David Craft, PhD

Assistant Professor
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Associate Member, Broad Institute

Education and Degrees

B.Sc.: Brown University, Mechanical Engineering, 1996
Ph.D.: Massachusetts Institute of Technology, Operations Research, 2004

Areas of Interest

Genomics, biological network modeling, machine learning, radiation for cancer control

Multi-criteria optimization in radiation therapy

Mathematics and statistics

Research statement 

My current focus is on the development of machine learning algorithms tailored to making predictions on datasets that are derived from networked systems. In order to do this, we are building various network simulations and using these simulations to produce artificial datasets. Since the ground truth data generation system is known, we can incorporate (partial) system knowledge into the machine learning algorithms and thus ascertain the value of such knowledge. This is in contrast to blind machine learning that is typically done in computational biology, where all prior known biology is ignored in favor of a pure data driven approach.We hypothesize that utilizing known network information, even in a limited way, should increase the power and interpretability of machine learning algorithms. The eventual application of these ideas will be in predicting patient specific responses (efficacy and toxicity) to cancer drugs and radiation.

I am also working on estimating fitness of copy number variations from large scale copy number data.

In the world of radiation therapy, I consider VMAT still an unsolved problem. It is highly non-convex, and yet there are many convex aspects to the problem. My group is working to tame those non convexities by smart heuristics. Keep an eye out for a paper on dynamic MLC delivery with the word "biquasiconvex", for which there are only 9 hits (now 10 I suppose) on google!


The value of prior knowledge in machine learning of complex network systems, Submitted. Datasets for download (including README instructions) and Matlab Boolean Network Creation Simulation package: RaBooNet

PICS: Pathway Informed Classification System for cancer analysis using gene expression data Cancer Informatics, 2016.

The price of target dose uniformity, International Journal of Biology, Physics, and Medicine, 2016.

Craft and Balvert VMAT papers: Fast approximate delivery of fluence maps: the single map case and the VMAT case. 2016. We rolled this paper into one to publish it: Fast approximate delivery of fluence maps for IMRT and VMAT. 2017

Within the next five years, most radiotherapy treatment schedules will be designed using spatiotemporal optimization, point/counterpoint. Medical Physics, 2016. 

Volumetric-modulated arc therapy using multicriteria optimization for body and extremity sarcoma, M. Young et al. JACMP 2016(submitted).

Multi-criteria optimization achieves superior normal tissue sparing in a planning study of intensity-modulated radiation therapy for RTOG 1308-eligible non-small cell lung cancer patients, Kamran et al, Radiotherapy and Oncology, 2016.

Shared data for intensity modulated radiation therapy (IMRT) optimization research: the CORT dataset GigaScience, 2015.

Optimization approaches to volumetric modulated arc therapy planning J Unkelbach, T Bortfeld, D Craft, M Alber, M Bangert… - Medical physics, 2015

A circular matrix-merging algorithm with application in volumetric intensity-modulated Arc therapy DZ Chen, D Craft, L Yang - Theoretical Computer Science, 2015

Three-dimensional conformal planning with low-segment multicriteria intensity modulated radiation therapy optimization, Kahn, Craft.  GigaScience, 2015.

Optimization approaches to volumetric modulated arc therapy planningUnkelbach, Bortfeld, Craft, et al, Med Phys, 2015.

Plan averaging for multicriteria navigation of sliding window IMRT and VMAT, Med Phys, 2014.

Multi-criteria optimization methods in radiation therapy planning: a review of technologies and directions. Springer, submitted.

Guaranteed Epsilon-Optimal Solutions with the Minimum Number of Beams for Stereotactic Body Radiation Therapy, Yarmand, Winey, Craft. PMB (2013)

A hybrid approach to beam angle optimization in intensity-modulated radiation therapy  Bertsimas, Cacchiani, Craft, Nohadani. Computers and Operations Research (2013).

Maximizing dosimetric benefits of IMRT in the treatment of localized prostate cancer through multicriteria optimization planning, Medical Dosimetry, 2013.

Deliverable navigation for multicriteria step and shoot IMRT treatment planning, Physics in Medicine and Biology, 2013.

The dependence of optimal fractionation schemes on the spatial dose distribution, Physics in Medicine and Biology, 2013.

