Today's post is about the presentations two participants to the Richard E. Rosenthal Early Career Connection program - Shokoufeh Mirzaei and Ehsan Salari - did of their work at the 2015 INFORMS Annual Meeting in Philadelphia, PA. (Nominations for the 2016 ECC program are now open and due March 4! More information is available here.)
Dr. Mirzaei (Shokoufeh thereafter), who is a tenure-track Assistant Professor at Cal State Pomona, gave a talk regarding open problems on computational structural biology and protein quality assessment. She explained why researchers care about the structure of the protein (shape affects function). Many diseases happen as a result of misfolding proteins (for instance Alzheimer's and Parkinson's) and it is important in the drug discovery process to understand a protein's interaction with other proteins. The goal of this line of work is to design new proteins with desired functions not currently found in nature, with the hope that computational work will be able to replace at least in part experimental work, i.e., drug trials on individuals. A challenge is that there is no clearly defined energy function so there is no clear objective to minimize. Criteria that can be used in the optimization framework include: hydrogen bonds, Van der Waals interactions, backbone and angle preferences, electrostatic interactions, and more. Those criteria lead to very nonlinear and non convex expressions, making the problem even more challenging.
Shokoufeh then discussed the Protein Data Bank (which offers opportunities for template-based, homology-based and free modeling) and the WeFold Coopetition, the purpose of which is to encourage "coopetition" (competition+cooperation) among labs to improve the state of knowledge regarding protein structure prediction. Certain classes of prediction targets have only seen modest gains over the past few years and such an event therefore had the potential of speeding up the rate of discovery. Open problems in the field include best scoring function and best metrics to compare two protein structures. Then Shokoufeh commented on the problem of creating a benchmark data set for testing different proteins and discussed computational approaches such as MESHI (using the clustering nature of proteins) and Support Vector Machine.
This is a field I know nothing about and I was struck by the clarity of Dr. Mirzaei's presentation as well as the effectiveness of her communication skills in making very complex problems understandable to a lay audience. She proved a very articulate and effective speaker who convincingly made the case for her research. In today's world, analytics professionals must not only have the quantitative tools to make a difference but also communicate their work effectively and there is no doubt Dr. Mirzaei will soon be a star in her domain.
Dr. Salari (Ehsan thereafter), Assistant Professor at Wichita State, gave a talk entitled: "Biologically-guided radiotherapy planning: fractionation decision in the presence of chemoradiotherapeutic drugs." His talk was based on his recent paper published in IIE Transactions in Healthcare Systems Engineering. You can find a technical paper version of the work here. Radiotherapy (RT) uses high-energy radiation beams to kill cancer cells by damaging DNA. The survival rate of cells when exposed to different rates of radiation follows a linear-quadratic model. RT treatments are delivered through daily fractions. A regimen is thus determined by the number of fractions and the radiation dose. Effects of fractionation are accounted for by using a concept called the biologically effective dose. (BED)
Chemotherapy can be done sequentially or concurrently with RT but increases the risks of complication. It is therefore important to determine the impact of chemotherapeutic agents on optimal RT fractionation regimens. Additivity and radio-sensitization both affect the linear-quadratic curve depicting the survival rate of cells. Ehsan proposed an approach to extend the BED model to quantify the radiation damage and studied the optimal radiation fractionation regimen and the drug administration scheme under 4 schemes: RT only, CRT with additive effects only, CRT with radio-sensitization effects only, CRT with combined effects. His presentation contained many insightful graphs on the structure of the optimal regimen, which you can also find in his paper.
Like Shokoufeh, Ehsan proved to be an exceptional researcher delivering a compelling, insightful presentation of quality far above the average presentation at the annual meeting. I am looking forward to reading other papers by him.