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The demand for anytime, anywhere, anyhow communications in future generation networks necessitates a paradigm shift from independent network services into a more harmonized system. This vision can be accomplished by integrating the existing and emerging access networks via a common Internet Protocol (IP) based platform. Nevertheless, owing to the inter-worked infrastructure, a malicious security threat in such a heterogeneous network is no more confined to its originating network domain, but can easily be propagated to other access networks. To address these security concerns, this paper proposes a biologically inspired security framework that governs the cooperation among network entities to identify security attacks, to perform security updates, and to inhibit attacks propagation in the heterogeneous network. The proposed framework incorporates two principal security components, in the form of anomaly detection framework and security control framework. Several plausible principles from two fields of biology, in particular the human immune system (HIS) and epidemiology have been adopted into the proposed security framework. Performance evaluation demonstrates the efficiency of the proposed biologically inspired security framework in detecting malicious anomalies such as denial-of-service (DoS), distributed DoS (DDoS), and worms, as well as restricting their propagations in the heterogeneous network.