Increasing Patient-Provider Interaction with “Pharma-C”

· Posted in Fun, HCI, Projects

This weekend I took part in The Pitt Challenge Hackathon hosted by the School of Pharmacy and the Clinical and Translational Science Institute. I found this hackathon interesting because it had specific goals and challenged the participants to “Change the way the world looks at Health.” I went to the event with absolutely no prior ideas about what to build. I enjoy participating in hackathons for a chance to work with a completely new group of team members every time. I joined a team of two software professionals Zee and Greg right after registration. We were then joined by a business major – Shoueb during the official team formation stage of the event. The hackathon organizers provided us with ample opportunities to have discussions with researchers, professors and practitioners about the problems they’d like to solve with technology.

We started with a lot of interesting ideas and everyone in the team had a lot to contribute. We realized that almost all of our ideas revolved around the concept of increasing the interaction between the patient and providers outside of the health care setting. Currently, the patients have little interaction with the health care providers apart from the short face-to-face meetings and sporadic phone calls. Providers are interested in knowing more about their patients during their normal activities. Patients would also feel better cared for when the providers are more vested in them. We began with a grand scheme of creating a three-way communication channel with patient, physicians and pharmacists. After having more discussions with the mentors, we soon understood our big challenges – ‘busy schedules’ and ‘incumbent systems.’ We decided to focus on patient-pharmacy interactions. We brainstormed ideas about how we can build a system that ties well with the existing systems and isn’t too demanding in terms of time, either from the pharmacists or the patients. We decided to call ourselves – “Pharma-Cand after appropriate amount of giggling over the name, we sat down to think about the tech.

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We wanted to design a system that could be less intrusive than phone calls, where both participants must be available at the same time, but also more visible than emails that could be left ignored in the promotions inbox. We began with an idea of using an email based system that could also appear as Google Now Cards as notifications on phones and smart devices. To our disappointment, we learned that Google Now only supports schemas for a limited number of activities (such as restaurant reservations, flights etc.). As a result, we moved on to a custom notification service. We agreed upon using the Pushover app which made it very easy to build a prototype for the hackathon.

We built a web-based system that could be connected to the existing loyalty programs from the pharmacies. The patients could opt for signing up for additional follow-up questions about their prescriptions. These questions could be generic ones such as: How many prescribed doses have you missed this week?, Is your prescribed medicine affordable?, Do you have questions about your current prescription?; or specific follow-up questions about the drugs they are taking. One could be interested in knowing how the patients are doing, whether the drug is having the desired effects or even reminding them about the common side-effects. Once signed up, a weekly script could send notifications to the participants and collect their responses from their preferred devices. Having such a system in place would help the pharmacists gather better information about the patients and offer interventions. They could look at the summary information screen when they make their follow-up calls according the existing systems in place. We believe the such a system could benefit both the pharmacies and the users without disrupting their regular workflows.

During the course of 24 hours, we finished building a working prototype and could demo everything in real-time to all our judges. One addition that improve the challenge would be to release some datasets for the participants to work with. We wanted to try some interesting data analysis methods for our problems but were limited to work on data collection hacks. Overall, I enjoyed taking part in the Pitt Challenge Hackathon and will look forward to their future events.

 

 


Machines learn to play Tabla

· Posted in Artificial Intelligence, Fun, Machine Learning

If you follow machine learning topics in the news, I am sure by now you would have come across Andrej Karpathy‘s blog post on The Unreasonable Effectiveness of Recurrent Neural Networks.[1] Apart from the post itself, I have found it very fascinating to read about the diverse applications that its readers have found for it. Since then I have spent several hours hacking with different machine learning models to compose tabla rhythms:

Although Tabla does not have a standardized musical notation that is accepted by all, it does have a language based on the ‘bols’ (literally, verbalize in English) or the sounds of the strokes played on it. These ‘bols’ may be expressed in written form which when pronounced in Indian languages sound similar to the drums. For example, the ‘theka’ for the commonly used 16-beat cycle – Teental is written as follows:

