What physicians need from AI

· Posted in Artificial Intelligence, HCI, Opinion

We have a small library in the graduate students’ office of the Intelligent Systems Program. Over 30 years of its existence, it has collected various visions and hopes about how applications of AI would change different fields around us. One such record is the Institute of Medicine committee report on improving the “patient record” from 1992. It emphasizes the importance of using Electronic Health Records for decision support systems and supporting data-driven quality measures for the then emerging technology. While the last few years have seen a rapid increase in EMR adoption, there hasn’t as much progress towards the goal of using this data for improving care. In contrast, however, physicians’ experiences tell a very different story about how EMRs end up getting in the way of taking care of their patients.

Why are EMRs causing harm when they were supposed to help?

There are many potential reasons for physicians’ problems with the current EMRs, but the main challenge in building them is to provide effective solutions for many complex tasks and scenarios involving collecting, finding and displaying large volumes of patient information. Physicians often like to compare their EMR to large wooden cabinets with lots of drawers and difficult access to the information they need. Documenting and finding the right pieces of information becomes a massive task as the information grows. And all these problems are only going to increase in the future. This is because we are moving towards collecting more and more data. Also, we can expect physicians’ processes to become more sophisticated as we advance towards solving harder health problems.

More data

The University of Pittsburgh Medical Center has over 9 PB of data, which is doubling every ~18 months. More innovation in medical devices and sensors, easier documentation procedures, patient reported outcomes… all are going to further add burden to the EMR software. We also need to ensure that the methods for capturing this data are convenient for the care providers, without causing significant disruptions in taking care of the patients.  Free-text reports offer easy mechanisms to capture rich information that can be easily communicated. But, we need to build better systems that can help analyze this information. More data can only provide favorable outcomes when we provide appropriate ways of handling and analyzing it.

Team based care

Sophisticated health care practices requires a team based effort. All of which must be coordinated by the EMR software as the primary means of communication between the team members. However, not all teams are interested in the same pieces of information and the current practices result in an information overload for the physicians. Some physicians come up with ad-hoc processes outside the EMR system to cope with these problems. For example, we often find ICU physicians using manually curated signout notes to communicate important information to their team members. These are examples of important pain points for the physicians that must be identified and addressed.

Technology to the rescue?

We have seen these problems in computer science before. We even trace the birth of the field of Human-Computer Interaction to ideas like MEMEX, which hoped to solve some of these very problems. We also have made a lot of progress in AI since then, which provides us practical tools to build real solutions. And we are employing some of these in EMRs as well – like Dragon for dictating patient notes, aggregating patient information among others. But, one could still claim that the development of EMRs “has not kept pace with the technology in other domains”. We have many open problems in the way of making the EMRs work better for everyone. As much as pop culture has left us desiring for things like the Star Trek Tricorder, what we really need instead are tools that can help make physicians wade through the sea of information and make better decisions. A more recent (2007) Institute of Medicine report envisions a Learning Health Care system that allows intelligent access to patient information. The role of the physicians must evolve towards becoming better data managers and analysts.  And we need computer scientists and engineers to find and solve some of the problems along the way.


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.


Mathematics, Tabla and the Arts

· Posted in Opinion

Spring break is here and I finally have ample time to practice my tabla. In the absence of a regular schedule and a teacher, I rely on online videos to improve my skills. Following my YouTube recommendations, I came across this talk given by Manjul Bhargava to a group of school children in Bangalore. Not many of you may know that Dr. Bhargava is not only the 2014 Fields Medal winner, but he is also an accomplished tabla player who has studied under one of the greatest tabla player of our times – Zakir Hussain.

I thought I should post this on my blog for it is certainly the kind of talk that I would have cherished as a kid attending it. Also, I really liked the way he simplified and explained a reasonably difficult concept to his audience. I am sure it would have made a lot of minds curious about the topic:

If you found this interesting, you can find a nice tutorial on it with the title Mathematics for Poets and Drummers by Dr. Rachel Hall (also has an extended version that I haven’t been through yet). Also if this talk inspired you to pick up tabla, I found this very useful series of videos on a YouTube channel by Tej Singh for beginning and intermediate tabla players.


Macbook 2011 Problem

· Posted in Opinion

issueUpdate: Apple finally owned up to the problem and is offering free repairs starting Feb 20, 2015.

As everyone was starting to queue up for the sale of iPhone 6 today, I was trying to get my macbook working again at the Genius bar. I had been facing problems with a garbled display since the last couple of days which then turned into a critical problem rendering my computer unable to start up. It would show the apple logo and the loading animation but then get stuck with a gray screen.

I am not sure how everyone’s experience at the Apple store has been but I have always had a terrible time explaining any of my problems to the “geniuses” out there. It takes a lot of patience to listen to the condescending way they would talk to you (You seem to be having a problem with the logic board – you know, the brain of the computer”). I don’t know if they are trained to talk like that to anyone not wearing a blue t-shirt or is it their everyday experiences that make them act like that.

Turns out that early 2011 version of the macbooks with ATI graphics cards came with a manufacturing defect that Apple is refusing to own up to. There are several threads on popular sites and on Apple’s discussion forums that talk about it. In fact, there has been a class action lawsuit has also been filed against Apple against this issue. You can also support the change.org petition and sign your name along with 15,000 supporters there:

In case you have been facing the same issue and are looking to buy some more time to get a final backup and move your stuff etc… Moving the graphics driver to a temporary directory helped me with that. Here‘s the StackExchange answer that you could make use of. And if you own a Macbook Pro from 2011 and haven’t faced this problem yet, please do bookmark the link for you would eventually need it anytime you do any graphics intensive work.

