Dynamic load balancing for the distributed mining of molecular structures

In molecular biology, it is often desirable to find common properties in large numbers of drug candidates. One family of methods stems from the data mining community, where algorithms to find frequent graphs have received increasing attention over the past years. However, the computational complexity of the underlying problem and the large amount of data to be explored essentially render sequential algorithms useless. In this paper, we present a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular compounds. This problem is characterized by a highly irregular search tree, whereby no reliable workload prediction is available. We describe the three main aspects of the proposed distributed algorithm, namely, a dynamic partitioning of the search space, a distribution process based on a peer-to-peer communication framework, and a novel receiverinitiated load balancing algorithm. The effectiveness of the distributed method has been evaluated on the well-known National Cancer Institute’s HIV-screening data set, where we were able to show close-to linear speedup in a network of workstations. The proposed approach also allows for dynamic resource aggregation in a non dedicated computational environment. These features make it suitable for large-scale, multi-domain, heterogeneous environments, such as computational grids

Computationally Data-Independent Memory Hard Functions

Memory hard functions (MHFs) are an important cryptographic primitive that are used to design egalitarian proofs of work and in the construction of moderately expensive key-derivation functions resistant to brute-force attacks. Broadly speaking, MHFs can be divided into two categories: data-dependent memory hard functions (dMHFs) and data-independent memory hard functions (iMHFs). iMHFs are resistant to certain side-channel attacks as the memory access pattern induced by the honest evaluation algorithm is independent of the potentially sensitive input e.g., password. While dMHFs are potentially vulnerable to side-channel attacks (the induced memory access pattern might leak useful information to a brute-force attacker), they can achieve higher cumulative memory complexity (CMC) in comparison than an iMHF. In particular, any iMHF that can be evaluated in N steps on a sequential machine has CMC at most ?((N^2 log log N)/log N). By contrast, the dMHF scrypt achieves maximal CMC ?(N^2) - though the CMC of scrypt would be reduced to just ?(N) after a side-channel attack. In this paper, we introduce the notion of computationally data-independent memory hard functions (ciMHFs). Intuitively, we require that memory access pattern induced by the (randomized) ciMHF evaluation algorithm appears to be independent from the standpoint of a computationally bounded eavesdropping attacker - even if the attacker selects the initial input. We then ask whether it is possible to circumvent known upper bound for iMHFs and build a ciMHF with CMC ?(N^2). Surprisingly, we answer the question in the affirmative when the ciMHF evaluation algorithm is executed on a two-tiered memory architecture (RAM/Cache). We introduce the notion of a k-restricted dynamic graph to quantify the continuum between unrestricted dMHFs (k=n) and iMHFs (k=1). For any ? > 0 we show how to construct a k-restricted dynamic graph with k=?(N^(1-?)) that provably achieves maximum cumulative pebbling cost ?(N^2). We can use k-restricted dynamic graphs to build a ciMHF provided that cache is large enough to hold k hash outputs and the dynamic graph satisfies a certain property that we call "amenable to shuffling". In particular, we prove that the induced memory access pattern is indistinguishable to a polynomial time attacker who can monitor the locations of read/write requests to RAM, but not cache. We also show that when k=o(N^(1/log log N))then any k-restricted graph with constant indegree has cumulative pebbling cost o(N^2). Our results almost completely characterize the spectrum of k-restricted dynamic graphs