Dha | Dhin | Dhin | Dha | Dha | Dhin | Dhin | Dha |
Dha | Tin  | Tin  | Ta  | Ta  | Dhin | Dhin | Dha

For this task, I made use of Abhijit Patait‘s software – TaalMala, which provides a GUI environment for composing Tabla rhythms by writing them out in this language. The bols can then be synthesized to produce the sound of the drum. In his software, Abhijit extended the tabla language to make it easier for users to compose tabla rhythms by adding a square brackets after each bol that specify the number of beats within which it must be played. You could also lay more emphasis on a particular bol by adding ‘+’ symbols which increased their intensity when synthesized to sound. Variations of standard bols can be defined as well based on different the hand strokes used:

Dha1 = Na + First Closed then Open Ge

Now that we are armed with this background knowledge, it is easy to see how we may attempt to learn tabla like a standard Natural Language Processing language model. Predictive modeling of tabla has been previously explored in "N-gram modeling of tabla sequences using variable-length hidden Markov models for improvisation and composition" (Avinash Sastry, 2011). But, I was not able to access the datasets used in the study and had to rely on the compositions that came with the TaalMala software.[2] This is comparatively a much smaller database than what you would otherwise use to train a neural network: It comprises of 207 rhythms with 6,840 bols in all. I trained a char-rnn and sampled some compositions after priming it with different seed text such as “Dha”, “Na” etc. Given below is a minute long composition sampled from my network. We can see that not only the network has learned the TaalMala notation but it has also understood some common phrases used in compositions such as the occurrence of the phrase “TiRa KiTa“, repetitions of “Tun Na” etc.:

Ti [0.50] | Ra | Ki | Te | Dha [0.50] | Ti [0.25] | Ra | Ki
| Ta | Tun [0.50] | Na | Dhin | Na 
| Tun | Na | Tun | Na | Dha | Dhet | Dha | Dhet | Dha | Dha
| Tun | Na | Dha | Tun | Na | Ti | Na | Dha | Ti | Te | Ki |
Ti | Dha [0.50] | Ti [0.25] | Ra | Ki | Te | Dhin [0.50] |
Dhin | Dhin | Dha | Ge | Ne | Dha | Dha | Tun | Na | Ti
[0.25] | Ra | Ki | Ta | Dha [0.50] | Ti [0.25] | Ra | Ki |
Te | Dha [1.00] | Ti | Dha | Ti [0.25] | Ra | Ki | Te | Dha
[0.50] | Dhet | Dhin | Dha | Tun | Na | Ti [0.25] | Ra | Ki
| Ta | Dha [0.50] | Ti [0.25] | Ra | Ki | Te | Ti | Ka | Tra
[0.50] | Ti | Ti | Te | Na [0.50] | Ki [0.50] | Dhin [0.13]
| Ta | Ti [0.25] | Ra | Ki | Te | Tra | Ka | Ti [0.25] | Ra
| Ki | Te | Dhin [0.50] | Na [0.25] | Ti [0.25] | Ra | Ki |
Te | Tra | Ka | Dha [0.34] | Ti [0.25] | Ra | Ki | Ta | Tra
| Ka | Tra [0.50] | Ki [0.50] | Tun [0.50] | Dha [0.50] | Ti
[0.25] | Ra | Ki | Ta | Tra | Ka | Ta | Te | Ti | Ta | Kat |
Ti | Dha | Ge | Na | Dha | Ti [0.25] | Ra | Ki | Te | Dha
[0.50] | Dhin | Dhin | Dhin | Dha | Tun | Na | Ti | Na | Ki
| Ta | Dha [0.50] | Dha | Ti [0.50] | Ra | Ki | Te | Tun
[0.50] | Tra [0.25] | Ti [0.25] | Ra | Ki | Te | Tun | Ka |
Ti [0.25] | Ra | Ki | Te | Dha [0.50] | Ki [0.25] | Ti | Dha
| Ti | Ta | Dha | Ti | Dha [0.50] | Ti | Na | Dha | Ti
[0.25] | Ra | Ki | Te | Dhin [0.50] | Na | Ti [0.25] | Ra |
Ki | Te | Tra | Ka | Dha [0.50] | Ti [0.50] | Ra | Ki | Te |
Tun [0.50] | Na | Ki [0.25] | Te | Dha | Ki | Dha [0.50] |
Ti [0.25] | Ra | Ki | Te | Dha [0.50] | Ti [0.25] | Ra | Ki
| Te | Dha [0.50] | Tun | Ti [0.25] | Ra | Ki | Te | Dhin
[0.50] | Na | Ti [0.25] | Te | Dha | Ki [0.25] | Te | Ki |
Te | Dhin [0.50] | Dhin | Dhin | Dhin | Dha | Dha | Tun | Na
| Na | Na | Ti [0.25] | Ra | Ki | Ta | Ta | Ka | Dhe [0.50]
| Ti [0.25] | Ra | Ki | Te | Ti | Re | Ki | Te | Dha [0.50]
| Ti | Dha | Ge | Na | Dha | Ti [0.25] | Ra | Ki | Te | Ti |
Te | Ti | Te | Ti | Te | Dha [0.50] | Ti [0.25] | Te | Ra |
Ki | Te | Dha [0.50] | Ki | Te | Dha | Ti [0.25]

