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1. Computing β-Stretch Paths in Drawings of Graphs

   Arkin, E ; Darabi, F ; Efrat, A ; Frank, F ; Fulek, R ; Kobourov, S ; Mitchell, J ( October 2020 , 17th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT))

   Let f be a drawing in the Euclidean plane of a graph G, which is understood to be a 1-dimensional simplicial complex. We assume that every edge of G is drawn by f as a curve of constant algebraic complexity, and the ratio of the length of the longest simple path to the the length of the shortest edge is poly(n). In the drawing f, a path P of G, or its image in the drawing π = f(P), is β-stretch if π is a simple (non-self-intersecting) curve, and for every pair of distinct points p ∈ P and q ∈ P , the length of the sub-curve of π connecting f(p) with f(q) is at most β∥f(p) − f(q)∥, where ∥.∥ denotes the Euclidean distance. We introduce and study the β-stretch Path Problem (βSP for short), in which we are given a pair of vertices s and t of G, and we are to decide whether in the given drawing of G there exists a β-stretch path P connecting s and t. We also output P if it exists. The βSP quantifies a notion of “near straightness” for paths in a graph G, motivated by gerrymandering regions in amore »map, where edges of G represent natural geographical/political boundaries that may be chosen to bound election districts. The notion of a β-stretch path naturally extends to cycles, and the extension gives a measure of how gerrymandered a district is. Furthermore, we show that the extension is closely related to several studied measures of local fatness of geometric shapes. We prove that βSP is strongly NP-complete. We complement this result by giving a quasi-polynomial time algorithm, that for a given ε > 0, β ∈ O(poly(log |V (G)|)), and s, t ∈ V (G), outputs a β-stretch path between s and t, if a (1 − ε)β-stretch path between s and t exists in the drawing.« less
2. Map-matching using shortest paths

   https://doi.org/10.1145/3191801.3191812  

   Chambers, Erin ; Fasy, Brittany Terese ; Wang, Yusu ; Wenk, Carola ( January 2018 , IWISC)

   We consider several variants of the map-matching problem, which seeks to find a path Q in graph G that has the smallest distance to a given trajectory P (which is likely not to be exactly on the graph). In a typical application setting, P models a noisy GPS trajectory from a person traveling on a road network, and the desired path Q should ideally correspond to the actual path in G that the person has traveled. Existing map-matching algorithms in the literature consider all possible paths in G as potential candidates for Q. We find solutions to the map-matching problem under different settings. In particular, we restrict the set of paths to shortest paths, or concatenations of shortest paths, in G. As a distance measure, we use the Fréchet distance, which is a suitable distance measure for curves since it takes the continuity of the curves into account.
3. Local Access to Huge Random Objects Through Partial Sampling

   Biswas, Amartya Shankha ; Rubinfeld, Ronitt ; Yodpinyanee, Anak ( January 2020 , 11th Innovations in Theoretical Computer Science Conference, ITCS 2020)

   Consider an algorithm performing a computation on a huge random object (for example a random graph or a "long" random walk). Is it necessary to generate the entire object prior to the computation, or is it possible to provide query access to the object and sample it incrementally "on-the-fly" (as requested by the algorithm)? Such an implementation should emulate the random object by answering queries in a manner consistent with an instance of the random object sampled from the true distribution (or close to it). This paradigm is useful when the algorithm is sub-linear and thus, sampling the entire object up front would ruin its efficiency. Our first set of results focus on undirected graphs with independent edge probabilities, i.e. each edge is chosen as an independent Bernoulli random variable. We provide a general implementation for this model under certain assumptions. Then, we use this to obtain the first efficient local implementations for the Erdös-Rényi G(n,p) model for all values of p, and the Stochastic Block model. As in previous local-access implementations for random graphs, we support Vertex-Pair and Next-Neighbor queries. In addition, we introduce a new Random-Neighbor query. Next, we give the first local-access implementation for All-Neighbors queries inmore »the (sparse and directed) Kleinberg’s Small-World model. Our implementations require no pre-processing time, and answer each query using O(poly(log n)) time, random bits, and additional space. Next, we show how to implement random Catalan objects, specifically focusing on Dyck paths (balanced random walks on the integer line that are always non-negative). Here, we support Height queries to find the location of the walk, and First-Return queries to find the time when the walk returns to a specified location. This in turn can be used to implement Next-Neighbor queries on random rooted ordered trees, and Matching-Bracket queries on random well bracketed expressions (the Dyck language). Finally, we introduce two features to define a new model that: (1) allows multiple independent (and even simultaneous) instantiations of the same implementation, to be consistent with each other without the need for communication, (2) allows us to generate a richer class of random objects that do not have a succinct description. Specifically, we study uniformly random valid q-colorings of an input graph G with maximum degree Δ. This is in contrast to prior work in the area, where the relevant random objects are defined as a distribution with O(1) parameters (for example, n and p in the G(n,p) model). The distribution over valid colorings is instead specified via a "huge" input (the underlying graph G), that is far too large to be read by a sub-linear time algorithm. Instead, our implementation accesses G through local neighborhood probes, and is able to answer queries to the color of any given vertex in sub-linear time for q ≥ 9Δ, in a manner that is consistent with a specific random valid coloring of G. Furthermore, the implementation is memory-less, and can maintain consistency with non-communicating copies of itself.« less
4. Space-efficient Query Evaluation over Probabilistic Event Streams

