Related papers: Izzy: a high-throughput metagenomic read simulator

As the complexity of state-of-the-art deep learning models increases by the month, implementation, interpretation, and traceability become ever-more-burdensome challenges for AI practitioners around the world. Several AI frameworks have…

Simulation is increasingly being used for generating large labelled datasets in many machine learning problems. Recent methods have focused on adjusting simulator parameters with the goal of maximising accuracy on a validation task, usually…

Seed scheduling is a prominent factor in determining the yields of hybrid fuzzing. Existing hybrid fuzzers schedule seeds based on fixed heuristics that aim to predict input utilities. However, such heuristics are not generalizable as there…

Objective and interpretable metrics to evaluate current artificial intelligent systems are of great importance, not only to analyze the current state of such systems but also to objectively measure progress in the future. In this work, we…

In this work, we present a novel, machine-learning approach for constructing Multiclass Interpretable Scoring Systems (MISS) - a fully data-driven methodology for generating single, sparse, and user-friendly scoring systems for multiclass…

Scientific inference is often undermined by the vast but rarely explored "multiverse" of defensible modelling choices, which can generate results as variable as the phenomena under study. We introduce RobustiPy, an open-source Python…

Microarray is one of the essential technologies used by the biologist to measure genome-wide expression levels of genes in a particular organism under some particular conditions or stimuli. As microarrays technologies have become more…

Simulators are an important tool in robotics that is used to develop robot software and generate synthetic data for machine learning algorithms. Faster simulation can result in better software validation and larger amounts of data. Previous…

In this paper, we present BIMS (Biomedical Information Management System). BIMS is a software architecture designed to provide a flexible computational framework to manage the information needs of a wide range of biomedical research…

This paper surveys and describes the implementation of parallelization of the Mizar proof checking and of related Mizar utilities. The implementation makes use of Mizar's compiler-like division into several relatively independent passes,…

Any complex dynamic system's ability to function successfully depends in significant part on the accuracy of the sensor data; hence sensor data validation is crucial. Because sensor data is utilized for monitoring and oversight, erroneous…

When physical testbeds are out of reach for evaluating a networked system, we frequently turn to simulation. In today's datacenter networks, bottlenecks are rarely at the network protocol level, but instead in end-host software or hardware…

Characterizing the entropy of a system is a crucial, and often computationally costly, step in understanding its thermodynamics. It plays a key role in the study of phase transitions, pattern formation, protein folding and more. Current…

Antimony is a high-level, human-readable text-based language designed for defining and sharing models in the systems biology community. It enables scientists to describe biochemical networks and systems using a simple and intuitive syntax.…

Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…

The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics…

Biological machine learning is often bottlenecked by a lack of scaled data. One promising route to relieving data bottlenecks is through high throughput screens, which can experimentally test the activity of $10^6-10^{12}$ protein sequences…

Background. Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or…

In this paper, a methodology is presented and employed for simulating the Internet of Things (IoT). The requirement for scalability, due to the possibly huge amount of involved sensors and devices, and the heterogeneous scenarios that might…

Security vulnerabilities play a vital role in network security system. Fuzzing technology is widely used as a vulnerability discovery technology to reduce damage in advance. However, traditional fuzzing techniques have many challenges, such…