Here’s a loop that I synthesized by pasting a composition sampled 4 times one after the another:

Of course, I also tried training n-gram models and the smoothing methods using the SRILM toolkit. Adding spaces between letters is a quick hack that can be used to train character level models using existing toolkits. Which one produces better compositions? I can’t tell for now but I am trying to collect more data and hope to add updates to this post as and when I find time to work on it. I am not confident if simple perplexity scores may be sufficient to judge the differences between two models, specially on the rhythmic quality of the compositions. There are many ways in which one can extend this work. One there is a possibility of training on different kinds of compositions: kaidas, relas, laggis etc., different rhythm cycles and also on compositions from different gharanas. All of this would required collecting a bigger composition database:

And then there is a scope for allowing humans to interactively edit compositions at places where AI goes wrong, but using the samples generated by it as an infinite source of inspiration.

Finally, here’s a link to the work in progress playlist of the rhythms I have sampled till now.

References

  1. Avinash Sastry (2011), N-gram modeling of tabla sequences using variable-length hidden Markov models for improvisation and composition. Available: https://smartech.gatech.edu/bitstream/handle/1853/42792/sastry_avinash_201112_mast.pdf?sequence=1.

Footnotes

  1. If you encountered a lot of new topics in this post, you may find this post on Understanding natural language using deep neural networks and the series of videos on Deep NN by Quoc Le helpful. ^
  2. On the other hand, Avinash Sastry‘s work uses a more elaborate Humdrum notation for writing tabla compositions but is not as easy to comprehend for tabla players. ^


Bike ride from Pittsburgh to DC

· Posted in Fun, Opinion

This week I did a 335 mi (540 km) bicycle tour from Pittsburgh to Washington DC along with a group of 3 other folks from the school. This is the longest I have ever biked and covered the distance over a period of 5 days. The entire trip is divided into two  trails – the 150 mile Great Allegheny Passage from Pittsburgh to Cumberland, followed by the 185.5 mile long Chesapeake and Ohio Canal (C&O Canal) Towpath.

We carried camping equipment on our bikes and enjoyed a lot of flexibility in deciding where to stay each night, although we roughly followed the original plan that our group agreed upon before starting the trip. We biked for 8-12 hours during the day and stayed overnight at each of the following cities:

Day City Miles Daily Mileage Elevation in feet
0 Pittsburgh, PA 0 0 720
1 Ohiopyle, PA 77 77 1,230
2 Frostburg, MD 134 57 1,832
3 Little Orleans, MD 193 59 450
4 Harpers Ferry, MD 273 80 264
5 Georgetown, Washington DC 335 62 10
Mile 0 of the GAP Trail. The C&O trail begins from there onwards.

Mile 0 of the GAP trail. The C&O trail begins from here onwards.

