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We introduce two Python frameworks to train neural networks on large datasets: Blocks and Fuel. Blocks is based on Theano, a linear algebra compiler with CUDA-support. It facilitates the training of complex neural network models by…

SparseChem provides fast and accurate machine learning models for biochemical applications. Especially, the package supports very high-dimensional sparse inputs, e.g., millions of features and millions of compounds. It is possible to train…

Machine Learning · Statistics 2022-03-10 Adam Arany , Jaak Simm , Martijn Oldenhof , Yves Moreau

In the realm of Business Process Management (BPM), process modeling plays a crucial role in translating complex process dynamics into comprehensible visual representations, facilitating the understanding, analysis, improvement, and…

Software Engineering · Computer Science 2024-07-01 Humam Kourani , Alessandro Berti , Daniel Schuster , Wil M. P. van der Aalst

Large Language Models (LLMs) have made great strides in areas such as language processing and computer vision. Despite the emergence of diverse techniques to improve few-shot learning capacity, current LLMs fall short in handling the…

Biomolecules · Quantitative Biology 2024-05-14 Xianggen Liu , Yan Guo , Haoran Li , Jin Liu , Shudong Huang , Bowen Ke , Jiancheng Lv

Neural networks have become integral to many fields due to their exceptional performance. The open-source community has witnessed a rapid influx of neural network (NN) repositories with fast-paced iterations, making it crucial for…

Software Engineering · Computer Science 2025-09-25 Xiaoning Ren , Yuhang Ye , Xiongfei Wu , Yueming Wu , Yinxing Xue

Neural processing units (NPUs) are gaining prominence in power-sensitive devices like client devices, with AI PCs being defined by their inclusion of these specialized processors. Running AI workloads efficiently on these devices requires…

Programming Languages · Computer Science 2025-07-22 Sarunas Kalade , Graham Schelle

In recent years, AI models that mine intrinsic patterns from molecular structures and protein sequences have shown promise in accelerating drug discovery. However, these methods partly lag behind real-world pharmaceutical approaches of…

Machine Learning · Computer Science 2023-10-17 Yizhen Luo , Xing Yi Liu , Kai Yang , Kui Huang , Massimo Hong , Jiahuan Zhang , Yushuai Wu , Zaiqing Nie

The molecular large language models have garnered widespread attention due to their promising potential on molecular applications. However, current molecular large language models face significant limitations in understanding molecules due…

Biomolecules · Quantitative Biology 2025-10-23 Zaifei Yang , Hong Chang , Ruibing Hou , Shiguang Shan , Xilin Chen

The rapid advancement of artificial intelligence, particularly autonomous agentic systems based on Large Language Models (LLMs), presents new opportunities to accelerate drug discovery by improving in-silico modeling and reducing dependence…

This paper presents the Model Gateway, a management platform for managing machine learning (ML) and scientific computational models in the drug discovery pipeline. The platform supports Large Language Model (LLM) Agents and Generative…

Software Engineering · Computer Science 2025-12-08 Yan-Shiun Wu , Nathan A. Morin

Large language models (LLMs) represent a significant advancement in integrating physical robots with AI-driven systems. We showcase the capabilities of our framework within the context of the real-world household competition. This research…

Robotics · Computer Science 2025-01-29 Shady Nasrat , Myungsu Kim , Seonil Lee , Jiho Lee , Yeoncheol Jang , Seung-joon Yi

Using language models (LMs) pre-trained in a self-supervised setting on large corpora and then fine-tuning for a downstream task has helped to deal with the problem of limited label data for supervised learning tasks such as Named Entity…

Computation and Language · Computer Science 2023-08-21 Pavlova Vera , Mohammed Makhlouf

Vision Language Models (VLMs) have shown strong performance on multimodal reasoning tasks, yet most evaluations focus on short videos and assume unconstrained computational resources. In industrial settings such as pharmaceutical content…

Computer Vision and Pattern Recognition · Computer Science 2026-01-09 Suyash Mishra , Qiang Li , Srikanth Patil , Satyanarayan Pati , Baddu Narendra

Sparse large language models (LLMs) with Mixture of Experts (MoE) and close to a trillion parameters are dominating the realm of most capable language models. However, the massive model scale poses significant challenges for the underlying…

The widespread application of Artificial Intelligence (AI) techniques has significantly influenced the development of new therapeutic agents. These computational methods can be used to design and predict the properties of generated…

Neural and Evolutionary Computing · Computer Science 2024-08-21 Arthur Cerveira , Frederico Kremer , Darling de Andrade Lourenço , Ulisses B Corrêa

Drug discovery can be viewed as a combinatorial search over an immense chemical space, motivating the development of deep generative models for de novo molecular design. Among these, GPT-based molecular language models (MLM) have shown…

Machine Learning · Computer Science 2026-02-02 Qianwei Yang , Dong Xu , Zhangfan Yang , Sisi Yuan , Zexuan Zhu , Jianqiang Li , Junkai Ji

Current pharmaceutical formulation development still strongly relies on the traditional trial-and-error approach by individual experiences of pharmaceutical scientists, which is laborious, time-consuming and costly. Recently, deep learning…

Machine Learning · Computer Science 2018-12-05 Yilong Yang , Zhuyifan Ye , Yan Su , Qianqian Zhao , Xiaoshan Li , Defang Ouyang

Large language models (LLMs) offer new opportunities for automated data extraction and property prediction across materials science, yet their use in superconductivity research remains limited. Here we construct a large experimental…

Materials Science · Physics 2025-12-12 Suman Itani , Yibo Zhang , Ranjit Itani , Jiadong Zang

Properties of molecules are indicative of their functions and thus are useful in many applications. With the advances of deep learning methods, computational approaches for predicting molecular properties are gaining increasing momentum.…

Quantitative Methods · Quantitative Biology 2021-07-07 Zhengyang Wang , Meng Liu , Youzhi Luo , Zhao Xu , Yaochen Xie , Limei Wang , Lei Cai , Qi Qi , Zhuoning Yuan , Tianbao Yang , Shuiwang Ji

In evidence-based medicine (EBM), defining a clinical question in terms of the specific patient problem aids the physicians to efficiently identify appropriate resources and search for the best available evidence for medical treatment. In…

Computation and Language · Computer Science 2019-11-12 Di Jin , Peter Szolovits