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Molecular similarity search has been widely used in drug discovery to identify structurally similar compounds from large molecular databases rapidly. With the increasing size of chemical libraries, there is growing interest in the efficient…
The time complexity of data clustering has been viewed as fundamentally quadratic, slowing with the number of data items, as each item is compared for similarity to preceding items. Clustering of large data sets has been infeasible without…
Bloom filters are a fundamental data structure for approximate membership queries, with applications ranging from data analytics to databases and genomics. Several variants have been proposed to accommodate parallel architectures. GPUs,…
We motivate and propose a new way of thinking about failure detectors which allows us to define, quite surprisingly, what it means to solve a distributed task \emph{wait-free} \emph{using a failure detector}. In our model, the system is…
Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities, however, poses many computational challenges when taking…
Simultaneous recordings from many neurons hide important information and the connections characterizing the network remain generally undiscovered despite the progresses of statistical and machine learning techniques. Discerning the presence…
Screening traditionally refers to the problem of detecting active inputs in the computer model. In this paper, we develop methodology that applies to screening, but the main focus is on detecting active inputs not in the computer model…
FPGA accelerators on the NIC enable the offloading of expensive packet processing tasks from the CPU. However, FPGAs have limited resources that may need to be shared among diverse applications, and programming them is difficult. We present…
In this paper an efficient model based diagnostic process is described for systems whose components possess a causal relation between their inputs and their outputs. In this diagnostic process, firstly, a set of focuses on likely broken…
Alignment-based conformance checking is the state-of-the-art approach for comparing observed process executions with normative process models. The standard exact solution relies on an A*-based heuristic search, which can exhibit exponential…
We present Parallel Feasible Pareto Frontier Entropy Search ($\{\text{PF}\}^2$ES) -- a novel information-theoretic acquisition function for multi-objective Bayesian optimization supporting unknown constraints and batch query. Due to the…
Essential protein plays a crucial role in the process of cell life. The identification of essential proteins can not only promote the development of drug target technology, but also contribute to the mechanism of biological evolution. There…
Phenotyping is the process of distinguishing groups of patients to identify different types of disease progression. A recent trend employs low-rank matrix and tensor factorization methods for their capability of dealing with multi-modal,…
Hippocampus segmentation plays a key role in diagnosing various brain disorders such as Alzheimer's disease, epilepsy, multiple sclerosis, cancer, depression and others. Nowadays, segmentation is still mainly performed manually by…
Abstract interpretation is a general framework for expressing static program analyses. It reduces the problem of extracting properties of a program to computing an approximation of the least fixpoint of a system of equations. The de facto…
Biclustering is a class of techniques that simultaneously clusters the rows and columns of a matrix to sort heterogeneous data into homogeneous blocks. Although many algorithms have been proposed to find biclusters, existing methods suffer…
Splotch is a rendering algorithm for exploration and visual discovery in particle-based datasets coming from astronomical observations or numerical simulations. The strengths of the approach are production of high quality imagery and…
The primary objective of SIRENE is to simulate the response to neutrino events of any type of high energy neutrino telescope. Additionally, it implements different geometries for a neutrino detector and different configurations and…
Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand…
Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. Their identification is therefore necessary not only to understand complex formation…