@article{847,
abstract = {The accumulation of genome-wide information on single nucleotide polymorphisms in humans provides an unprecedented opportunity to detect the evolutionary forces responsible for heterogeneity of the level of genetic variability across loci. Previous studies have shown that history of recombination events has produced long haplotype blocks in the human genome, which contribute to this heterogeneity. Other factors, however, such as natural selection or the heterogeneity of mutation rates across loci, may also lead to heterogeneity of genetic variability. We compared synonymous and non-synonymous variability within human genes with their divergence from murine orthologs. We separately analyzed the non-synonymous variants predicted to damage protein structure or function and the variants predicted to be functionally benign. The predictions were based on comparative sequence analysis and, in some cases, on the analysis of protein structure. A strong correlation between non-synonymous, benign variability and non-synonymous human-mouse divergence suggests that selection played an important role in shaping the pattern of variability in coding regions of human genes. However, the lack of correlation between deleterious variability and evolutionary divergence shows that a substantial proportion of the observed non-synonymous single-nucleotide polymorphisms reduces fitness and never reaches fixation. Evolutionary and medical implications of the impact of selection on human polymorphisms are discussed.},
author = {Sunyaev, Shamil R and Fyodor Kondrashov and Bork, Peer and Ramensky, Vasily},
journal = {Human Molecular Genetics},
number = {24},
pages = {3325 -- 3330},
publisher = {Oxford University Press},
title = {{Impact of selection, mutation rate and genetic drift on human genetic variation}},
doi = {10.1093/hmg/ddg359},
volume = {12},
year = {2003},
}
@article{876,
abstract = {Alternative splicing is thought to be a major source of functional diversity in animal proteins. We analyzed the evolutionary conservation of proteins encoded by alternatively spliced genes and predicted the ancestral state for 73 cases of alternative splicing (25 insertions and 48 deletions). The amino acid sequences of most of the inserts in proteins produced by alternative splicing are as conserved as the surrounding sequences. Thus, alternative splicing often creates novel isoforms by the insertion of new, functional protein sequences that probably originated from noncoding sequences of introns.},
author = {Fyodor Kondrashov and Koonin, Eugene V},
journal = {Trends in Genetics},
number = {3},
pages = {115 -- 119},
publisher = {Elsevier},
title = {{Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences}},
doi = {10.1016/S0168-9525(02)00029-X},
volume = {19},
year = {2003},
}
@article{1457,
abstract = {Among the major mathematical approaches to mirror symmetry are those of Batyrev-Borisov and Stromdnger-Yau-Zaslow (SYZ). The first is explicit and amenable to computation but is not clearly related to the physical motivation; the second is the opposite. Furthermore, it is far from obvious that mirror partners in one sense will also be mirror partners in the other. This paper concerns a class of examples that can be shown to satisfy the requirements of SYZ, but whose Hodge numbers are also equal. This provides significant evidence in support of SYZ. Moreover, the examples are of great interest in their own right: they are spaces of flat SLr-connections on a smooth curve. The mirror is the corresponding space for the Langlands dual group PGLr. These examples therefore throw a bridge from mirror symmetry to the duality theory of Lie groups and, more broadly, to the geometric Langlands program.},
author = {Tamas Hausel and Thaddeus, Michael},
journal = {Inventiones Mathematicae},
number = {1},
pages = {197 -- 229},
publisher = {Springer},
title = {{Mirror symmetry, langlands duality, and the Hitchin system}},
doi = {10.1007/s00222-003-0286-7},
volume = {153},
year = {2003},
}
@article{1458,
