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Pangenome variation graphs (PVGs) allow for the representation of genetic diversity in a more nuanced way than traditional reference-based approaches. Here we focus on how PVGs are a powerful tool for studying genetic variation in viruses,…

Genomics · Quantitative Biology 2025-06-18 Tim Downing

The convolutional neural network (CNN), which is one of the deep learning models, has seen much success in a variety of computer vision tasks. However, designing CNN architectures still requires expert knowledge and a lot of trial and…

Neural and Evolutionary Computing · Computer Science 2017-08-14 Masanori Suganuma , Shinichi Shirakawa , Tomoharu Nagao

Prompt-based techniques have demostrated great potential for improving the few-shot generalization of pretrained language models. However, their performance heavily relies on the manual design of prompts and thus requires a lot of human…

Computation and Language · Computer Science 2022-11-01 Hanwei Xu , Yujun Chen , Yulun Du , Nan Shao , Yanggang Wang , Haiyu Li , Zhilin Yang

The techniques of data-driven backmapping from coarse-grained (CG) to fine-grained (FG) representation often struggle with accuracy, unstable training, and physical realism, especially when applied to complex systems such as proteins. In…

Machine Learning · Computer Science 2025-05-26 Georgios Kementzidis , Erin Wong , John Nicholson , Ruichen Xu , Yuefan Deng

Compositional generalization is a key ability of humans that enables us to learn new concepts from only a handful examples. Neural machine learning models, including the now ubiquitous Transformers, struggle to generalize in this way, and…

Machine Learning · Computer Science 2024-01-19 Tim Klinger , Luke Liu , Soham Dan , Maxwell Crouse , Parikshit Ram , Alexander Gray

Gaussian processes (GPs) are popular nonparametric statistical models for learning unknown functions and quantifying the spatiotemporal uncertainty in data. Recent works have extended GPs to model scalar and vector quantities distributed…

In molecular dynamics simulations, rare events, such as protein folding, are typically studied using enhanced sampling techniques, most of which are based on the definition of a collective variable (CV) along which acceleration occurs.…

Chemical Physics · Physics 2024-07-22 Soojung Yang , Juno Nam , Johannes C. B. Dietschreit , Rafael Gómez-Bombarelli

Neural processes are a family of models which use neural networks to directly parametrise a map from data sets to predictions. Directly parametrising this map enables the use of expressive neural networks in small-data problems where neural…

Machine Learning · Statistics 2024-08-20 Wessel P. Bruinsma

We present SketchGPT, a flexible framework that employs a sequence-to-sequence autoregressive model for sketch generation, and completion, and an interpretation case study for sketch recognition. By mapping complex sketches into simplified…

Computer Vision and Pattern Recognition · Computer Science 2024-05-07 Adarsh Tiwari , Sanket Biswas , Josep Lladós

Symbolic Regression (SR) aims to discover interpretable equations from observational data, with the potential to reveal underlying principles behind natural phenomena. However, existing approaches often fall into the Pseudo-Equation Trap:…

Machine Learning · Computer Science 2026-02-17 Jing Xiao , Xinhai Chen , Jiaming Peng , Qinglin Wang , Menghan Jia , Zhiquan Lai , Guangping Yu , Dongsheng Li , Tiejun Li , Jie Liu

A key challenge with controlling complex dynamical systems is to accurately model them. However, this requirement is very hard to satisfy in practice. Data-driven approaches such as Gaussian processes (GPs) have proved quite effective by…

Robotics · Computer Science 2022-03-08 Mouhyemen Khan , Akash Patel , Abhijit Chatterjee

This paper introduces Multi-population Ensemble Genetic Programming (MEGP), a computational intelligence framework that integrates cooperative coevolution and the multiview learning paradigm to address classification challenges in…

Neural and Evolutionary Computing · Computer Science 2025-09-25 Mohammad Sadegh Khorshidi , Navid Yazdanjue , Hassan Gharoun , Mohammad Reza Nikoo , Fang Chen , Amir H. Gandomi

Regression analysis is used for prediction and to understand the effect of independent variables on dependent variables. Symbolic regression (SR) automates the search for non-linear regression models, delivering a set of hypotheses that…

Machine Learning · Computer Science 2025-04-09 Fabricio Olivetti de Franca , Gabriel Kronberger

Conditional visual generation has witnessed remarkable progress with the advent of diffusion models (DMs), especially in tasks like control-to-image generation. However, challenges such as expensive computational cost, high inference…

Computer Vision and Pattern Recognition · Computer Science 2024-10-03 Xiang Li , Kai Qiu , Hao Chen , Jason Kuen , Zhe Lin , Rita Singh , Bhiksha Raj

Symbolic regression (SR) is a powerful technique for discovering the underlying mathematical expressions from observed data. Inspired by the success of deep learning, recent deep generative SR methods have shown promising results. However,…

Machine Learning · Computer Science 2024-06-04 Wenqiang Li , Weijun Li , Lina Yu , Min Wu , Linjun Sun , Jingyi Liu , Yanjie Li , Shu Wei , Yusong Deng , Meilan Hao

In the last few years the systematic adoption of deep learning to visual generation has produced impressive results that, amongst others, definitely benefit from the massive exploration of convolutional architectures. In this paper, we…

Machine Learning · Computer Science 2020-02-10 Giuseppe Marra , Francesco Giannini , Michelangelo Diligenti , Marco Gori

Deep generative models such as conditional variational autoencoders (CVAEs) have shown great promise for predicting trajectories of surrounding agents in autonomous vehicle planning. State-of-the-art models have achieved remarkable accuracy…

Robotics · Computer Science 2025-10-14 Yongxi Cao , Julian F. Schumann , Jens Kober , Joni Pajarinen , Arkady Zgonnikov

Computational fluid dynamics (CFD) analysis is widely used in engineering. Although CFD calculations are accurate, the computational cost associated with complex systems makes it difficult to obtain empirical equations between system…

Fluid Dynamics · Physics 2022-04-08 Mehrad Ansari , Heta A. Gandhi , David G. Foster , Andrew D. White

Symbolic regression automates the process of learning closed-form mathematical models from data. Standard approaches to symbolic regression, as well as newer deep learning approaches, rely on heuristic model selection criteria, heuristic…

Machine Learning · Statistics 2025-07-29 Roger Guimera , Marta Sales-Pardo

Instrumental variable (IV) regression is a standard strategy for learning causal relationships between confounded treatment and outcome variables from observational data by utilizing an instrumental variable, which affects the outcome only…

Machine Learning · Computer Science 2023-06-28 Liyuan Xu , Yutian Chen , Siddarth Srinivasan , Nando de Freitas , Arnaud Doucet , Arthur Gretton