Balanced Allocation on Graphs: A Random Walk Approach

In this paper we propose algorithms for allocating $n$ sequential balls into $n$ bins that are interconnected as a $d$-regular $n$-vertex graph $G$, where $d\ge3$ can be any integer.Let $l$ be a given positive integer. In each round $t$, $1\le t\le n$, ball $t$ picks a node of $G$ uniformly at random and performs a non-backtracking random walk of length $l$ from the chosen node.Then it allocates itself on one of the visited nodes with minimum load (ties are broken uniformly at random). Suppose that $G$ has a sufficiently large girth and $d=\omega(\log n)$. Then we establish an upper bound for the maximum number of balls at any bin after allocating $n$ balls by the algorithm, called {\it maximum load}, in terms of $l$ with high probability. We also show that the upper bound is at most an $O(\log\log n)$ factor above the lower bound that is proved for the algorithm. In particular, we show that if we set $l=\lfloor(\log n)^{\frac{1+\epsilon}{2}}\rfloor$, for every constant $\epsilon\in (0, 1)$, and $G$ has girth at least $\omega(l)$, then the maximum load attained by the algorithm is bounded by $O(1/\epsilon)$ with high probability.Finally, we slightly modify the algorithm to have similar results for balanced allocation on $d$-regular graph with $d\in[3, O(\log n)]$ and sufficiently large girth

Accurate prediction of gene feedback circuit behavior from component properties

A basic assumption underlying synthetic biology is that analysis of genetic circuit elements, such as regulatory proteins and promoters, can be used to understand and predict the behavior of circuits containing those elements. To test this assumption, we used time‐lapse fluorescence microscopy to quantitatively analyze two autoregulatory negative feedback circuits. By measuring the gene regulation functions of the corresponding repressor–promoter interactions, we accurately predicted the expression level of the autoregulatory feedback loops, in molecular units. This demonstration that quantitative characterization of regulatory elements can predict the behavior of genetic circuits supports a fundamental requirement of synthetic biology

Multiplexed DNA-Modified Electrodes

We report the use of silicon chips with 16 DNA-modified electrodes (DME chips) utilizing DNA-mediated charge transport for multiplexed detection of DNA and DNA-binding protein targets. Four DNA sequences were simultaneously distinguished on a single DME chip with 4-fold redundancy, including one incorporating a single base mismatch. These chips also enabled investigation of the sequence-specific activity of the restriction enzyme Alu1. DME chips supported dense DNA monolayer formation with high reproducibility, as confirmed by statistical comparison to commercially available rod electrodes. The working electrode areas on the chips were reduced to 10 μm in diameter, revealing microelectrode behavior that is beneficial for high sensitivity and rapid kinetic analysis. These results illustrate how DME chips facilitate sensitive and selective detection of DNA and DNA-binding protein targets in a robust and internally standardized multiplexed format

Designing algorithms to aid discovery by chemical robots

Recently, automated robotic systems have become very efficient, thanks to improved coupling between sensor systems and algorithms, of which the latter have been gaining significance thanks to the increase in computing power over the past few decades. However, intelligent automated chemistry platforms for discovery orientated tasks need to be able to cope with the unknown, which is a profoundly hard problem. In this Outlook, we describe how recent advances in the design and application of algorithms, coupled with the increased amount of chemical data available, and automation and control systems may allow more productive chemical research and the development of chemical robots able to target discovery. This is shown through examples of workflow and data processing with automation and control, and through the use of both well-used and cutting-edge algorithms illustrated using recent studies in chemistry. Finally, several algorithms are presented in relation to chemical robots and chemical intelligence for knowledge discovery

Improved Approximation Algorithms for Relay Placement

In the relay placement problem the input is a set of sensors and a number $r \ge 1$, the communication range of a relay. In the one-tier version of the problem the objective is to place a minimum number of relays so that between every pair of sensors there is a path through sensors and/or relays such that the consecutive vertices of the path are within distance $r$ if both vertices are relays and within distance 1 otherwise. The two-tier version adds the restrictions that the path must go through relays, and not through sensors. We present a 3.11-approximation algorithm for the one-tier version and a PTAS for the two-tier version. We also show that the one-tier version admits no PTAS, assuming P $\ne$ NP.Comment: 1+29 pages, 12 figure

Counting Hamilton cycles in sparse random directed graphs

Let D(n,p) be the random directed graph on n vertices where each of the n(n-1) possible arcs is present independently with probability p. A celebrated result of Frieze shows that if $p\ge(\log n+\omega(1))/n$ then D(n,p) typically has a directed Hamilton cycle, and this is best possible. In this paper, we obtain a strengthening of this result, showing that under the same condition, the number of directed Hamilton cycles in D(n,p) is typically $n!(p(1+o(1)))^{n}$. We also prove a hitting-time version of this statement, showing that in the random directed graph process, as soon as every vertex has in-/out-degrees at least 1, there are typically $n!(\log n/n(1+o(1)))^{n}$ directed Hamilton cycles

Derandomized Construction of Combinatorial Batch Codes

Combinatorial Batch Codes (CBCs), replication-based variant of Batch Codes introduced by Ishai et al. in STOC 2004, abstracts the following data distribution problem: $n$ data items are to be replicated among $m$ servers in such a way that any $k$ of the $n$ data items can be retrieved by reading at most one item from each server with the total amount of storage over $m$ servers restricted to $N$. Given parameters $m, c,$ and $k$, where $c$ and $k$ are constants, one of the challenging problems is to construct $c$-uniform CBCs (CBCs where each data item is replicated among exactly $c$ servers) which maximizes the value of $n$. In this work, we present explicit construction of $c$-uniform CBCs with $\Omega(m^{c-1+{1 \over k}})$ data items. The construction has the property that the servers are almost regular, i.e., number of data items stored in each server is in the range $[{nc \over m}-\sqrt{{n\over 2}\ln (4m)}, {nc \over m}+\sqrt{{n \over 2}\ln (4m)}]$. The construction is obtained through better analysis and derandomization of the randomized construction presented by Ishai et al. Analysis reveals almost regularity of the servers, an aspect that so far has not been addressed in the literature. The derandomization leads to explicit construction for a wide range of values of $c$ (for given $m$ and $k$) where no other explicit construction with similar parameters, i.e., with $n = \Omega(m^{c-1+{1 \over k}})$, is known. Finally, we discuss possibility of parallel derandomization of the construction

Subsampling in Smoothed Range Spaces

We consider smoothed versions of geometric range spaces, so an element of the ground set (e.g. a point) can be contained in a range with a non-binary value in $[0,1]$. Similar notions have been considered for kernels; we extend them to more general types of ranges. We then consider approximations of these range spaces through $\varepsilon$-nets and $\varepsilon$-samples (aka $\varepsilon$-approximations). We characterize when size bounds for $\varepsilon$-samples on kernels can be extended to these more general smoothed range spaces. We also describe new generalizations for $\varepsilon$-nets to these range spaces and show when results from binary range spaces can carry over to these smoothed ones.Comment: This is the full version of the paper which appeared in ALT 2015. 16 pages, 3 figures. In Algorithmic Learning Theory, pp. 224-238. Springer International Publishing, 201