Cyber-physical systems (CPS) connect the physical and digital domains and are often realized as spatially distributed. CPS is built on the Internet of Things (IoT) and Internet of Services, which use cloud architecture to link a swarm of devices over a decentralized network. Modern CPSs are undergoing a foundational shift as Industry 4.0 is continually expanding its boundaries of digitization. From automating the industrial manufacturing process to interconnecting sensor devices within buildings, Industry 4.0 is about developing solutions for the digitized industry. An extensive amount of engineering efforts are put to design dynamically scalable and robust automation solutions that have the capacity to integrate heterogeneous CPS. Such heterogeneous systems must be able to communicate and exchange information with each other in real-time even if they are based on different underlying technologies, protocols, or semantic definitions in the form of ontologies. This development is subject to interoperability challenges and knowledge gaps that are addressed by engineers and researchers, in particular, machine learning approaches are considered to automate costly engineering processes. For example, challenges related to predictive maintenance operations and automatic translation of messages transmitted between heterogeneous devices are investigated using supervised and unsupervised machine learning approaches. In this thesis, a machine learning-based collaboration and automation-oriented IIoT framework named Cloud-based Collaborative Learning (CCL) is developed. CCL is based on a service-oriented architecture (SOA) offering a scalable CPS framework that provides machine learning-as-a-Service (MLaaS). Furthermore, interoperability in the context of the IIoT is investigated. I consider the ontology of an IoT device to be its language, and the structure of that ontology to be its grammar. In particular, the use of aggregated language and structural encoders is investigated to improve the alignment of entities in heterogeneous ontologies. Existing techniques of entity alignment are based on different approaches to integrating structural information, which overlook the fact that even if a node pair has similar entity labels, they may not belong to the same ontological context, and vice versa. To address these challenges, a model based on a modification of the BERT_INT model on graph triples is developed. The developed model is an iterative model for alignment of heterogeneous IIoT ontologies enabling alignments within nodes as well as relations. When compared to the state-of-the-art BERT_INT, on DBPK15 language dataset the developed model exceeds the baseline model by (HR@1/10, MRR) of 2.1%. This motivated the development of a proof-of-concept for conducting an empirical investigation of the developed model for alignment between heterogeneous IIoT ontologies. For this purpose, a dataset was generated from smart building systems and SOSA and SSN ontologies graphs. Experiments and analysis including an ablation study on the proposed language and structural encoders demonstrate the effectiveness of the model. The suggested approach, on the other hand, highlights prospective future studies that may extend beyond the scope of a single thesis. For instance, to strengthen the ablation study, a generalized IIoT ontology that is designed for any type of IoT devices (beyond sensors), such as SAREF can be tested for ontology alignment. Next potential future work is to conduct a crowdsourcing process for generating a validation dataset for IIoT ontology alignment and annotations. Lastly, this work can be considered as a step towards enabling translation between heterogeneous IoT sensor devices, therefore, the proposed model can be extended to a translation module in which based on the ontology graphs of any device, the model can interpret the messages transmitted from that device. This idea is at an abstract level as of now and needs extensive efforts and empirical study for full maturity.