 

Edits:

1. Zach Clawson has compiled a list of actions that you could possibly take if you are facing a similar problem – https://people.cam.cornell.edu/~zc227/extras/early2011mbp_graphics.html.

2. I had written this post as a rant after a rather disappointing visit to the Apple Store. I have edited some portions since then for providing a more objective view.

3. Add bug report screenshot:

Bug report I filed The update making it a dupe

 

I have filed a bug report for this issue as well to make sure that it is in their system (which they later updated to be a duplicate of another issue – see picture).

 


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. ^


A Symphony of Drums

· Posted in Opinion

I spent my afternoon today at Tablaphilia – a tabla symphony composed by Pt. Samir Chatterjee. It was incredible to listen to 22 drummers playing together on a single stage in harmony and conducted in a symphony. Do you find it strange when I talk about harmonics while describing something performed on drums? A lot of people new to Tabla certainly do. You could sense the confusion in the audience as they watched the band “tune” their drums. Most drums, such as the ones used in a rock performance produce only in-harmonic vibrations. You’d probably prefer a dry sound without any ‘ring’ on these drums contrary to what you get from a Tabla.

tabla

A tabla is usually played as a set of two drums. The one on the left is the bass drum while the right one has a pitch and can produce harmonic overtones.

Tabla is part of a family of musical drums including Mridangam and Pakhawaj, which can produce harmonic overtones. In fact, tabla featured relatively much later in Indian music. There are several theories about its origins, such as the legend involving the famous musician – Amir Khusro [1] , and how he invented tabla when a jealous competitor broke his drum. Many also believe that Tabla may have more ancient roots in the instrument known as Tripushkara, which had three different parts like a drum kit: horizontal, vertical and embraced. I find this theory more convincing but the absolute beginnings of tabla remain unclear. However, we do know that Tabla became popular in the 17th century, when there was a need to have a drum that could give faster and complex rhythm structures required for the then emerging Sufi music style. The “finger and palm” technique used on the Tabla was much more suited for it than the heavier sounding Pakhawaj.

Alright, coming back to the central theme of the post: what allows a drum to produce harmonics? Without going into its mathematics (read, I can’t :D), allow me to refresh your memory about some concepts in harmonics. Perhaps you remember the experiments performed with the sound column and a tuning fork in your Physics lab. [2] You’d recall that a string vibrates at some fundamental frequency and its integer multiples are known as harmonics. Stringed instruments can vibrate in a harmonic series, and a unique combination of these harmonics make them sound the way they do. But what about a membrane such as the ones that used on these drums? Turns out that the drum-head on the pitch drum (the right one; See picture.) can also produce five such harmonics giving its musical effect. These are responsible for the different bols that are played on the tabla. There are two papers by the Nobel prize-winning physicist CV Raman, who has explored them in a lot of detail: "Musical drums with harmonic overtones" (C.V. Raman and S. Kumar, 1920)  and "The Indian musical drums" (C.V. Raman, 1934)

Unlike most drums, tabla has a sophisticated mechanism to alter its pitch. All tablas are designed to have a pitch that can vary between a certain range. This is done by beating along the sides of the head and adjusting the tension in the straps on the side with wooden blocks. By carefully tuning several tablas, you can derive different notes used in music and have something as amazing like this:

It was exhilarating to hear the “notes” played by the drummers during the concert piece today  as the tablas provided both rhythm and melody. As I was enjoying the music, I couldn’t help but wonder about the engineering skills and knowledge required to build these instruments. Most artisans responsible for building them have no formal training about the theory behind it. All the ingredients that go into making the drum, its shape, the three layers of membrane on the head and even the placement of the black spot (or syahi) contribute to the unique sounds of the instrument. Some of the techniques for building the drum have been passed within families over hundreds of years. The exact recipe for making the syahi, is still kept as a closely guarded secret in these families. This loading of the membrane with the syahi allows the tabla to produce overtones. Did you notice that it is placed off the center on the bass (the left drum) though? The membrane also has different regions which when struck in a certain manner produce the overtones. When you go about counting the different parameters and factors, it makes you wonder about how by mere experience, the makers of tabla could design it.

Listening to Tablaphilia was an incredibly unique experience. I always enjoy when students play together in a tabla class while learning a piece but having a complete performance like this was very new for me. Usually, tabla performances are either done solo or they give company to a melody instrument but never as an ensemble. Some connoisseurs of Indian music would argue that a format like this doesn’t offer any room for improvisations. Agreed; but then what is music without variety and experimentation. I look forward to more such symphonies and concerts.

References

  1. C.V. Raman (1934), The Indian musical drums. Available: http://www.ias.ac.in/jarch/proca/1/179-188.pdf.
  2. C.V. Raman and S. Kumar (1920), Musical drums with harmonic overtones. Available: http://www.nature.com/nature/journal/v104/n2620/abs/104500a0.html.

Footnotes

  1. Amir Khusro, the second; as I am told, but I couldn’t find a reference online ^
  2. The Wikipedia article on Harmonics has some really neat illustrations. ^