   https://doi.org/10.1145/3373718.3394747  

   Alur, Rajeev ; Chen, Yu ; Jothimurugan, Kishor ; Khanna, Sanjeev ( May 2020 , LICS'20: 35th Annual ACM/IEEE Symposium on Logic in Computer Science)

   Real-time decision making in IoT applications relies upon space-efficient evaluation of queries over streaming data. To model the uncertainty in the classification of data being processed, we consider the model of probabilistic strings --- sequences of discrete probability distributions over a finite set of events, and initiate the study of space complexity of streaming computation for different classes of queries over such probabilistic strings. We first consider the problem of computing the probability that a word, sampled from the distribution defined by the probabilistic string read so far, is accepted by a given deterministic finite automaton. We show that this regular pattern matching problem can be solved using space that is only poly-logarithmic in the string length (and polynomial in the size of the DFA) if we are allowed a multiplicative approximation error. Then we show how to generalize this result to quantitative queries specified by additive cost register automata --- these are automata that map strings to numerical values using finite control and registers that get updated using linear transformations. Finally, we consider the case when updates in such an automaton involve tests, and in particular, when there is a counter variable that can be either incremented or decrementedmore »but decrements only apply when the counter value is non-zero. In this case, the desired answer depends on the probability distribution over the set of possible counter values that can range from 0 to n for a string of length n. Under a mild assumption, namely probabilities of the individual events are bounded away from 0 and 1, we show that there is an algorithm that can compute all n entries of this probability distribution vector to within additive 1/poly(n) error using space that is only Õ(n). In establishing these results, we introduce several new technical ideas that may prove useful for designing space-efficient algorithms for other query models over probabilistic strings.« less
5. Validating Paired-end Read Alignments in Sequence Graphs

   https://doi.org/10.1101/682799  

   Jain, Chirag ; Zhang, Haowen ; Dilthey, Alexander ; Aluru, Srinivas ( September 2019 , Leibniz international proceedings in informatics)

   Graph based non-linear reference structures such as variation graphs and colored de Bruijn graphs enable incorporation of full genomic diversity within a population. However, transitioning from a simple string-based reference to graphs requires addressing many computational challenges, one of which concerns accurately mapping sequencing read sets to graphs. Paired-end Illumina sequencing is a commonly used sequencing platform in genomics, where the paired-end distance constraints allow disambiguation of repeats. Many recent works have explored provably good index-based and alignment-based strategies for mapping individual reads to graphs. However, validating distance constraints efficiently over graphs is not trivial, and existing sequence to graph mappers rely on heuristics. We introduce a mathematical formulation of the problem, and provide a new algorithm to solve it exactly. We take advantage of the high sparsity of reference graphs, and use sparse matrix-matrix multiplications (SpGEMM) to build an index which can be queried efficiently by a mapping algorithm for validating the distance constraints. Effectiveness of the algorithm is demonstrated using real reference graphs, including a human MHC variation graph, and a pan-genome de-Bruijn graph built using genomes of 20 B. anthracis strains. While the one-time indexing time can vary from a few minutes to a few hours usingmore »our algorithm, answering a million distance queries takes less than a second.« less