abstract = {The moduli space of stable bundles of rank $2$ and degree $1$ on a Riemann surface has rational cohomology generated by the so-called universal classes. The work of Baranovsky, King-Newstead, Siebert-Tian and Zagier provided a complete set of relations between these classes, expressed in terms of a recursion in the genus. This paper accomplishes the same thing for the noncompact moduli spaces of Higgs bundles, in the sense of Hitchin and Simpson. There are many more independent relations than for stable bundles, but in a sense the answer is simpler, since the formulas are completely explicit, not recursive. The results of Kirwan on equivariant cohomology for holomorphic circle actions are of key importance.},
author = {Tamas Hausel and Thaddeus, Michael},
journal = {Journal of the American Mathematical Society},
number = {2},
pages = {303 -- 329},
publisher = {American Mathematical Society},
title = {{Relations in the cohomology ring of the moduli space of rank 2 Higgs bundles}},
doi = {10.1090/S0894-0347-02-00417-4},
volume = {16},
year = {2003},
}
@article{1459,
abstract = {In this paper we explicitly calculate the analogue of the 't Hooft SU (2) Yang-Mills instantons on Gibbons-Hawking multi-centered gravitational instantons, which come in two parallel families: the multi-Eguchi-Hanson, or Ak ALE gravitational instantons and the multi-Taub-NUT spaces, or Ak ALF gravitational instantons. We calculate their energy and find the reducible ones. Following Kronheimer we also exploit the U(1) invariance of our solutions and study the corresponding explicit singular SU (2) magnetic monopole solutions of the Bogomolny equations on flat ℝ3.},
author = {Etesi, Gábor and Tamas Hausel},
journal = {Communications in Mathematical Physics},
number = {2},
pages = {275 -- 288},
publisher = {Springer},
title = {{On Yang-Mills instantons over multi-centered gravitational instantons}},
doi = {10.1007/s00220-003-0806-8},
volume = {235},
year = {2003},
}
@inproceedings{3170,
abstract = {Geodesic active contours and graph cuts are two standard image segmentation techniques. We introduce a new segmentation method combining some of their benefits. Our main intuition is that any cut on a graph embedded in some continuous space can be interpreted as a contour (in 2D) or a surface (in 3D). We show how to build a grid graph and set its edge weights so that the cost of cuts is arbitrarily close to the length (area) of the corresponding contours (surfaces) for any anisotropic Riemannian metric. There are two interesting consequences of this technical result. First, graph cut algorithms can be used to find globally minimum geodesic contours (minimal surfaces in 3D) under arbitrary Riemannian metric for a given set of boundary conditions. Second, we show how to minimize metrication artifacts in existing graph-cut based methods in vision. Theoretically speaking, our work provides an interesting link between several branches of mathematics -differential geometry, integral geometry, and combinatorial optimization. The main technical problem is solved using Cauchy-Crofton formula from integral geometry.},
author = {Boykov, Yuri and Vladimir Kolmogorov},
pages = {26 -- 33},
publisher = {IEEE},
title = {{Computing geodesics and minimal surfaces via graph cuts}},
doi = {10.1109/ICCV.2003.1238310},
volume = {1},
year = {2003},
}
@inproceedings{3171,
abstract = {Reconstructing a 3-D scene from more than one camera is a classical problem in computer vision. One of the major sources of difficulty is the fact that not all scene elements are visible from all cameras. In the last few years, two promising approaches have been developed 11,12 that formulate the scene reconstruction problem in terms of energy minimization, and minimize the energy using graph cuts. These energy minimization approaches treat the input images symmetrically, handle visibility constraints correctly, and allow spatial smoothness to be enforced. However, these algorithm propose different problem formulations, and handle a limited class of smoothness terms. One algorithm 11 uses a problem formulation that is restricted to two-camera stereo, and imposes smoothness between a pair of cameras. The other algorithm 12 can handle an arbitrary number of cameras, but imposes smoothness only with respect to a single camera. In this paper we give a more general energy minimization formulation for the problem, which allows a larger class of spatial smoothness constraints. We show that our formulation includes both of the previous approaches as special cases, as well as permitting new energy functions. Experimental results on real data with ground truth are also included. },
