English
Related papers

Related papers: COCACOLA: binning metagenomic contigs using sequen…

200 papers

Online contextual reasoning and association across consecutive video frames are critical to perceive instances in visual tracking. However, most current top-performing trackers persistently lean on sparse temporal relationships between…

Computer Vision and Pattern Recognition · Computer Science 2024-01-04 Yaozong Zheng , Bineng Zhong , Qihua Liang , Zhiyi Mo , Shengping Zhang , Xianxian Li

An oritatami system (OS) is a theoretical model of self-assembly via co-transcriptional folding. It consists of a growing chain of beads which can form bonds with each other as they are transcribed. During the transcription process, the…

Data Structures and Algorithms · Computer Science 2018-07-16 Erik D. Demaine , Jacob Hendricks , Meagan Olsen , Matthew J. Patitz , Trent A. Rogers , Nicolas Schabanel , Shinnosuke Seki , Hadley Thomas

Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in…

Quantitative Methods · Quantitative Biology 2024-06-03 Qizhi Pei , Lijun Wu , Kaiyuan Gao , Xiaozhuan Liang , Yin Fang , Jinhua Zhu , Shufang Xie , Tao Qin , Rui Yan

Accurate segmentation and classification of nuclei in histology images is critical but challenging due to nuclei heterogeneity, staining variations, and tissue complexity. Existing methods often struggle with limited dataset variability,…

Image and Video Processing · Electrical Eng. & Systems 2025-01-22 Wenhua Zhang , Sen Yang , Meiwei Luo , Chuan He , Yuchen Li , Jun Zhang , Xiyue Wang , Fang Wang

Large Language Models (LLMs) achieve state-of-the-art performance across various NLP tasks but face deployment challenges due to high computational costs and memory constraints. Knowledge distillation (KD) is a promising solution,…

Computation and Language · Computer Science 2025-03-04 Anh Duc Le , Tu Vu , Nam Le Hai , Nguyen Thi Ngoc Diep , Linh Ngo Van , Trung Le , Thien Huu Nguyen

Interpreting the internal behavior of large language models trained on code remains a critical challenge, particularly for applications demanding trust, transparency, and semantic robustness. We propose Code Concept Analysis (CoCoA): a…

Software Engineering · Computer Science 2025-10-06 Arushi Sharma , Vedant Pungliya , Christopher J. Quinn , Ali Jannesari

Optical Coherence Tomography Angiography (OCTA) is a crucial imaging technique for visualizing retinal vasculature and diagnosing eye diseases such as diabetic retinopathy and glaucoma. However, precise segmentation of OCTA vasculature…

Image and Video Processing · Electrical Eng. & Systems 2025-01-03 Shun Zou , Zhuo Zhang , Guangwei Gao

Research on LLM technologies is rapidly emerging, with most of them employ a 'fast thinking' approach to inference. Most LLMs generate the final result based solely on a single query and LLM's reasoning capabilities. However, with the…

Computation and Language · Computer Science 2025-11-14 Jianfeng Pan , Senyou Deng , Shaomang Huang

Although dominant in natural language processing, transformer-based models remain challenged by the task of long-sequence processing, because the computational cost of self-attention operations in transformers swells quadratically with the…

Computation and Language · Computer Science 2024-07-08 Jiawen Xie , Pengyu Cheng , Xiao Liang , Yong Dai , Nan Du

Convolution is the main building block of convolutional neural networks (CNN). We observe that an optimized CNN often has highly correlated filters as the number of channels increases with depth, reducing the expressive power of feature…

Computer Vision and Pattern Recognition · Computer Science 2020-09-28 Xudong Wang , Stella X. Yu

We present Agglomerative Token Clustering (ATC), a novel token merging method that consistently outperforms previous token merging and pruning methods across image classification, image synthesis, and object detection & segmentation tasks.…

Computer Vision and Pattern Recognition · Computer Science 2024-09-19 Joakim Bruslund Haurum , Sergio Escalera , Graham W. Taylor , Thomas B. Moeslund

Convolutional neural networks (CNNs) are widely applied in real-time applications on resource-constrained devices. To accelerate CNN inference, prior works proposed to distribute the inference workload across multiple devices. However, they…

Distributed, Parallel, and Cluster Computing · Computer Science 2025-01-14 Xing Liu , Chao Huang , Ming Tang

Fixed-point quantization and binarization are two reduction methods adopted to deploy Convolutional Neural Networks (CNN) on end-nodes powered by low-power micro-controller units (MCUs). While most of the existing works use them as…

Computer Vision and Pattern Recognition · Computer Science 2020-01-28 Luca Mocerino , Andrea Calimera

We present SuperConga, an open-source framework for simulating equilibrium properties of unconventional and ballistic singlet superconductors, confined to two-dimensional (2D) mesoscopic grains in a perpendicular external magnetic field, at…

Superconductivity · Physics 2023-03-23 P. Holmvall , N. Wall Wennerdal , M. Håkansson , P. Stadler , O. Shevtsov , T. Löfwander , M. Fogelström

Advances in high-throughput technologies have originated an ever-increasing availability of omics datasets. The integration of multiple heterogeneous data sources is currently an issue for biology and bioinformatics. Multiple kernel…

Machine Learning · Statistics 2024-12-04 Mitja Briscik , Gabriele Tazza , Marie-Agnes Dillies , László Vidács , Sébastien Dejean

The scaling of Large Language Models (LLMs) is increasingly limited by data quality. Most methods handle data mixing and sample selection separately, which can break the structure in code corpora. We introduce \textbf{UniGeM}, a framework…

Machine Learning · Computer Science 2026-02-04 Changhao Wang , Yunfei Yu , Xinhao Yao , Jiaolong Yang , Riccardo Cantoro , Chaobo Li , Qing Cui , Jun Zhou

Stance detection on social media is challenging for Large Language Models (LLMs), as emerging slang and colloquial language in online conversations often contain deeply implicit stance labels. Chain-of-Thought (COT) prompting has recently…

Computation and Language · Computer Science 2023-10-31 Joseph Gatto , Omar Sharif , Sarah Masud Preum

One of the most striking findings in modern research on large language models (LLMs) is that scaling up compute during training leads to better results. However, less attention has been given to the benefits of scaling compute during…

Computation and Language · Computer Science 2024-11-21 Sean Welleck , Amanda Bertsch , Matthew Finlayson , Hailey Schoelkopf , Alex Xie , Graham Neubig , Ilia Kulikov , Zaid Harchaoui

The detection of genomic structural variation (SV) has advanced tremendously in recent years due to progress in high-throughput sequencing technologies. Novel sequence insertions, insertions without similarity to a human reference genome,…

Genomics · Quantitative Biology 2015-04-09 Birte Kehr , Páll Melsted , Bjarni V. Halldórsson

The architecture of deep convolutional networks (CNNs) has evolved for years, becoming more accurate and faster. However, it is still challenging to design reasonable network structures that aim at obtaining the best accuracy under a…

Computer Vision and Pattern Recognition · Computer Science 2021-10-01 Lu Rao