Related papers: PyPanda: a Python Package for Gene Regulatory Netw…
Genome-wide association studies generate very large datasets that require scalable analysis algorithms. In this report we describe the GEDI software package, which implements efficient algorithms for performing several common tasks in the…
PyOD is an open-source Python toolbox for performing scalable outlier detection on multivariate data. Uniquely, it provides access to a wide range of outlier detection algorithms, including established outlier ensembles and more recent…
In this paper, we propose a novel adaptive modulation and coding (AMC) algorithm dedicated to reduce the feedback frequency of the channel state information (CSI). There have been already plenty of works on AMC so as to exploit the…
We make Bayesian Additive Regression Networks (BARN) available as a Python package, \texttt{barmpy}, with documentation at \url{https://dvbuntu.github.io/barmpy/} for general machine learning practitioners. Our object-oriented design is…
Determining gene regulatory network (GRN) structure is a central problem in biology, with a variety of inference methods available for different types of data. For a widely prevalent and challenging use case, namely single-cell gene…
Fact-checking tabular data is essential for ensuring the accuracy of structured information. However, existing methods often rely on black-box models with opaque reasoning. We introduce RePanda, a structured fact verification approach that…
This paper introduces PyMatching, a fast open-source Python package for decoding quantum error-correcting codes with the minimum-weight perfect matching (MWPM) algorithm. PyMatching includes the standard MWPM decoder as well as a variant,…
Transparently checkpointing MPI for fault tolerance and load balancing is a long-standing problem in HPC. The problem has been complicated by the need to provide checkpoint-restart services for all combinations of an MPI implementation over…
Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is…
Data gridding is a common task in astronomy and many other science disciplines. It refers to the resampling of irregularly sampled data to a regular grid. We present cygrid, a library module for the general purpose programming language…
Neural Networks are notoriously difficult to inspect. We introduce comgra, an open source python library for use with PyTorch. Comgra extracts data about the internal activations of a model and organizes it in a GUI (graphical user…
Open-source process mining provides many algorithms for the analysis of event data which could be used to analyze mainstream processes (e.g., O2C, P2P, CRM). However, compared to commercial tools, they lack the performance and struggle to…
Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological {\em networks} holds similar promise. Biological networks generally model interactions between biomolecules…
This paper describes SPINDLE - an open source Python module implementing an efficient and accurate parser for written Dutch that transforms raw text input to programs for meaning composition, expressed as {\lambda} terms. The parser…
PyBADS is a Python implementation of the Bayesian Adaptive Direct Search (BADS) algorithm for fast and robust black-box optimization (Acerbi and Ma 2017). BADS is an optimization algorithm designed to efficiently solve difficult…
Distilling knowledge from large Vision-Language Models (VLMs) into lightweight networks is crucial yet challenging in Fine-Grained Visual Classification (FGVC), due to the reliance on fixed prompts and global alignment. To address this, we…
Deep autoencoders are often extended with a supervised or adversarial loss to learn latent representations with desirable properties, such as greater predictivity of labels and outcomes or fairness with respects to a sensitive variable.…
Evolutionary computing, particularly genetic algorithm (GA), is a combinatorial optimization method inspired by natural selection and the transmission of genetic information, which is widely used to identify optimal solutions to complex…
Over the last two decades, alongside the increased availability of large network datasets, we have witnessed the rapid rise of network science. For many systems, however, the data we have access to is not a direct description of the…
High-level scripting languages are in many ways polar opposites to GPUs. GPUs are highly parallel, subject to hardware subtleties, and designed for maximum throughput, and they offer a tremendous advance in the performance achievable for a…