Related papers: A Field Approach to 3D Gene Expression Pattern Cha…

In this paper, we investigate the problem of automatically controllable artistic character line drawing generation from photographs by proposing a Vector Flow Aware and Line Controllable Image-to-Image Translation architecture, which can be…

This paper proposes a novel method, Explicit Flow Matching (ExFM), for training and analyzing flow-based generative models. ExFM leverages a theoretically grounded loss function, ExFM loss (a tractable form of Flow Matching (FM) loss), to…

We propose an effective method to improve Protein Function Prediction (PFP) utilizing hierarchical features of Gene Ontology (GO) terms. Our method consists of a language model for encoding the protein sequence and a Graph Convolutional…

The ability of neural radiance fields or NeRFs to conduct accurate 3D modelling has motivated application of the technique to scene representation. Previous approaches have mainly followed a centralised learning paradigm, which assumes that…

A problem of substantial interest is to systematically map variation in chromatin structure to gene expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for…

We develop a formalism to describe the equilibrium distributions for segments of confined branched networks consisting of stiff filaments. This is applicable to certain situations of cytoskeleton in cells, such as for example actin…

We consider the problem of predicting gene expressions from DNA sequences. A key challenge of this task is to find the regulatory elements that control gene expressions. Here, we introduce Seq2Exp, a Sequence to Expression network…

Gene expression profiling provides critical insights into cellular heterogeneity, biological processes and disease mechanisms. There has been an increasing interest in computational approaches that can predict gene expression directly from…

Neuro-encoded expression programming(NEEP) that aims to offer a novel continuous representation of combinatorial encoding for genetic programming methods is proposed in this paper. Genetic programming with linear representation uses…

Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes.…

This paper proposes a novel framework for large-scale scene reconstruction based on 3D Gaussian splatting (3DGS) and aims to address the scalability and accuracy challenges faced by existing methods. For tackling the scalability issue, we…

Embryonic development involves pattern formation characterized by the emergence of spatially localized domains characterized by distinct cell fates resulting from differential gene expression. The boundaries demarcating these domains are…

We study the effect of fluid flow on three-dimensional (3D) dendrite growth using a phase-field model on an adaptive finite element grid. In order to simulate 3D fluid flow, we use an averaging method for the flow problem coupled to the…

Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…

Methods allowing the synthesis of realistic cell shapes could help generate training data sets to improve cell tracking and segmentation in biomedical images. Deep generative models for cell shape synthesis require a light-weight and…

Transcription factors are able to associate to their binding sites on DNA faster than the physical limit posed by diffusion. Such high association rates can be achieved by alternating between three-dimensional diffusion and one-dimensional…

Robotic grasping of house-hold objects has made remarkable progress in recent years. Yet, human grasps are still difficult to synthesize realistically. There are several key reasons: (1) the human hand has many degrees of freedom (more than…

In this paper we describe two new computational operators, called complex entropic form (CEF) and generalized complex entropic form (GEF), for pattern characterization of spatially extended systems. Besides of being a measure of regularity,…

The formation of protein patterns inside cells is generically described by reaction-diffusion models. The study of such systems goes back to Turing, who showed how patterns can emerge from a homogenous steady state when two reactive…

Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…