Related papers: CLP-based protein fragment assembly
CLeFAPS, a fast and flexible pairwise structural alignment algorithm based on a rigid-body framework, namely CLePAPS, is proposed. Instead of allowing twists (or bends), the flexible in CLeFAPS means: (a) flexibilization of the algorithm's…
A basic assumption of molecular biology is that proteins sharing close three-dimensional (3D) structures are likely to share a common function and in most cases derive from a same ancestor. Computing the similarity between two protein…
ACLP is a system which combines abductive reasoning and constraint solving by integrating the frameworks of Abductive Logic Programming (ALP) and Constraint Logic Programming (CLP). It forms a general high-level knowledge representation…
This paper proposes the use of Constraint Logic Programming (CLP) to model SQL queries in a data-independent abstract layer by focusing on some semantic properties for signalling possible errors in such queries. First, we define a…
In this work we introduce a novel approach, based on sampling, for finding assignments that are likely to be solutions to stochastic constraint satisfaction problems and constraint optimisation problems. Our approach reduces the size of the…
Semi-supervised clustering is a basic problem in various applications. Most existing methods require knowledge of the ideal cluster number, which is often difficult to obtain in practice. Besides, satisfying the must-link constraints is…
Identification and alignment of three-dimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of…
Detectability of failures of linear programming (LP) decoding and its potential for improvement by adding new constraints motivate the use of an adaptive approach in selecting the constraints for the LP problem. In this paper, we make a…
Clustering attempts to partition data instances into several distinctive groups, while the similarities among data belonging to the common partition can be principally reserved. Furthermore, incomplete data frequently occurs in many…
Despite the constant evolution of similarity searching research, it continues to face the same challenges stemming from the complexity of the data, such as the curse of dimensionality and computationally expensive distance functions.…
Contrastive Language-Image Pre-training (CLIP) has achieved widely applications in various computer vision tasks, e.g., text-to-image generation, Image-Text retrieval and Image captioning. However, CLIP suffers from high memory and…
Learning from 3D protein structures has gained wide interest in protein modeling and structural bioinformatics. Unfortunately, the number of available structures is orders of magnitude lower than the training data sizes commonly used in…
Logic programming with tabling and constraints (TCLP, tabled constraint logic programming) has been shown to be more expressive and, in some cases, more efficient than LP, CLP, or LP with tabling. In this paper we provide insights regarding…
The remarkable structural diversity of modern proteins reflects millions of years of evolution, during which sequence space has expanded while many structural features remain conserved. This conservation is evident not only among homologous…
A new approach to solving a large class of factorable nonlinear programming (NLP) problems to global optimality is presented in this paper. Unlike the traditional strategy of partitioning the decision-variable space employed in many…
This paper presents a new, parallel implementation of clustering and demonstrates its utility in greatly speeding up the process of identifying homologous proteins. Clustering is a technique to reduce the number of comparison needed to find…
Scheduling flexible sources to promote the integration of renewable generation is one fundamental problem for operating active distribution networks (ADNs). However, existing works are usually based on power flow models, which require…
A particularly successful role for Inductive Logic Programming (ILP) is as a tool for discovering useful relational features for subsequent use in a predictive model. Conceptually, the case for using ILP to construct relational features…
In this paper, we present a novel approach for conformal prediction (CP), in which we aim to identify a set of promising prediction candidates -- in place of a single prediction. This set is guaranteed to contain a correct answer with high…
Computational protein structure determination involves optimization in a problem space much too large to exhaustively search. Existing approaches include optimization algorithms such as gradient descent and simulated annealing, but these…