Related papers: Profile Conditional Random Fields for Modeling Pro…

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…

Accurate prediction of inter-residue contacts of a protein is important to calcu- lating its tertiary structure. Analysis of co-evolutionary events among residues has been proved effective to inferring inter-residue contacts. The Markov…

The need to measure sequence similarity arises in information extraction, object identity, data mining, biological sequence analysis, and other domains. This paper presents discriminative string-edit CRFs, a finitestate conditional random…

Conditional random field (CRF) and Structural Support Vector Machine (Structural SVM) are two state-of-the-art methods for structured prediction which captures the interdependencies among output variables. The success of these methods is…

Time series of conformational dynamics in proteins are usually evaluated with hidden Markov models (HMMs). This approach works well if the number of states and their connectivity is known. However, for the multi-domain protein Hsp90, a…

Pairwise Markov Random Fields (MRFs) or undirected graphical models are parsimonious representations of joint probability distributions. Variables correspond to nodes of a graph, with edges between nodes corresponding to conditional…

Coarse-grained models have proven helpful for simulating complex systems over long timescales to provide molecular insights into various processes. Methodologies for systematic parameterization of the underlying energy function, or force…

Gaussian conditional random fields (GCRF) are a well-known used structured model for continuous outputs that uses multiple unstructured predictors to form its features and at the same time exploits dependence structure among outputs, which…

Context-free and context-sensitive formal grammars are often regarded as more appropriate to model proteins than regular level models such as finite state automata and Hidden Markov Models. In theory, the claim is well founded in the fact…

Under certain conditions, the dynamics of coarse-grained models of solvated proteins can be described using a Markov state model, which tracks the evolution of populations of configurations. The transition rates among states that appear in…

By providing new insights into the distribution of a protein's torsion angles, recent statistical models for this data have pointed the way to more efficient methods for protein structure prediction. Most current approaches have…

Recent years have seen substantial advances in the development of biofunctional materials using synthetic polymers. The growing problem of elusive sequence-functionality relations for most biomaterials has driven researchers to seek more…

Hidden Markov Models (HMMs) are powerful tools for modeling sequential data, where the underlying states evolve in a stochastic manner and are only indirectly observable. Traditional HMM approaches are well-established for linear sequences,…

Flow matching (FM) is a family of training algorithms for fitting continuous normalizing flows (CNFs). Conditional flow matching (CFM) exploits the fact that the marginal vector field of a CNF can be learned by fitting least-squares…

Factorization machines (FM) are a popular model class to learn pairwise interactions by a low-rank approximation. Different from existing FM-based approaches which use a fixed rank for all features, this paper proposes a Rank-Aware FM…

We introduce a probabilistic formalism subsuming Markov random fields of bounded tree width and probabilistic context free grammars. Our models are based on a representation of Boolean formulas that we call case-factor diagrams (CFDs). CFDs…

Revealing the functional sites of biological sequences, such as evolutionary conserved, structurally interacting or co-evolving protein sites, is a fundamental, and yet challenging task. Different frameworks and models were developed to…

Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…

The use of hierarchical Conditional Random Field model deal with the problem of labeling images . At the time of labeling a new image, selection of the nearest cluster and using the related CRF model to label this image. When one give input…

Hidden Markov Models (HMMs) and Probabilistic Context-Free Grammars (PCFGs) are widely used structured models, both of which can be represented as factor graph grammars (FGGs), a powerful formalism capable of describing a wide range of…