Exploring Trade-offs between VMAT Treatment Quality and Delivery Efficiency, Salari et al, Physics in Medicine and Biology, 2012.

Optimal partial-arcs in VMAT treatment planning,Jeremiah Wala, Ehsan Salari, Wei Chen and David Craft, Physics in Medicine and Biology, 2012.

Including robustness in multi-criteria optimization for intensity-modulated proton therapy, Wei Chen, Jan Unkelbach, Alexei Trofimov, Thomas Madden, Hanne Kooy, Thomas Bortfeld and David Craft, 2012 Phys. Med. Biol. 57.

Multicriteria VMAT optimization, Medical Physics, 2012 

Improved planning time and plan quality through multicriteria optimization for intensity-modulated radiotherapy.International Journal of Radiation Oncology * Biology * Physics, 2011

A fast optimization algorithm for multicriteria intensity modulated proton therapy planning. Chen, Herman, Craft, Madden, Zhang, Kooy. Medical Physics, 2010; 37(9).

Simultaneous navigation of multiple Pareto surfaces, with an application to multicriteria IMRT planning with multiple beam angle configurations. Medical Physics 2010;37(2).

Calculating and Controlling the Error of Discrete Representations of Pareto Surfaces in Convex Multi-Criteria Optimization. Physica Medica. 2010.

Multicriteria Optimization in IMRT Treatment Planning For Locally Advanced Cancer of the Pancreatic Head. International Journal of Radiation Oncology * Biology * Physics, 2008;72(4):1208-1214.

Evaluating Target Cold Spots By the Use of Tail EUDs. International Journal of Radiation Oncology * Biology * Physics, 2008;71:880-889.

How Many Plan Are Needed in an IMRT Multi-Objective Plan Database. Physics in Medicine and Biology. 2008;53:2785-2796.

An approach for practical multiobjective IMRT treatment planning, Int J Radiat Oncol Biol Phys. 2007;69(5):1600-1607

The tradeoff between treatment plan quality and intensity field complexity in IMRT, Red Journal, volume 67 number 5, April 2007

Local beam angle optimization with linear programming and gradient search. Phys. Med. Biol. -- March 2007 -- Vol. 52, pp. N127-N135.

Dose-volume objectives in multi-criteria optimization (Halabi et al., Phys. Med. Biol. -- August, 2006 -- Volume 51, pp. 3809-3818)

Approximating convex Pareto surfaces in multiobjective radiotherapy planning(Medical Physics -- September 2006 -- Volume 33, Issue 9, pp. 3399-3407)

Exploration of tradeoffs in intensity-modulated radiotherapy (2005, Physics in Medicine and Biology)

Maximizing Operating Room and Recovery Room Capacity in an Era of Constrained Resources, Arch Surg. 2006;141:389-395.

Surgeon Profiling: A Key to Optimum Operating Room Use, Arch Surg. 2007;142:365-370

Ph.D. Thesis: Local energy management through mathematical modeling and optimization

Analyzing Bioterror Response Logistics: The Case of Anthrax (May 2005, Management Science, Volume 51, Number 5)

Analyzing bioterror response logistics: The case of smallpox (2003, Mathematical Biosciences, Volume 185 Issue 1)

Emergency response to a smallpox attack: The case for mass vaccination (2002, Proceedings of the National Academy of Sciences)          - Work discussed in the New York Times, July 9, 2002

Emergency Response to an Anthrax Attack (2003, Proceedings of the National Academy of Sciences)

A Mathematical Model of the Impact of Novel Treatments on the A-Beta Burden in the Alzheimer's Brain, CSF and Plasma (2001, Bulletin of Mathematical Biology)

Bower, A.F. and Craft, D. (1998) Analysis of failure mechanisms in the interconnect lines of microelectronic circuits. Fatigue & Fracture of Engineering Materials & Structures 21 611-630


Some of Infinity: peaks in the landscape of mathematics, (Center of Math, in progress) 2016.

Urban Foraging, Finding and eating wild plants in the city, Service Berry Press, 2011.


Return To Their Natural Coast, 2012

Furniture Music, 2016


My foraging tours schedule at foragelive.com

Located in: Research