Related papers: Mapache: a flexible pipeline to map ancient DNA
Transcriptome assembly from RNA-Seq reads is an active area of bioinformatics research. The ever-declining cost and the increasing depth of RNA-Seq have provided unprecedented opportunities to better identify expressed transcripts. However,…
Communication and networking research introduces new protocols and standards with an increasing number of researchers relying on real experiments rather than simulations to evaluate the performance of their new protocols. A number of…
In autonomous driving, mapping is critical for motion planning but remains an under-utilized resource for perception tasks such as 3D object detection. Maps can provide robust structural priors of the static environment, helping resolve…
Ancient mitochondrial DNA has been used in a wide variety of palaeontological and archaeological studies, ranging from population dynamics of extinct species to patterns of domestication. Most of these studies have traditionally been based…
Circular RNAs (circRNAs) are important components of the non-coding RNA regulatory network. Previous circRNA identification primarily relies on high-throughput RNA sequencing (RNA-seq) data combined with alignment-based algorithms that…
The field of connectomics faces unprecedented "big data" challenges. To reconstruct neuronal connectivity, automated pixel-level segmentation is required for petabytes of streaming electron microscopy data. Existing algorithms provide…
Path planning is a key component in mobile robotics. A wide range of path planning algorithms exist, but few attempts have been made to benchmark the algorithms holistically or unify their interface. Moreover, with the recent advances in…
Motivation: Identifying the molecular pathways more prone to disruption during a pathological process is a key task in network medicine and, more in general, in systems biology. Results: In this work we propose a pipeline that couples a…
Automated machine learning makes it easier for data scientists to develop pipelines by searching over possible choices for hyperparameters, algorithms, and even pipeline topologies. Unfortunately, the syntax for automated machine learning…
We propose a general method for optimally approximating an arbitrary matrix $\mathbf{M}$ by a structured matrix $\mathbf{T}$ (circulant, Toeplitz/Hankel, etc.) and examine its use for estimating the spectra of genomic linkage disequilibrium…
Recent advances in computational methods for designing biological sequences have sparked the development of metrics to evaluate these methods performance in terms of the fidelity of the designed sequences to a target distribution and their…
DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the…
Paper maps remain widely used for hiking and sightseeing because they contain curated trails and locally relevant annotations that are often missing from digital navigation applications such as Google Maps. We propose a pipeline to extract…
Using a single tool to build and compare recommender systems significantly reduces the time to market for new models. In addition, the comparison results when using such tools look more consistent. This is why many different tools and…
We present the first public release of ShapePipe, an open-source and modular weak-lensing measurement, analysis, and validation pipeline written in Python. We describe the design of the software and justify the choices made. We provide a…
Rapid analysis of DNA sequences is important in preventing the evolution of different viruses and bacteria during an early phase, early diagnosis of genetic predispositions to certain diseases (cancer, cardiovascular diseases), and in DNA…
A method based on mapping a symbolic sequence into a set of patterns (strings resulting from the sequence parsing) is proposed as a tool for the reconstruction of ancestral sequences. The set union of patterns comprises all the patterns…
The Mixture of Experts architecture allows for outrageously large neural networks by scaling model parameter size independently from computational demand (FLOPs). However, current DNN frameworks cannot effectively support the dynamic data…
The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene…
Big Data today is being generated at an unprecedented rate from various sources such as sensors, applications, and devices, and it often needs to be enriched based on other reference information to support complex analytical queries.…