Updating CSCI 205

CSCI 205 has been a highly successful course for our majors. It is a lot of work for students, and likewise for the instructors who teach it (myself and Prof. Chris Dancy.) But, the rewards have been plenty, as the course teaches a lot about there is a lot of material that is out of date. The course will still relying on Java 7, and used Netbeans.

I’ve taken quite a bit of extra time this semester to update some of the course. As of Fall 2019, the course has been updated in the following ways:

  • We are now using IntelliJ IDEA
  • The course has been updated to Java 12
  • Many videos have been re-recorded to address the updated content, including:
    • Heavier emphasis on lambda expressions than ever before
    • Teaching more java.nio and java.nio2 along with java.io
    • Added new material on socket programming with java.net
    • Added new material on multithreading and concurrency in Java
    • Introduced the Java Stream API (not to be confused with the I/O streams)
  • The final project has been overhauled. Every student now must use Gitlab for all their Scrum task board and sprint management (This has worked surprisingly well!)
  • Expanded the JavaFX material 

It’s a start. There is a lot to be done still.

In a recent discussion with Chris Dancy, he expressed significant interest in incorporating elements of engineering social justice into the course. This represents a broader move by the engineering community at large to start helping our students recognize the impact that their choices have on humanity. I am at fault here. Like many of us, we focus on the goals without teaching our students the impacts that their choices have. Well, that’s not entirely true. I discuss impact – computational resource impact. That’s not enough. I do not give enough attention to social, moral or ethical impact. So, I believe this will be the next set of revisions we make to the course. Chris may likely start on some of those changes in Spring 2020. But, we’ll likely make a more substantial effort to incorporate this into the project over the summer. It’s time for engineers to emphasize people as more important considerations than profits.

My joy with ILTM

I had the joy of becoming a core faculty member of the Institute of Leadership in Technology and Management for the past two summers (Summer 2017, 2018). I found this to be one of the most transformative experiences available to Bucknell students since I’ve been here. I was honored to be part of this program. I worked with some absolutely wonderful students in ILTM! However, as a result of this opportunity, my scholarship was substantially halted for the last two summers. Thus, I have not taken on any new students for quite some time.

I was also on sabbatical during the entire 2017-18 academic year. During this time, I continued to work on interesting projects collaboratively with Dr. Vanessa Troiani at Geisinger Autism and Developmental Medicine Institute. As much as I’ve found much pleasure working in various areas of bioinformatics, I decided it was time for me to explore other areas of sequential data analysis. Dr. Troiani and her lab members have invigorated me with new opportunities in pattern mining mass quantities of eye-tracking data. This ultimately led to another collaborative project involving Dr. Troiani and our own Prof. Evan Peck. Slowly, the research agenda is ramping back up again. I applied to 5 different grant opportunities, of which, to date, one has been awarded, and a much larger one is currently under review.

I’ve also become more involved in interdisciplinary teaching and research opportunities across the university. Bucknell is at a point now where we can truly provide some very interesting transformative experiences to our students – rare opportunities that very few colleges can offer. To do so, however, we must leverage the opportunities that exist across disciplines. Thus, I’ve been intentional in my pursuits to identify new opportunities outside of my own department, and my own home – the College of Engineering. For instance, I’ve had great joy working with my collegue, Prof. Abby Flynt, on both teaching and research projects. (We both recently received the Presidential Award for Teaching Excellence for 2018, and co-mentored a wonderful student, Alexander Murph, who completed an honors thesis and is now at UNC Chapel Hill pursuing his PhD in Statistics!)

Speaking of new, unique opportunities for interdisciplinary work. I’m looking forward to seeing new things happen with our new College of Management, where I expect some interesting collaborations with new faculty who will be part of their new Analytics and Operations Management program. I’ve been spending time with them recently serving on a committee to help them hire new faculty for this exciting program.

Of course, I can’t forget our wonderful friends in Biology, who were so instrumental in collaborating on my bioinformatics projects very early on during my pre-tenure days here. Needless to say, there are great colleagues across this university, with lots of data! It’s a rich place for a data scientist!

Sequential data mining and analysis – it will always remain my primary area of focus, and it’s exciting to be able to afford the risks with tenure to be able to stretch my core interests toward new areas. Fortunately, sequential data are ubiquitous. Thus, I’ve branched away from biological sequence analysis and delved into numerous other areas of sequential data. I will update soon.

