Related papers: Calculating complexity of large randomized librari…
The past decade highlighted the usefulness of social network simulations that run on k-regular, n-size, connected graphs. These can be seen as small-scale models of human social networks of large societies. By narrowing down onto k-regular…
Drug discovery has become a main challenge in our society, following the Covid-19 pandemic. Even pharmaceutical companies are already using computing to accelerate drug discovery. They are increasingly interested in Quantum Computing with a…
The new and growing field of Quantitative Dependency Syntax has emerged at the crossroads between Dependency Syntax and Quantitative Linguistics. One of the main concerns in this field is the statistical patterns of syntactic dependency…
Gradients of probabilistic model likelihoods with respect to their parameters are essential for modern computational statistics and machine learning. These calculations are readily available for arbitrary models via automatic…
The fact that we can build models from data, and therefore refine our models with more data from experiments, is usually given for granted in scientific inquiry. However, how much information can we extract, and how precise can we expect…
Protein aggregation is an important field of investigation because it is closely related to the problem of neurodegenerative diseases, to the development of biomaterials, and to the growth of cellular structures such as cyto-skeleton.…
We present here a new package to automatically generate a complete library of 2 to 2 squared amplitudes at leading order in any New Physics models. The package is written in C++ and based on the MARTY software. The numerical library…
Machine learning solutions are very popular in the field of chemoinformatics, where they have numerous applications, such as novel drug discovery or molecular property prediction. Molecular fingerprints are algorithms commonly used for…
The interpretation of count data originating from the current generation of DNA sequencing platforms requires special attention. In particular, the per-sample library sizes often vary by orders of magnitude from the same sequencing run, and…
Software systems often leverage on open source software libraries to reuse functionalities. Such libraries are readily available through software package managers like npm for JavaScript. Due to the huge amount of packages available in such…
Software systems are expansive, exhibiting behaviors characteristic of complex systems, such as self-organization and emergence. These systems, highlighted by advancements in Large Language Models (LLMs) and other AI applications developed…
The GC-content is very variable in different genome regions and species but although many hypothesis we still do not know the reason why. Here we show that a relationship exists with the mutation rate, in particular we noticed a new…
Modern randomization methods in clinical trials are invariably adaptive, meaning that the assignment of the next subject to a treatment group uses the accumulated information in the trial. Some of the recent adaptive randomization methods…
Many big-data clusters store data in large partitions that support access at a coarse, partition-level granularity. As a result, approximate query processing via row-level sampling is inefficient, often requiring reads of many partitions.…
Evaluating the computational reproducibility of data analysis pipelines has become a critical issue. It is, however, a cumbersome process for analyses that involve data from large populations of subjects, due to their computational and…
Statistical analysis of DNA mixtures is known to pose computational challenges due to the enormous state space of possible DNA profiles. We propose a Bayesian network representation for genotypes, allowing computations to be performed…
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…
Challenges of assessing complexity and clonality in populations of mixed species arise in diverse areas of modern biology, including estimating diversity and clonality in microbiome populations, measuring patterns of T and B cell clonality,…
The method of random projections has become very popular for large-scale applications in statistical learning, information retrieval, bio-informatics and other applications. Using a well-designed coding scheme for the projected data, which…
In [3], algorithms to compute the density of the distance to a random variable uniformly distributed in (a) a ball, (b) a disk, (c) a line segment, or (d) a polygone were introduced. For case (d), the algorithm, based on Green's theorem,…