Group testing problems in experimental molecular biology

In group testing, the task is to determine the distinguished members of a set of objects L by asking subset queries of the form ``does the subset Q of L contain a distinguished object?'' The primary biological application of group testing is for screening libraries of clones with hybridization probes. This is a crucial step in constructing physical maps and for finding genes. Group testing has also been considered for sequencing by hybridization. Another important application includes screening libraries of reagents for useful chemically active zones. This preliminary report discusses some of the constrained group testing problems which arise in biology.Comment: 7 page

Scienceography: the study of how science is written

Scientific literature has itself been the subject of much scientific study, for a variety of reasons: understanding how results are communicated, how ideas spread, and assessing the influence of areas or individuals. However, most prior work has focused on extracting and analyzing citation and stylistic patterns. In this work, we introduce the notion of 'scienceography', which focuses on the writing of science. We provide a first large scale study using data derived from the arXiv e-print repository. Crucially, our data includes the "source code" of scientific papers-the LaTEX source-which enables us to study features not present in the "final product", such as the tools used and private comments between authors. Our study identifies broad patterns and trends in two example areas-computer science and mathematics-as well as highlighting key differences in the way that science is written in these fields. Finally, we outline future directions to extend the new topic of scienceography.Comment: 13 pages,16 figures. Sixth International Conference on FUN WITH ALGORITHMS, 201

First Author Advantage: Citation Labeling in Research

Citations among research papers, and the networks they form, are the primary object of study in scientometrics. The act of making a citation reflects the citer's knowledge of the related literature, and of the work being cited. We aim to gain insight into this process by studying citation keys: user-chosen labels to identify a cited work. Our main observation is that the first listed author is disproportionately represented in such labels, implying a strong mental bias towards the first author.Comment: Computational Scientometrics: Theory and Applications at The 22nd CIKM 201

Radix Sorting With No Extra Space

It is well known that n integers in the range [1,n^c] can be sorted in O(n) time in the RAM model using radix sorting. More generally, integers in any range [1,U] can be sorted in O(n sqrt{loglog n}) time. However, these algorithms use O(n) words of extra memory. Is this necessary? We present a simple, stable, integer sorting algorithm for words of size O(log n), which works in O(n) time and uses only O(1) words of extra memory on a RAM model. This is the integer sorting case most useful in practice. We extend this result with same bounds to the case when the keys are read-only, which is of theoretical interest. Another interesting question is the case of arbitrary c. Here we present a black-box transformation from any RAM sorting algorithm to a sorting algorithm which uses only O(1) extra space and has the same running time. This settles the complexity of in-place sorting in terms of the complexity of sorting.Comment: Full version of paper accepted to ESA 2007. (17 pages