Related papers: Unravelling the Architecture of Membrane Proteins …

Superpixel-based Higher-order Conditional Random Fields (CRFs) are effective in enforcing long-range consistency in pixel-wise labeling problems, such as semantic segmentation. However, their major short coming is considerably longer time…

This paper proposes hybrid semi-Markov conditional random fields (SCRFs) for neural sequence labeling in natural language processing. Based on conventional conditional random fields (CRFs), SCRFs have been designed for the tasks of…

We introduce a conditional Generative Adversarial Network (cGAN) approach to generate cloud reflectance fields (CRFs) conditioned on large scale meteorological variables such as sea surface temperature and relative humidity. We show that…

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…

Many deep learning architectures for semantic segmentation involve a Fully Convolutional Neural Network (FCN) followed by a Conditional Random Field (CRF) to carry out inference over an image. These models typically involve unary potentials…

The techniques of data-driven backmapping from coarse-grained (CG) to fine-grained (FG) representation often struggle with accuracy, unstable training, and physical realism, especially when applied to complex systems such as proteins. In…

In this work we introduce a fully-connected graph structure in the Deep Gaussian Conditional Random Field (G-CRF) model. For this we express the pairwise interactions between pixels as the inner-products of low-dimensional embeddings,…

We propose a novel discriminative model for sequence labeling called Bregman conditional random fields (BCRF). Contrary to standard linear-chain conditional random fields, BCRF allows fast parallelizable inference algorithms based on…

This paper describes a parsing model that combines the exact dynamic programming of CRF parsing with the rich nonlinear featurization of neural net approaches. Our model is structurally a CRF that factors over anchored rule productions, but…

The Distributional Random Forest (DRF) is a recently introduced Random Forest algorithm to estimate multivariate conditional distributions. Due to its general estimation procedure, it can be employed to estimate a wide range of targets such…

Prediction of one-dimensional protein structures such as secondary structures and contact numbers is useful for the three-dimensional structure prediction and important for the understanding of sequence-structure relationship. Here we…

The increase of vehicle in highways may cause traffic congestion as well as in the normal roadways. Predicting the traffic flow in highways especially, is demanded to solve this congestion problem. Predictions on time-series multivariate…

This paper proposes a general framework for internal patch-based image restoration based on Conditional Random Fields (CRF). Unlike related models based on Markov Random Fields (MRF), our approach explicitly formulates the posterior…

In this work we propose a structured prediction technique that combines the virtues of Gaussian Conditional Random Fields (G-CRF) with Deep Learning: (a) our structured prediction task has a unique global optimum that is obtained exactly…

Capturing the conditional covariances or correlations among the elements of a multivariate response vector based on covariates is important to various fields including neuroscience, epidemiology and biomedicine. We propose a new method…

Graph neural networks (GNNs) have emerged as powerful tools for learning protein structures by capturing spatial relationships at the residue level. However, existing GNN-based methods often face challenges in learning multiscale…

Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which…

Multiplexed immunofluorescence provides an unprecedented opportunity for studying specific cell-to-cell and cell microenvironment interactions. We employ graph neural networks to combine features obtained from tissue morphology with…

We propose a novel methodology, forest floor, to visualize and interpret random forest (RF) models. RF is a popular and useful tool for non-linear multi-variate classification and regression, which yields a good trade-off between robustness…

While recent NeRF-based generative models achieve the generation of diverse 3D-aware images, these approaches have limitations when generating images that contain user-specified characteristics. In this paper, we propose a novel model,…