author = {Vladimir Kolmogorov and Zabih, Ramin and Gortler, Steven},
pages = {501 -- 516},
publisher = {Springer},
title = {{Generalized multi camera scene reconstruction using graph cuts}},
doi = {10.1007/978-3-540-45063-4_32},
volume = {2683},
year = {2003},
}
@inproceedings{3174,
abstract = {We address visual correspondence problems without assuming that scene points have similar intensities in different views. This situation is common, usually due to non-lambertian scenes or to differences between cameras. We use maximization of mutual information, a powerful technique for registering images that requires no a priori model of the relationship between scene intensities in different views. However, it has proven difficult to use mutual information to compute dense visual correspondence. Comparing fixed-size windows via mutual information suffers from the well-known problems of fixed windows, namely poor performance at discontinuities and in low-texture regions. In this paper, we show how to compute visual correspondence using mutual information without suffering from these problems. Using 'a simple approximation, mutual information can be incorporated into the standard energy minimization framework used in early vision. The energy can then be efficiently minimized using graph cuts, which preserve discontinuities and handle low-texture regions. The resulting algorithm combines the accurate disparity maps that come from graph cuts with the tolerance for intensity changes that comes from mutual information.},
author = {Kim, Junhwan and Vladimir Kolmogorov and Zabih, Ramin},
pages = {1033 -- 1040},
publisher = {IEEE},
title = {{Visual correspondence using energy minimization and mutual information}},
doi = {10.1109/ICCV.2003.1238463},
volume = {2},
year = {2003},
}
@article{3209,
abstract = {We show that the fixed alphabet shortest common supersequence (SCS) and the fixed alphabet longest common subsequence (LCS) problems parameterized in the number of strings are W[1]-hard. Unless W[1]=FPT, this rules out the existence of algorithms with time complexity of O(f(k)nα) for those problems. Here n is the size of the problem instance, α is constant, k is the number of strings and f is any function of k. The fixed alphabet version of the LCS problem is of particular interest considering the importance of sequence comparison (e.g. multiple sequence alignment) in the fixed length alphabet world of DNA and protein sequences.},
author = {Krzysztof Pietrzak},
journal = {Journal of Computer and System Sciences},
number = {4},
pages = {757 -- 771},
publisher = {Elsevier},
title = {{On the parameterized complexity of the fixed alphabet shortest common supersequence and longest common subsequence problems}},
doi = {10.1016/S0022-0000(03)00078-3},
volume = {67},
year = {2003},
}
@inproceedings{3210,
abstract = {Luby and Rackoff showed how to construct a (super-)pseudo-random permutation {0,1}2n→ {0,1}2n from some number r of pseudo-random functions {0,1}n → {0,1}n. Their construction, motivated by DES, consists of a cascade of r Feistel permutations. A Feistel permutation 1for a pseudo-random function f is defined as (L, R) → (R,L ⊕ f (R)), where L and R are the left and right part of the input and ⊕ denotes bitwise XOR or, in this paper, any other group operation on {0,1}n. The only non-trivial step of the security proof consists of proving that the cascade of r Feistel permutations with independent uniform random functions {0,1}n → {0,1}n, denoted Ψ2nr is indistinguishable from a uniform random permutation {0,1}2n → {0,1}2n by any computationally unbounded adaptive distinguisher making at most O(2cn) combined chosen plaintext/ciphertext queries for any c < α, where a is a security parameter. Luby and Rackoff proved α = 1/2 for r = 4. A natural problem, proposed by Pieprzyk is to improve on α for larger r. The best known result, α = 3/4 for r = 6, is due to Patarin. In this paper we prove a = 1 -O(1/r), i.e., the trivial upper bound α = 1 can be approached. The proof uses some new techniques that can be of independent interest. },
author = {Maurer, Ueli M and Krzysztof Pietrzak},
pages = {544 -- 561},
publisher = {Springer},
title = {{The security of many round Luby Rackoff pseudo random permutations}},
doi = {10.1007/3-540-39200-9_34},
volume = {2656},
year = {2003},
}