Hi Sean I'm asking my team's manager to see if we can present. I work as Architect / cTakes Implementer with a team at the UCSF Bakar Institute for computational health sciences.
Peter On Mon, Jul 6, 2020 at 6:20 AM Finan, Sean <sean.fi...@childrens.harvard.edu> wrote: > I can't believe that I forgot to mention ... > > > There will also be a presentation (maybe two?) by a group that has adapted > ctakes to work with two other languages. They have also integrated ctakes > with other tools such as FreeLing and HeidelTime. So cool ... > > > Cheers, > > Sean > > > ________________________________ > From: Finan, Sean > Sent: Monday, July 6, 2020 9:08 AM > To: dev@ctakes.apache.org; u...@ctakes.apache.org > Subject: ApacheCon 2020 > > > Hi all, > > > The ctakes representation at ApacheCon 2020 is looking good! > > > ApacheCon 2020 runs September 29 through October 1. > > Submission runs through Sunday, July 12. Technically it is 8:00 a.m. > Eastern time Monday, but please don't procrastinate. > > Registration is free. > > > I am excited to announce that we have three groups interested in giving > presentations on their configuration and use of ctakes at a large scale! > > We also have a presentation on the installation of the ctakes Rest service > using the ctakes-rest module! > > > Knowledge on these topics is always extremely valuable to our users, and I > for one really want to see how sites use ctakes when given different > resources, requirements and restrictions. Because of that, I am trying to > put together (technology allowing) a roundtable discussion with those > presenters. That should be of value to every user no matter what your > situation. > > > We still need more presentations! To encourage you, here is a little > information: > > > 1. What you do is interesting! If you think that nobody out there cares > about what you've done and how, then you probably aren't fully aware of how > large and diverse our user base really is. People want to know about > things like integration, customization, clinical specialty application, > augmentation and favorite capability fascination. > > 2. Submission is very simple. This is not like a scientific conference > that requires a complete paper describing your work. You only need to > submit a blurb that loosely covers your topic and major talking point(s). > Half a dozen sentences will suffice. In fact, what I sent last week (far > below) could pass muster for a submission. Go for something that will be > on a brochure / schedule. > > 3. The audience is made up of people just like you. Developers, > Bioinformaticians, IT Specialists, Students, Medical Researchers, AI > Explorers and far more Hackers than Rock Stars. > > 4. Slick presentation skills are not necessary. Don't worry if you have > never spoken to a room full of listeners. Don't worry if English isn't > your first language. Don't worry if your slides are "sloppy". Your > presentation will not be graded. > > 5. You don't need to prepare your whole talk before submitting. Idea > now, details later. > > 6. Registration is FREE. > > > Right now the speaking time is anything up to 50 minutes. If you don't > want to present a full 50 minutes then that is ok ... The rest can be > filled with extra question/answer or somebody else may fill the remaining > time with a presentation on a similar topic. > > > I am going to put together a lightning round. If you think that you can > cover some material in five to fifteen minutes then this is for you! > Lightning rounds can be fun as you can make an impact with two or three > slides and barely enough speaking to run out of breath. This is really a > free-for-all. You can pack the time with data, give a short demonstration, > compare using ctakes to breaking a mustang, or even do some on-topic > (ctakes, nlp, AI, bioinformatics) stand up. Anything goes. This was an > interesting (full) talk last year: > https://aceu19.apachecon.com/session/confessions-middle-aged-coder-turned-gravel-grinder. > If you want to be in the lightning round, just write me a couple of > sentences on your strike and I will put together the full submission for > ApacheCon. Does it get any easier? > > > I will present one or two things, but to maximize impact I would like to > know what most interests / would help all of you. So, please write me a > topic or two that would best apply to your work. > > > Some links ... > > > ApacheCon Home Page: https://www.apachecon.com/ > > ApacheCon Registration: https://hopin.to/events/apachecon-home > > ApacheCon Submission: https://acna2020.jamhosted.net/cfp.html > > > Lastly, so that we don't crash a server, I would like to have a rough head > count for attendance estimation. If you think that you will watch any > presentation of ctakes then please send me ( seanfi...@apache.org ) an > email with the subject "Attend" and "+1" in the body. > > > Cheers, > > Sean > > > ________________________________ > From: Finan, Sean > Sent: Monday, June 29, 2020 11:02 AM > To: dev@ctakes.apache.org > Subject: ApacheCon 2020 > > > Hi all, > > > General admission to ApacheCon 2020 is free: > https://hopin.to/events/apachecon-home > > > I think that price of admission and travel costs have held back ctakes > users from attending past conferences, and lack of a sizable audience has > diminished the comparative value of ctakes presentations in the eyes of > ApacheCon planners. Because of the "at home" nature of this year's > conference, an app with smaller presence and less hip buzz has a better > chance of grabbing some time on the schedule. > > > The predetermined tracks are still an ill fit when it comes to the nature > of ctakes. https://apachecon.com/acah2020/cfp.html > > However, I think that we can still use this opportunity to deliver some > powerful introduction and training videos, as well as user stories and > clinical project application. Perhaps we can argue for a NLP track and do > some coordination with projects like OpenNLP and UIMA. > > > There are a scant two weeks to come up with presentations, and less time > to propose a track/topic. The call for presentations ends July 13th. That > is a deadline that requires immediate attention by anybody who wants to > show off their project or expertise. > > > Apache wants to have a single point of contact for each project, and I am > volunteering