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Designing radiotherapy treatments is a complicated and important task that affects patient care, and modern delivery systems enable a physician more flexibility than can be considered. Consequently, treatment design is increasingly automated by techniques of optimization, and many of the advances in the design process are accomplished by a collaboration… (More)

- Allen Holder
- Operations Research
- 2005

- Allen Holder
- Health care management science
- 2003

A new linear programming model used to aid in the design of radiotherapy plans is introduced. This model incorporates elastic constraints, and when solved with a path following interior point method, produces favorable plans. A sound mathematical analysis shows how to interpret the solution, and hence, the treatment planner receives meaningful knowledge… (More)

- Yosi Shibberu, Allen Holder
- IEEE/ACM Transactions on Computational Biology…
- 2011

A new intrinsic geometry based on a spectral analysis is used to motivate methods for aligning protein folds. The geometry is induced by the fact that a distance matrix can be scaled so that its eigenvalues are positive. We provide a mathematically rigorous development of the intrinsic geometry underlying our spectral approach and use it to motivate two… (More)

- Julio-Roberto Hasfura-Buenaga, Allen Holder, Jeffrey Stuart
- 2001

The data describing an asymptotic linear program rely on a single parameter , usually referred to as time, and unlike parametric linear programming, asymptotic linear programming is concerned with the steady state behavior as time increases to infinity. The fundamental result of this work shows that the optimal partition for an asymptotic linear program… (More)

- Yosi Shibberu, Allen Holder, Kyla Lutz
- ISBRA
- 2010

We address the problem of aligning the 3D structures of two proteins. Our pairwise comparisons are based on a new optimization model that is succinctly expressed in terms of linear transformations and highlights the problem's intrinsic geometry. The optimization problem is approximately solved with a new polynomial time algorithm. The worst-case analysis of… (More)

- Ali Ebrahim, Eivind Almaas, +38 authors Ines Thiele
- Molecular systems biology
- 2015

This paper reviews the history, within psycho-analysis, of narcissism and shows that it cannot be understood as a unitary concept. This is reflected in much of the extensive literature on the topic. The definition of narcissism solely in terms of the libidinal drive cathexis of the self representation is rejected. Instead, narcissism is defined as the sum… (More)

- Gino J. Lim, Allen Holder, Josh Reese, MSTR
- 2009

In this paper we introduce a p-median problem based clustering heuristic for selecting efficient beam angles for intensity modulated radiation therapy. The essence of the method described here is the clustering of beam angles according to probability that an angle will be observed in the final solution and similarities among different angles and the… (More)