list
>>>>>> ml at lists.noisebridge.net
>>>>>> https://www.noisebridge.net/mailman/listinfo/ml
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _____________________________________________________________
>>>>>> J-Fan - Your Ultimate Japanese Entertainment Directory!
>>>>>> http://j-fan.com
>>>>>> _______________________________________________
>>>>>> ml mailing list
>>>>>> ml at lists.noisebridge.net
>>>>>> https://www.noisebridge.net/mailman/listinfo/ml
>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> ml mailing list
>>>>> ml at lists.noisebridge.net
>>>>> https://www.noisebridge.net/mailman/listinfo/ml
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> ml mailing list
>>>> ml at lists.noisebridge.net
>>>> https://www.noisebridge.net/mailman/listinfo/ml
>>>>
>>>>
>>>
>>> _______________________________________________
>>> ml mailing list
>>> ml at lists.noisebridge.net
>>> https://www.noisebridge.net/mailman/listinfo/ml
>>>
>>>
>>
>>
>> --
>> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.noisebridge.net/pipermail/ml/attachments/20100817/56a4e402/attachment-0001.htm 


More information about the ml mailing list