My post tenure feelings

So, is tenure all it’s cracked up to be? Well, I’m now in the midst of my third year post tenure. Or is it my second? I don’t even know. I’m burnt out, thanks to the vicious down side of tenure – SERVICE! Once a faculty member receives tenure, it seems as though you are put on a list by the administration throughout the college and university. This list is special. I believe the title of the list is, “PEOPLE WHO WE CAN GUILT INTO SERVING ON COMMITTEES NOW THAT THEY HAVE TENURE.” This semester, I honestly have lost count of the committees and the other opportunities where I have said “yes” to volunteer for opportunities to help my colleagues. The result, I regularly have a minimum of 10-15 additional hours per week dedicated to service obligations; that has recently reached 20+. Those are hours that are on top of my normal teaching hours in and out of the classroom, which are easily 40+ hours, and that doesn’t include my normal teaching/service duties, such as academic advising, department meetings, mandatory caffeine pursuits, and so on. (An academic has no concept of a 40-hour work week. It doesn’t exist.) This is a huge challenge that I’m struggling with. It is due, in part, to a very young, vibrant department of faculty who are going through the tenure process. Thus, the relatively few of us who have tenure take on a lot of the service obligations to protect them as they work through tenure. And, of course, I know, I know… the real reason? Because I often find it difficult to say, “NO!” Like I said, I work at a great place with wonderful colleagues. I believe it’s important to pay it forward. I had people senior to me who were once in my shoes and protected me from excessive service obligations, and I will do the same. The challenge is the imbalance in the department. We’ve had a lot of people retiring in recent years. In time, the balance should be back to normal as others get through the tenure review process, and they can share the service burdens.

Anyway, the most important thing that has me excited? First, I’m teaching BOTH a data mining AND a data science course this Spring! Second – this summer 2019 is mine! All mine! [Insert-evil-laugh-here]. I have not had a summer for research since 2016. So, I have several projects that are ramping up, and I am looking for new students to work with me this summer. Funding is available. Send me an e-mail if you are interested.

Summer 2016

It has been quite some time since I’ve updated current events. Thanks to our students, we have had a pretty active summer…

  • Robert Cowen is continuing his work with me on word prediction models. We have good results and are writing our first paper. The first draft should be complete by the beginning of September.
  • Morgan Eckenroth has started work on the development of a virtual reality app (using Google Cardboard) that will be used by autistic children to help assess (and hopefully retrain) biases in their visual processing
  • Khai Nguyen is working on a collaborative project, funded together by the College of Engineering, Chemical Engineering, and Computer Science. The aim of the project is to develop a new application for aerosol researchers in Chem Eng.
  • Ryan Stecher is working on a collaborative project with Dr. Aaron Mitchel in Psychology to develop and finalize a web-based series of perception tests.
  • Tongyu Yang has been investigating the use of deep learning to help autism researchers better understand why autistic children have substantial interest in certain types of images

Summer 2015

We have an active summer in store. Three students are working on entirely different research projects, while Rachel Ren is wrapping up her work.

  • Son Pham is working on investigating the use of Deep Learning for protein sequence classification. Deep Learning has recently gained substantial recognition due to its success with automated image recognition and speech classification. Very few have examined its use in bioinformatics. Son will help me explore this untapped area in bioinformatics.
  • Jason Hammett will be applying data mining techniques to years of regional climate data, including local stats for the Susquehanna River, to develop explanatory and predictive models for anomalistic weather events around the Susquehanna River Valley.
  • Robert Cowen will be continuing the wonderful work that I started with Bucknell Student Stephanie Gonthier last year on word prediction. Robert will be collaborating with myself and speech pathologists at the Geisinger-Bucknell Autism and Developmental Medicine Institute (ADMI) to develop a preliminary version of a new augmentative and alternative communication (AAC) app that will utilize my word prediction model. This first version will be developed to run on Android tablets.
  • Rachel Ren is graciously staying for a month after graduating to help submit a paper based on her extensive work completed for her honors thesis. Stayed tuned!

Spring 2015

Rachel Ren successfully defended her honors thesis, titled, “Predicting Protein Contact Maps by Bagging Decision Trees”. Congratulations, Rachel! Additionally, Rachel will be attending graduate school starting in the fall at Columbia University, where she will pursue a Masters in Computer Science. Rachel intends to focus on research in machine learning.

Congratulations, Rachel! Bucknell is proud of you! We wish you the very best as you pursue your graduate work.