Fast Searching in Packed Strings

Given strings $P$ and $Q$ the (exact) string matching problem is to find all positions of substrings in $Q$ matching $P$. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time which is optimal if we can only read one character at the time. However, most strings are stored in a computer in a packed representation with several characters in a single word, giving us the opportunity to read multiple characters simultaneously. In this paper we study the worst-case complexity of string matching on strings given in packed representation. Let $m \leq n$ be the lengths $P$ and $Q$, respectively, and let $\sigma$ denote the size of the alphabet. On a standard unit-cost word-RAM with logarithmic word size we present an algorithm using time O\left(\frac{n}{\log_\sigma n} + m + \occ\right). Here \occ is the number of occurrences of $P$ in $Q$. For $m = o(n)$ this improves the $O(n)$ bound of the Knuth-Morris-Pratt algorithm. Furthermore, if $m = O(n/\log_\sigma n)$ our algorithm is optimal since any algorithm must spend at least \Omega(\frac{(n+m)\log \sigma}{\log n} + \occ) = \Omega(\frac{n}{\log_\sigma n} + \occ) time to read the input and report all occurrences. The result is obtained by a novel automaton construction based on the Knuth-Morris-Pratt algorithm combined with a new compact representation of subautomata allowing an optimal tabulation-based simulation.Comment: To appear in Journal of Discrete Algorithms. Special Issue on CPM 200

Streaming algorithms for 2-coloring uniform hypergraphs

We consider the problem of two-coloring n-uniform hypergraphs. It is known that any such hypergraph with at most 1/10√n/ln n 2n hyperedges can be two-colored [7]. In fact, there is an efficient (requiring polynomial time in the size of the input) randomized algorithm that produces such a coloring. As stated [7], this algorithm requires random access to the hyperedge set of the input hypergraph. In this paper, we show that a variant of this algorithm can be implemented in the streaming model (with just one pass over the input), using space O(|V|B), where V is the vertex set of the hypergraph and each vertex is represented by B bits. (Note that the number of hyperedges in the hypergraph can be superpolynomial in |V|, and it is not feasible to store the entire hypergraph in memory.) We also consider the question of the minimum number of hyperedges in non-two-colorable n-uniform hypergraphs. Erdos showed that there exist non-2-colorable n-uniform hypegraphs with O(n2 2n) hyperedges and Θ(n2) vertices. We show that the choice Θ(n2) for the number of vertices in Erdös's construction is crucial: any hypergraph with at most 2n2/t vertices and 2nexp(t/8) hyperedges is 2-colorable. (We present a simple randomized streaming algorithm to construct the two-coloring.) Thus, for example, if the number of vertices is at most n1.5, then any non-2-colorable hypergraph must have at least 2n exp(√n/8) » n22n hyperedges. We observe that the exponential dependence on t in our result is optimal up to constant factors

Efficient exact pattern-matching in proteomic sequences

This paper proposes a novel algorithm for complete exact pattern-matching focusing the specificities of protein sequences (alphabet of 20 symbols) but, also highly efficient considering larger alphabets. The searching strategy uses large search windows allowing multiple alignments per iteration. A new filtering heuristic, named compatibility rule, contributed decisively to the efficiency improvement. The new algorithm’s performance is, on average, superior in comparison with its best-rated competitors

Dynamic analysis of repetitive decision-free discreteevent processes: The algebra of timed marked graphs and algorithmic issues

A model to analyze certain classes of discrete event dynamic systems is presented. Previous research on timed marked graphs is reviewed and extended. This model is useful to analyze asynchronous and repetitive production processes. In particular, applications to certain classes of flexible manufacturing systems are provided in a companion paper. Here, an algebraic representation of timed marked graphs in terms of reccurrence equations is provided. These equations are linear in a nonconventional algebra, that is described. Also, an algorithm to properly characterize the periodic behavior of repetitive production processes is descrbed. This model extends the concepts from PERT/CPM analysis to repetitive production processes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44155/1/10479_2005_Article_BF02248590.pd

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Lower Bounds for Howard’s Algorithm for Finding Minimum Mean-Cost Cycles

Howard’s policy iteration algorithm is one of the most widely used algorithms for finding optimal policies for controlling Markov Decision Processes (MDPs). When applied to weighted directed graphs, which may be viewed as Deterministic MDPs (DMDPs), Howard’s algorithm can be used to find Minimum Mean-Cost cycles (MMCC). Experimental studies suggest that Howard’s algorithm works extremely well in this context. The theoretical complexity of Howard’s algorithm for finding MMCCs is a mystery. No polynomial time bound is known on its running time. Prior to this work, there were only linear lower bounds on the number of iterations performed by Howard’s algorithm. We provide the first weighted graphs on which Howard’s algorithm performs Ω(n²) iterations, where n is the number of vertices in the graph