If there’s one change I could make in this schedule, it would be to avoid staying over at Harpers Ferry which involved climbing a foot bridge without any ramp for the bikes. It is even more difficult if you are carrying a lot of weight on your bike racks. On the positive side, it allowed us to experience the main streets of Harpers Ferry which is rightly called “a place in time”. Another tip that you could use is to take the Western Maryland Trail near Hancock. It runs parallel to the route and is a paved one, which provides a welcome break after long hours of riding on the C&O trail.

There are lots of campsites near the trail. There are hiker-biker camps near most major towns on the C&O trail and are free to use. We also camped at commercial campgrounds, like at the Trail Inn Campground in Frostburg, where we could use a shower. You can also get your laundry done at these places and save some luggage space. For food and drinks – I suggest that you follow the general long distance biking guidelines about eating at regular intervals while on the bike. I also strongly recommend using a hydration backpack though it adds to the weight you have carry on your shoulders.

Here's a picture of our bikes with our panniers and the camping equipment.

Here’s a picture of our bikes with our panniers and the camping equipment.

I used a hybrid bike – Raleigh Misceo and was very comfortable riding it through all parts of the trail. I was expecting a couple of flat tires specially on the C&O sections with loose gravel and other debris on the trail, but didn’t face any problems. As long as you are not using a road bike with narrow tires you should be good on these trails. Finally for getting back to Pittsburgh we rented a minivan and put our bikes in the trunk which had ample space for 4 bikes with their front wheels taken off.

If you decide to take this tour in future, we have plenty of online guides available for each of the GAP and C&O Canal trails. For a paper-based guide, I would recommend buying the Trailbook published by the Allegheny Trail Alliance. We also created a small webapp called the GAP Map that helped us plan our trip and prepare a schedule.

Here are some of the scenic views along the tour as captured from my phone camera:

Monongehala River

View of the Monongehala river.

McKeesport

A short stop near Buena Vista.

Cumberland

Along the trail near Cumberland.

East Continental Divide

Elevation Chart marking the good news for us at the East Continental Divide.

C&O Trail Bridge

One of many bridges on the C&O Trail.

C&O Canal Bike Path

Bike path on the C&O Canal trail. It also has several lock houses along the way which have been renovated and can be used for overnight stay.

Harpers Ferry

Shops in Harpers Ferry.

C&O Canal

A section of the C&O Canal that once ferried goods between Washington DC and Cumberland.


Ugly Pic Tweet

· Posted in Fun, Opinion, Projects

Lately I have observed the twitterrati follow a trend of tweeting “text” as images. My timeline was completely filled with such tweets today.

This is even encouraged by twitter as it expands all picture tweets by default.

So to further spread this epidemic (to convince Twitter to do something about it), I re-purposed one of my Interactive System Design class assignments [1] into a Ugly-Pic-Tweeter.

Go ahead, start posting your own ugly pic tweets. May you fill your followers timelines with them!

 

Footnotes

  1. Thanks Julio for teaming up for the original assignment 🙂 ^


Machines understand Rahul Gandhi!

· Posted in Fun, Machine Learning, Man vs. Machine, Opinion

I have a (bad) habit of checking my Twitter feed while at work. Yesterday after my machine learning class, I found my timeline to be filled with Tweets mocking Rahul Gandhi about his first-ever television interview. Naturally, I was curious to know why and I tried to give it a listen. Most of his answers made no sense to me whatsoever! But then guess what? Who else is bad at responding to questions in natural language? The machines are! Maybe it was time to put them to a test and see if the machines could understand Mr. Gandhi. Making use of the transcript made available by the Times of India and some free NLP tools(ets), I spent a couple of hours (unproductive, ofcourse :P) trying to make sense of the interview.

Here’s a wordle summary of his answers, that would at least give you an overview about what was being spoken about during the interview:

Screen Shot 2014-01-28 at 4.36.43 pm

Such system. Many people. Wow! Apparently the word ‘system’ was used 70 times during the entire interview.

Here are some of the most used (best) words from the transcript. The number times they were used are mentioned in parenthesis.

