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The identification of cellular objectives is one of the central topics in the research of microbial metabolic networks. In particular, the information about a cellular objective is needed in flux balance analysis which is a commonly used…
In this paper we study the adaptivity of submodular maximization. Adaptivity quantifies the number of sequential rounds that an algorithm makes when function evaluations can be executed in parallel. Adaptivity is a fundamental concept that…
Biomolecular condensates self-assemble when proteins and nucleic acids spontaneously demix to form droplets within the crowded intracellular milieu. This simple mechanism underlies the formation of a wide variety of membraneless…
This paper proposes a control algorithm for stable implementation of asynchronous parallel quadratic programming (PQP) through dual decomposition technique. In general, distributed and parallel optimization requires synchronization of data…
Due to the ubiquity of batch data processing in cloud computing, the related problem of scheduling malleable batch tasks and its extensions have received significant attention recently. In this paper, we consider a fundamental model where a…
In distributed computing systems with stragglers, various forms of redundancy can improve the average delay performance. We study the optimal replication of data in systems where the job execution time is a stochastically decreasing and…
Eukaryotic DNA replication follows a specific temporal program, with some genomic regions consistently replicating earlier than others, yet what determines this program is largely unknown. Highly transcribed regions have been observed to…
Scientific workflows have been predominantly used for complex and large scale data analysis and scientific computation/automation and the need for robust workflow scheduling techniques has grown considerably. But, most of the existing…
This paper presents a centralized recursive optimal scheduling method for a battery system that consists of parallel connected battery modules with different open circuit voltages and battery impedance characteristics. Examples of such a…
New automated and high-throughput methods allow the manipulation and selection of numerous bacterial populations. In this manuscript we are interested in the neutral diversity patterns that emerge from such a setup in which many bacterial…
Genome replication, a key process for a cell, relies on stochastic initiation by replication origins, causing a variability of replication timing from cell to cell. While stochastic models of eukaryotic replication are widely available, the…
In serial batch (s-batch) scheduling, jobs from similar families are grouped into batches and processed sequentially to avoid repetitive setups that are required when processing consecutive jobs of different families. Despite its large…
Pipeline parallelism has been widely explored, but most existing schedules lack a systematic methodology. In this paper, we propose a framework to decompose pipeline schedules as repeating a building block, and show that the lifespan of the…
We consider the problem of sequential anomaly identification over multiple independent data streams, under the presence of a sampling constraint. The goal is to quickly identify those that exhibit anomalous statistical behavior, when it is…
Catalytically active colloids maintain non-equilibrium conditions in which they produce and deplete chemicals and hence effectively act as sources and sinks of molecules. While individual colloids that are symmetrically coated do not…
We study the problem of scheduling a general computational DAG on multiple processors in a 2-level memory hierarchy. This setting is a natural generalization of several prominent models in the literature, and it simultaneously captures…
Spontaneous self-replication in cellular automata has long been considered rare, with most known examples requiring careful design or artificial initialization. In this paper, we present formal, causal evidence that such replication can…
Pipeline parallelism is one of the key components for large-scale distributed training, yet its efficiency suffers from pipeline bubbles which were deemed inevitable. In this work, we introduce a scheduling strategy that, to our knowledge,…
When integrating hard, soft and non-real-time tasks in general purpose operating systems, it is necessary to provide temporal isolation so that the timing properties of one task do not depend on the behaviour of the others. However, strict…
This study presents a theoretical model for a self-replicating mechanical system inspired by biological processes within living cells and supported by computer simulations. The model decomposes self-replication into core components, each of…