Related papers: Training-free Measures Based on Algorithmic Probab…

Bayesian network (BN) structure discovery algorithms typically either make assumptions about the sparsity of the true underlying network, or are limited by computational constraints to networks with a small number of variables. While these…

Nucleosome organization in eukaryotic genomes has a deep impact on gene function. Although progress has been recently made in the identification of various concurring factors influencing nucleosome positioning, it is still unclear whether…

In recent years, deep learning algorithms have outperformed the state-of-the art methods in several areas thanks to the efficient methods for training and for preventing overfitting, advancement in computer hardware, the availability of…

Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a…

A mesoscopic model which allows us to identify and quantify the strength of binding sites in DNA sequences is proposed. The model is based on the Peyrard-Bishop-Dauxois model for the DNA chain coupled to a Brownian particle which explores…

Model-free deep reinforcement learning algorithms have been shown to be capable of learning a wide range of robotic skills, but typically require a very large number of samples to achieve good performance. Model-based algorithms, in…

As the size and richness of available datasets grow larger, the opportunities for solving increasingly challenging problems with algorithms learning directly from data grow at the same pace. Consequently, the capability of learning…

Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…

Spatial models for occupancy data are used to estimate and map the true presence of a species, which may depend on biotic and abiotic factors as well as spatial autocorrelation. Traditionally researchers have accounted for spatial…

We propose a new alignment-free algorithm by constructing a compact vector representation on $\mathbb{R}^{24}$ of a DNA sequence of arbitrary length. Each component of this vector is obtained from a representative sequence, the elements of…

Inspired by the success of unsupervised pre-training paradigms, researchers have applied these approaches to DNA pre-training. However, we argue that these approaches alone yield suboptimal results because pure DNA sequences lack sufficient…

Non protein coding regions of the human genome contain many complex patterns which regulate the cellular activity. Studying the human genome is limited by the lack of understanding of its features and their complex interactions. However,…

Flow matching models generate high-fidelity molecular geometries but incur significant computational costs during inference, requiring hundreds of network evaluations. This inference overhead becomes the primary bottleneck when such models…

Machine learning methods have shown promise in predicting molecular properties, and given sufficient training data machine learning approaches can enable rapid high-throughput virtual screening of large libraries of compounds. Graph-based…

In this article, we review existing probabilistic models for modeling abundance of fixed-length strings (k-mers) in DNA sequencing data. These models capture dependence of the abundance on various phenomena, such as the size and repeat…

In autonomous navigation of mobile robots, sensors suffer from massive occlusion in cluttered environments, leaving significant amount of space unknown during planning. In practice, treating the unknown space in optimistic or pessimistic…

The time and effort involved in hand-designing deep neural networks is immense. This has prompted the development of Neural Architecture Search (NAS) techniques to automate this design. However, NAS algorithms tend to be slow and expensive;…

Architecture plays an important role in deciding the performance of deep neural networks. However, the search for the optimal architecture is often hindered by the vast search space, making it a time-intensive process. Recently, a novel…

Deep learning-based nuclei segmentation and classification in pathology images typically rely on large-scale pixel-level manual annotations, which are costly and difficult to obtain across diverse tissues and staining conditions. To address…

The training of large language models (LLMs) is expensive. In this paper, we study data-efficient approaches for pre-training LLMs, i.e., techniques that aim to optimize the Pareto frontier of model quality and training resource/data…