Related papers: Explicit Path CGR: Maintaining Sequence Fidelity i…

Biological classification with interpretability remains a challenging task. For this, we introduce a novel encoding framework, Multi-Scale Reversible Chaos Game Representation (MS-RCGR), that transforms biological sequences into…

Accurate molecular sequence analysis is a key task in the field of bioinformatics. To apply molecular sequence classification algorithms, we first need to generate the appropriate representations of the sequences. Traditional numeric…

Traditional feature engineering approaches for molecular sequence classification suffer from sparsity issues and computational complexity, while deep learning models often underperform on tabular biological data. This paper introduces a…

DNA sequences are fundamental for encoding genetic information. The genetic information may not only be understood by symbolic sequences but also from the hidden signals inside the sequences. The symbolic sequences need to be transformed…

This paper establishes formal mathematical foundations linking Chaos Game Representations (CGR) of DNA sequences to their underlying $k$-mer frequencies. We prove that the Frequency CGR (FCGR) of order $k$ is mathematically equivalent to a…

The generalization ability of Convolutional neural networks (CNNs) for biometrics drops greatly due to the adverse effects of various occlusions. To this end, we propose a novel unified framework integrated the merits of both CNNs and…

This study proposes CGRclust, a novel combination of unsupervised twin contrastive clustering of Chaos Game Representations (CGR) of DNA sequences, with convolutional neural networks (CNNs). To the best of our knowledge, CGRclust is the…

Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation. However, such CG procedure induces information losses, which makes…

Stochastic process-based molecular graph generators have become the state of the art for template-free single-step retrosynthesis. However, these models are typically trained only on product-reactant pairs, thereby acquiring…

Absolute Pose Regression (APR) has emerged as a compelling paradigm for visual localization. However, APR models typically operate as black boxes, directly regressing a 6-DoF pose from a query image, which can lead to memorizing training…

Advances in deep learning models have revolutionized the study of biomolecule systems and their mechanisms. Graph representation learning, in particular, is important for accurately capturing the geometric information of biomolecules at…

One common belief is that with complex models and pre-training on large-scale datasets, transformer-based methods for referring expression comprehension (REC) perform much better than existing graph-based methods. We observe that since most…

We view the reconstruction of CAD models in the boundary representation (B-Rep) as the detection of geometric primitives of different orders, i.e. vertices, edges and surface patches, and the correspondence of primitives, which are…

The analysis of sequences (e.g., protein, DNA, and SMILES string) is essential for disease diagnosis, biomaterial engineering, genetic engineering, and drug discovery domains. Conventional analytical methods focus on transforming sequences…

Implicit neural representations have emerged as a powerful tool in learning 3D geometry, offering unparalleled advantages over conventional representations like mesh-based methods. A common type of INR implicitly encodes a shape's boundary…

Graph convolutional networks (GCNs) have been widely used and achieved remarkable results in skeleton-based action recognition. In GCNs, graph topology dominates feature aggregation and therefore is the key to extracting representative…

Continual Graph Learning (CGL) enables models to incrementally learn from streaming graph-structured data without forgetting previously acquired knowledge. Experience replay is a common solution that reuses a subset of past samples during…

Occlusion is a common problem with biometric recognition in the wild. The generalization ability of CNNs greatly decreases due to the adverse effects of various occlusions. To this end, we propose a novel unified framework integrating the…

Large Language Model agents often retrieve context from knowledge bases that lack structural consistency with the agent's current reasoning state, leading to incoherent reasoning chains. We introduce Path-Constrained Retrieval (PCR), a…

Research question answering requires accurate retrieval and contextual understanding of scientific literature. However, current Retrieval-Augmented Generation (RAG) methods often struggle to balance complex document relationships with…