To create a safe bicycle infrastructure system, this article develops an intelligent embedded learning system using a combination of deep neural networks. The learning system is used as a case study in the Northumbria region in England’s northeast. It is made up of three components: (a) input data unit, (b) knowledge processing unit, and (c) output unit. It is demonstrated that various infrastructure characteristics influence bikers’ safe interactions, which is used to estimate the riskiest age and gender rider groups. Two accurate prediction models are built, with a male accuracy of 88 per cent and a female accuracy of 95 per cent. The findings concluded that different infrastructures pose varying levels of risk to users of different ages and genders. Certain aspects of the infrastructure are hazardous to all bikers. However, the cyclist’s characteristics determine the level of risk that any infrastructure feature presents. Following validation, the built learning system is interoperable under various scenarios, including current heterogeneous and future semi-autonomous and autonomous transportation systems. The results contribute towards understanding the risk variation of various infrastructure types. The study’s findings will help to improve safety and lead to the construction of a sustainable integrated cycling transportation system.