to be that person for ctakes. I am volunteering, not laying > claim, so if you think that you are a better fit for the position please > let me know. > > > I have written some ideas for presentations below. If you want to take > one (modify as you like) then please write me and post to the devlist. If > you have ideas for another presentation topic, please let me and the > devlist know - even if you aren't volunteering to do the presentation > yourself perhaps somebody else will. Again ... two weeks. > > > Thank you, > > Sean > > > > * The following talk ideas are by and large directed toward training. > That does not mean that topics should stay within that scope. > > > ================================================================= > > > Customizing cTAKES: First Principles > > Built using Apache UIMA, cTAKES is modular and extensible. Why is it > frequently treated as a black box? Is it lack of need, sparsity of > resources, or simply fear of the unknown? > > This is a quick start tutorial on adding custom elements to cTAKES. We > illustrate creating simple classes to input, process and output data. This > involves a concise overview of Apache uimaFIT and the cTAKES type system, > as well as building a UIMA pipeline using piper files. > > > ================================================================= > > > Loading a shippable with cTAKES DockHand > > Customizing a simple pipeline need not be left to cTAKES experts. Making > a cTAKES installation need not be confined to source code checkouts or > lengthy multi-stage binary downloads. > > We introduce cTAKES DockHand, a compact single-file installation tool that > allows one to construct custom pipelines as well as local installations, > Rest Services and Dockerfiles. > > > ================================================================== > > > Secret Engines of cTAKES > > The cTAKES default natural language processing pipeline is a standard in > the clinical research community. What is past that standard? While the > default clinical pipeline uses almost 20 engines, there are dozens more in > various cTAKES modules. > > We present and discuss the top 10 annotation engines you never knew you > had. > > > ==================================================== > > > Does cTAKES Know "The Best Words"? > > Named Entity Recognition is at the core of all complete natural language > processing tools. Out of the box cTAKES uses a dictionary containing part > of the Unified Medical Language System (UMLS) that covers most common > clinical terms. But it also comes with a custom dictionary creator. > > If you think that your clinical research is directed, then you should > probably have a directed dictionary. UMLS subsets, non-english > dictionaries and novel custom dictionaries have all been successfully used > with cTAKES. > > This is an overview of cTAKES named entity recognition with the essential > what, why and how of custom dictionaries as the centerpiece. > > > ==================================================== > > Academic Software: Performance or Performance? > > A conundrum faced by all academic software projects is how to make the > best of a small amount of resources. Clinical natural language processing > projects that use cTAKES are not exempt, and balancing accuracy of results > against speed of processing often becomes central when it is time to put > things into production (or just please the boss). > > More than a history of cTAKES and its evolutionary efforts in precision, > speed and usability, this presentation contains examples of how to best > utilize each aspect. > > > ================================================================ > > > Diet cTAKES > > One reason cTAKES is a popular framework in clinical natural language > processing tools is its use of Apache Maven for project management. > Navigating cTAKES dependencies can be difficult, leading to a common > practice of consuming the whole project. Much of what ends up in your > system may lead to unnecessary bloat. > > Going piecemeal through the values and weights of cTAKES modules and > resources, this presentation will assist any cTAKES user in trimming > project bulk from gigabytes to megabytes. > > > ================================================================ > > > cTAKES Saved my Life > > The title is inappropriate when it comes to healthcare in practice. > However, I used Apache cTAKES for my clinical research project on ________, > and its [versatile / comprehensive / speedy / ?] nature was important in > completing things [on time / accurately / ?]. > > We share our real-world experiences with using cTAKES, discuss why we > chose it, issues we faced and how we overcame unexpected problems. > > > ================================================================ > > > Large-scale cTAKES, an Installation Story > > At our _____ facility, we needed to process _____ [patients / notes / term > lists / ?] on a ______ system. > > We present a real-world application of cTAKES on a large scale, our needs > for _____ input and ____ output. We compare and contrast cTAKES with other > [clinical] NLP platforms that we tried and explain why we chose [it / > another] in the end. > > We will also share the novel [techniques / code / integration] that we > used for the success of our installation. > > > ================================================================ > > > My Engine is Faster than Yours > > We have created a cTAKES annotation engine that performs the task of > _____. This is [newer / faster / more comprehensive] than existing > engines in [cTAKES / other]. > > We will present [numbers , usage , capabilities / i/o ] of the engine and > its [model / data ]. > We will also commit the code and documentation to Apache cTAKES. > > > ================================================================ > > > cTAKES on the Catwalk > > We have created a Machine Learning model that can be used in cTAKES for > ______. The model uses the third party ______ for [newer / faster / more > comprehensive] results. > > We will present the essentials of model creation as well as [numbers , > usage , capabilities / i/o ] of our model. We will also advocate for the > third party _____ and how we integrated it with cTAKES. > We will also commit the code [model] and documentation to Apache cTAKES. > > > > > > > > >
