It looks like you are trying to use FACTORIE with clojure. As someone who both loves clojure and works at the lab that builds FACTORIE, I wouldn't recommend this. FACTORIE's codebase is written in a very imperative style, and is filled with mutable state. If I got my hands on a FACTORIE object in clojure I would find it very disorienting. FACTORIE also makes aggressive use of scala features in ways that won't translate well to compiled java (which is the level at which clojure and scala must interact).
If you already have a large clojure codebase and need a good implementation of a linear-chain CRF (based on your use of ChainModel
above), I'd recommend looking at MALLET. It's pure java and was developed by the same lab.