  1. system (70)
  2. people (66)
  3. going (52)
  4. party (51)
  5. country (44)
  6. want (34)
  7. congress (34)
  8. power (32)
  9. political (31)
  10. issue (26)

Next, I set out to generate a summary of his answers. And lo! to my surprise, it made perfect sense (contrary to what you usually get from a summarizer). This is the summary generated from the online tool at http://freesummarizer.com/:

What I feel is that this country needs to look at the fundamental issues at hand, the fundamental political issue at hand is that our Political system is controlled by too few people and we absolutely have to change the way our political system is structured, we have to change our Political parties, we have to make them more transparent, we have to change the processes that we use to elect candidates, we have to empower women in the political parties, that is where the meat of the issue but I don’t hear that discussion, I don’t hear the discussion about how are we actually choosing that candidate, that is never the discussion.

That ascribes huge power to the Congress party, I think the Congress party’s strength comes when we open up when we bring in new people, that is historically been the case and that is what I want to do.

The Gujarat riots took place frankly because of the way our system is structured, because of the fact that people do not have a voice in the system. And what I want to do. He was CM when Gujarat happened The congress party and the BJP have two completely different philosophies, our attack on the BJP is based on the idea that this country needs to move forward democratically, it needs push democracy deeper into the country, it needs to push democracy into the villagers, it needs to give women democratic powers, it needs to give youngsters democratic powers.

You are talking about India, we have had a 1 hour conversation here, you haven’t asked me 1 question about how we are going to build this country, how we are going to take this country forward, you haven’t asked me one question on how we are going to empower our people, you haven’t asked me one question on what we are going to do for youngsters, you are not interested in that.

There is the Congress Party that believes in openness, that believes in RTI, that believes in Panchayati Raj, that believes in giving people power. The Congress party is an extremely powerful system and all the Congress party needs to do is bring in younger fresher faces in the election which is what we are going to do and we are going to win the election.

In retrospect, repeating a few points several times is a good enough cue for an auto-summarizer to identify important sentences. This interview was perfect for a task like this as Mr. Gandhi repeated the same set of (rote) answers for almost every question that he was asked. Perhaps this is what he was hoping for? To make sure that when lazy journalists use automatic tools to do their jobs, it would give them a perfect output!

Now coming to the interesting bit. If you were a human listener like me and wanted to read the answers that he really did attempt to answer [1] , what would you do? Fear not! I have built an SVM classifier from this transcript that you could make use of in future. I used LightSide, an open source platform created by CMU LTI researchers to understand features from the transcript of his answers. Let’s get into the details then.

When you go for a interview, you could either choose to answer a question or try to avoid by cleverly diverting from the main question asked. In Rahul’s case, we have answers that can be mainly grouped into three categories – a) the questions that he answered, b) he managed to successfully avoid and c) the LOL category (the answer bears no resemblance to the question asked). I combined categories (b) and (c) to come up with classes: ANSWERED or UNANSWERED. You may check out my list of classes here and read the interview answers from the Times of India article here. They follow the same order as in the transcript with the exception of single line questions-answers that would’ve otherwise served as noise for machine learning. I selected a total of 114 questions in all out which 45 were answered and the remaining 69 were either successfully avoided or belonged to the LOL category [2] .

For feature extraction, I used quite simple language features like Bigrams, Trigrams, Line length after excluding stop words etc. You can download them in the LightSide feature format. I used the SVM plugin to learning the classification categories from the feature. Here is the final model that the tool built using the extracted features. And the results were surprising (or probably not :). With 10-fold cross validation, the resulting model had an accuracy of over 72%! An accuracy percentage like this is considered to be exceptional (in case you are not familiar with the field). The machines indeed understand Rahul Gandhi!

Unfortunately, I did not have enough data to run a couple of tests separately. We’ll have to probably wait for Mr. Gandhi to give his next interview for that. Hope that the Congress party members work as hard as the NLP researchers so that we can have a good competition by then!

Footnotes

  1. He did make an effort to answer about 40% of the questions to his credit ^
  2. These are solely based on my personal opinion. ^