Related papers: Izzy: a high-throughput metagenomic read simulator
Machine learning models often learn latent embedding representations that capture the domain semantics of their training data. These embedding representations are valuable for interpreting trained models, building new models, and analyzing…
Accurately capturing feature interactions is essential in recommender systems, and recent trends show that scaling up model capacity could be a key driver for next-level predictive performance. While prior work has explored various model…
Current metagenome assemblers developed for short sequence reads or noisy long readswere not optimized for accurate long reads. Here we describe hifiasm-meta, a new metagenome assembler that exploits the high accuracy of recent data.…
MetaScope is a fast and accurate tool for analyzing (host-associated) metagenome datasets. Sequence alignment of reads against the host genome (if requested) and against microbial Genbank is performed using a new DNA aligner called SASS.…
At the CMS experiment, a growing reliance on the fast Monte Carlo application (FastSim) will accompany the high luminosity and detector granularity expected in Phase 2. The FastSim chain is roughly 10 times faster than the application based…
An active area of research interest is the inference of ecological models of complex microbial communities. Inferring such ecological models entails understanding the interactions between microbes and how they affect each other's growth.…
ZV-Sim is an open-source, modular Python framework for probabilistic simulation and analysis of pre-emergent novel zoonotic diseases using pervasive sensing data. It incorporates customizable Human and Animal Presence agents that leverage…
Fuzzing is a commonly used technique designed to test software by automatically crafting program inputs. Currently, the most successful fuzzing algorithms emphasize simple, low-overhead strategies with the ability to efficiently monitor…
Large-scale network experiments is a challenging problem. Simulations, emulations, and real-world testbeds all have their advantages and disadvantages. In this paper we present LiteLab, a light-weight platform specialized for large-scale…
Metagenomics offers a way to analyze biotopes at the genomic level and to reach functional and taxonomical conclusions. The bio-analyzes of large metagenomic projects face critical limitations: complex metagenomes cannot be assembled and…
The human-associated microbiome is closely tied to human health and is of substantial clinical interest. Metagenomics-based tools are emerging for clinical diagnostics, tracking the spread of diseases, and surveillance of potential…
For validating low level embedded software, engineers use simulators that take the real binary as input. Like the real hardware, these full-system simulators are organized as a set of components. The main component is the CPU simulator…
Motivation: Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulators do not always take full advantage of modern hardware and often have a field-specific software design. Results:…
Large general-purpose transformer models have recently become the mainstay in the realm of speech analysis. In particular, Whisper achieves state-of-the-art results in relevant tasks such as speech recognition, translation, language…
Fuzz testing has enjoyed great success at discovering security critical bugs in real software. Recently, researchers have devoted significant effort to devising new fuzzing techniques, strategies, and algorithms. Such new ideas are…
The ever increasing demands placed upon machine performance have resulted in the need for more comprehensive particle accelerator modeling. Computer simulations are key to the success of particle accelerators. Many aspects of particle…
The Agent Based Model community has a rich and diverse ecosystem of libraries, platforms, and applications to help modelers develop rigorous simulations. Despite this robust and diverse ecosystem, the complexity of life from microbial…
ZigBee is a fairly new but promising wireless sensor network standard that offers the advantages of simple and low resource communication. Nevertheless, security is of great concern to ZigBee, and enhancements are prescribed in the latest…
Fuzzing is a security testing methodology effective in finding bugs. In a nutshell, a fuzzer sends multiple slightly malformed messages to the software under test, hoping for crashes or weird system behaviour. The methodology is relatively…
Chiplet architectures are on the rise as they promise to overcome the scaling challenges of monolithic chips. A key component of such architectures is an efficient inter-chiplet interconnect (ICI). The ICI design space is huge as there are…