English
Related papers

Related papers: HelixFold: An Efficient Implementation of AlphaFol…

200 papers

As LLMs scale to multi-million-token KV histories, real-time autoregressive decoding under tight Token-to-Token Latency (TTL) constraints faces growing pressure. Two core bottlenecks dominate: accessing Feed-Forward Network (FFN) weights…

Distributed, Parallel, and Cluster Computing · Computer Science 2025-07-11 Nidhi Bhatia , Ankit More , Ritika Borkar , Tiyasa Mitra , Ramon Matas , Ritchie Zhao , Maximilian Golub , Dheevatsa Mudigere , Brian Pharris , Bita Darvish Rouhani

Protein inverse folding aims to design an amino acid sequence that will fold into a given backbone structure, serving as a central task in protein design. Two main paradigms have been widely explored. Template-based methods exploit…

Machine Learning · Computer Science 2026-03-17 Yiran Zhu , Changxi Chi , Hongxin Xiang , Wenjie Du , Xiaoqi Wang , Jun Xia

This study develops a cloud-based deep learning system for early prediction of diabetes, leveraging the distributed computing capabilities of the AWS cloud platform and deep learning technologies to achieve efficient and accurate risk…

Distributed, Parallel, and Cluster Computing · Computer Science 2025-01-07 Yang Zhang , Fa Wang , Xin Huang , Xintao Li , Sibei Liu , Hansong Zhang

Accurately modeling the protein fitness landscapes holds great importance for protein engineering. Recently, due to their capacity and representation ability, pre-trained protein language models have achieved state-of-the-art performance in…

Biomolecules · Quantitative Biology 2024-02-06 Ziyi Zhou , Liang Zhang , Yuanxi Yu , Mingchen Li , Liang Hong , Pan Tan

Following AI scaling trends, frontier models continue to grow in size and continue to be trained on larger datasets. Training these models requires huge investments in exascale computational resources, which has in turn driven developtment…

Machine Learning · Computer Science 2025-09-18 Hiroki Naganuma , Xinzhi Zhang , Man-Chung Yue , Ioannis Mitliagkas , Philipp A. Witte , Russell J. Hewett , Yin Tat Lee

Training recommendation models pose significant challenges regarding resource utilization and performance. Prior research has proposed an approach that categorizes embeddings into popular and non-popular classes to reduce the training time…

Information Retrieval · Computer Science 2024-04-09 Yassaman Ebrahimzadeh Maboud , Muhammad Adnan , Divya Mahajan , Prashant J. Nair

Ensembles, where multiple neural networks are trained individually and their predictions are averaged, have been shown to be widely successful for improving both the accuracy and predictive uncertainty of single neural networks. However, an…

Machine Learning · Computer Science 2020-02-21 Yeming Wen , Dustin Tran , Jimmy Ba

Being accurate, efficient, and compact is essential to a facial landmark detector for practical use. To simultaneously consider the three concerns, this paper investigates a neat model with promising detection accuracy under wild…

Computer Vision and Pattern Recognition · Computer Science 2019-03-05 Xiaojie Guo , Siyuan Li , Jinke Yu , Jiawan Zhang , Jiayi Ma , Lin Ma , Wei Liu , Haibin Ling

Time series imputation benefits from leveraging cross-feature correlations, yet existing attention-based methods re-discover feature relationships at each layer, lacking persistent anchors to maintain consistent representations. To address…

Machine Learning · Computer Science 2026-05-05 Fengming Zhang , Wenjie Du , Huan Zhang , Ke Yu , Shen Qu

We break the linear link between the layer size and its inference cost by introducing the fast feedforward (FFF) architecture, a log-time alternative to feedforward networks. We demonstrate that FFFs are up to 220x faster than feedforward…

Machine Learning · Computer Science 2023-09-19 Peter Belcak , Roger Wattenhofer

Diffusion and flow-matching models achieve remarkable generative performance but at the cost of many sampling steps, this slows inference and limits applicability to time-critical tasks. The ReFlow procedure can accelerate sampling by…

Machine Learning · Computer Science 2024-10-11 Beomsu Kim , Yu-Guan Hsieh , Michal Klein , Marco Cuturi , Jong Chul Ye , Bahjat Kawar , James Thornton

While federated learning leverages distributed client resources, it faces challenges due to heterogeneous client capabilities. This necessitates allocating models suited to clients' resources and careful parameter aggregation to accommodate…

Machine Learning · Computer Science 2024-10-04 Yujin Shin , Kichang Lee , Sungmin Lee , You Rim Choi , Hyung-Sin Kim , JeongGil Ko

We present LFM2, a family of Liquid Foundation Models designed for efficient on-device deployment and strong task capabilities. Using hardware-in-the-loop architecture search under edge latency and memory constraints, we obtain a compact…

As an essential tool of secure distributed machine learning, vertical federated learning (VFL) based on homomorphic encryption (HE) suffers from severe efficiency problems due to data inflation and time-consuming operations. To this core,…

Cryptography and Security · Computer Science 2024-05-02 Liu Yang , Shuowei Cai , Di Chai , Junxue Zhang , Han Tian , Yilun Jin , Kun Guo , Kai Chen , Qiang Yang

RNA secondary structure prediction is widely used to understand RNA function. Recently, there has been a shift away from the classical minimum free energy (MFE) methods to partition function-based methods that account for folding ensembles…

Biomolecules · Quantitative Biology 2024-02-08 He Zhang , Liang Zhang , David H. Mathews , Liang Huang

Maximizing parallelism level in applications can be achieved by minimizing overheads due to load imbalances and waiting time due to memory latencies. Compiler optimization is one of the most effective solutions to tackle this problem. The…

Distributed, Parallel, and Cluster Computing · Computer Science 2017-03-29 Zahra Khatami , Hartmut Kaiser , J. Ramanujam

Deploying LLM agents at scale typically requires choosing between quality and cost. Existing cost-reduction approaches fail to preserve agility: the ability to iterate rapidly without human time bottlenecks. Prompt engineering is brittle…

Machine Learning · Computer Science 2026-04-21 Vishnu Sarukkai , Asanshay Gupta , James Hong , Michaël Gharbi , Kayvon Fatahalian

Deep neural networks (DNNs) exploit many layers and a large number of parameters to achieve excellent performance. The training process of DNN models generally handles large-scale input data with many sparse features, which incurs high…

Distributed, Parallel, and Cluster Computing · Computer Science 2023-06-08 Ji Liu , Zhihua Wu , Dianhai Yu , Yanjun Ma , Danlei Feng , Minxu Zhang , Xinxuan Wu , Xuefeng Yao , Dejing Dou

To optimize large Transformer model training, both efficient parallel computing and advanced data management are indispensable. However, current methods often assume a stable and uniform training workload, neglecting data-induced…

Distributed, Parallel, and Cluster Computing · Computer Science 2025-10-16 Haoyang Li , Fangcheng Fu , Sheng Lin , Hao Ge , Xuanyu Wang , Jiawen Niu , Jinbao Xue , Yangyu Tao , Di Wang , Jie Jiang , Bin Cui

Even with the significant advances of AlphaFold-Multimer (AF-Multimer) and AlphaFold3 (AF3) in protein complex structure prediction, their accuracy is still not comparable with monomer structure prediction. Efficient quality assessment (QA)…

Biomolecules · Quantitative Biology 2024-10-24 Bingqing Han , Yipeng Zhang , Longlong Li , Xinqi Gong , Kelin Xia