Single machine scheduling with job-dependent machine deterioration

We consider the single machine scheduling problem with job-dependent machine deterioration. In the problem, we are given a single machine with an initial non-negative maintenance level, and a set of jobs each with a non-preemptive processing time and a machine deterioration. Such a machine deterioration quantifies the decrement in the machine maintenance level after processing the job. To avoid machine breakdown, one should guarantee a non-negative maintenance level at any time point; and whenever necessary, a maintenance activity must be allocated for restoring the machine maintenance level. The goal of the problem is to schedule the jobs and the maintenance activities such that the total completion time of jobs is minimized. There are two variants of maintenance activities: in the partial maintenance case each activity can be allocated to increase the machine maintenance level to any level not exceeding the maximum; in the full maintenance case every activity must be allocated to increase the machine maintenance level to the maximum. In a recent work, the problem in the full maintenance case has been proven NP-hard; several special cases of the problem in the partial maintenance case were shown solvable in polynomial time, but the complexity of the general problem is left open. In this paper we first prove that the problem in the partial maintenance case is NP-hard, thus settling the open problem; we then design a $2$-approximation algorithm.Comment: 15 page

Planar graphs are acyclically edge (Δ+5)(\Delta + 5)-colorable

An edge coloring of a graph $G$ is to color all the edges in the graph such that adjacent edges receive different colors. It is acyclic if each cycle in the graph receives at least three colors. Fiam{\v{c}}ik (1978) and Alon, Sudakov and Zaks (2001) conjectured that every simple graph with maximum degree $\Delta$ is acyclically edge $(\Delta + 2)$-colorable -- the well-known acyclic edge coloring conjecture (AECC). Despite many major breakthroughs and minor improvements, the conjecture remains open even for planar graphs. In this paper, we prove that planar graphs are acyclically edge $(\Delta + 5)$-colorable. Our proof has two main steps: Using discharging methods, we first show that every non-trivial planar graph must have one of the eight groups of well characterized local structures; and then acyclically edge color the graph using no more than $\Delta + 5$ colors by an induction on the number of edges.Comment: Full version with 120 page

A stable gene selection in microarray data analysis

BACKGROUND: Microarray data analysis is notorious for involving a huge number of genes compared to a relatively small number of samples. Gene selection is to detect the most significantly differentially expressed genes under different conditions, and it has been a central research focus. In general, a better gene selection method can improve the performance of classification significantly. One of the difficulties in gene selection is that the numbers of samples under different conditions vary a lot. RESULTS: Two novel gene selection methods are proposed in this paper, which are not affected by the unbalanced sample class sizes and do not assume any explicit statistical model on the gene expression values. They were evaluated on eight publicly available microarray datasets, using leave-one-out cross-validation and 5-fold cross-validation. The performance is measured by the classification accuracies using the top ranked genes based on the training datasets. CONCLUSION: The experimental results showed that the proposed gene selection methods are efficient, effective, and robust in identifying differentially expressed genes. Adopting the existing SVM-based and KNN-based classifiers, the selected genes by our proposed methods in general give more accurate classification results, typically when the sample class sizes in the training dataset are unbalanced

ComPhy: Prokaryotic Composite Distance Phylogenies Inferred from Whole-Genome Gene Sets

doi:10.1186/1471-2105-10-S1-S5With the increasing availability of whole genome sequences, it is becoming more and more important to use complete genome sequences for inferring species phylogenies. We developed a new tool ComPhy, 'Composite Distance Phylogeny', based on a composite distance matrix calculated from the comparison of complete gene sets between genome pairs to produce a prokaryotic phylogeny. The composite distance between two genomes is defined by three components: Gene Dispersion Distance (GDD), Genome Breakpoint Distance (GBD) and Gene Content Distance (GCD). GDD quantifies the dispersion of orthologous genes along the genomic coordinates from one genome to another; GBD measures the shared breakpoints between two genomes; GCD measures the level of shared orthologs between two genomes. The phylogenetic tree is constructed from the composite distance matrix using a neighbor joining method. We tested our method on 9 datasets from 398 completely sequenced prokaryotic genomes. We have achieved above 90% agreement in quartet topologies between the tree created by our method and the tree from the Bergey's taxonomy. In comparison to several other phylogenetic analysis methods, our method showed consistently better performance. ComPhy is a fast and robust tool for genome-wide inference of evolutionary relationship among genomes."This work was supported in part by NSF/ITR-IIS-0407204.

Randomized algorithms for fully online multiprocessor scheduling with testing

We contribute the first randomized algorithm that is an integration of arbitrarily many deterministic algorithms for the fully online multiprocessor scheduling with testing problem. When there are two machines, we show that with two component algorithms its expected competitive ratio is already strictly smaller than the best proven deterministic competitive ratio lower bound. Such algorithmic results are rarely seen in the literature. Multiprocessor scheduling is one of the first combinatorial optimization problems that have received numerous studies. Recently, several research groups examined its testing variant, in which each job $J_j$ arrives with an upper bound $u_j$ on the processing time and a testing operation of length $t_j$; one can choose to execute $J_j$ for $u_j$ time, or to test $J_j$ for $t_j$ time to obtain the exact processing time $p_j$ followed by immediately executing the job for $p_j$ time. Our target problem is the fully online version, in which the jobs arrive in sequence so that the testing decision needs to be made at the job arrival as well as the designated machine. We propose an expected $(\sqrt{\varphi + 3} + 1) (\approx 3.1490)$-competitive randomized algorithm as a non-uniform probability distribution over arbitrarily many deterministic algorithms, where $\varphi = \frac {\sqrt{5} + 1}2$ is the Golden ratio. When there are two machines, we show that our randomized algorithm based on two deterministic algorithms is already expected $\frac {3 \varphi + 3 \sqrt{13 - 7\varphi}}4 (\approx 2.1839)$-competitive. Besides, we use Yao's principle to prove lower bounds of $1.6682$ and $1.6522$ on the expected competitive ratio for any randomized algorithm at the presence of at least three machines and only two machines, respectively, and prove a lower bound of $2.2117$ on the competitive ratio for any deterministic algorithm when there are only two machines.Comment: 21 pages with 1 plot; an extended abstract to be submitte