Conditional random fields (CRF) are widely used for sequence labeling such as natural language processing and biological sequence analysis. Most CRF models use a linear potential function to represent the relationship between input features and output. However, in many real-world applications such as protein structure prediction and handwriting recognition, the relationship between input features and output is highly complex and nonlinear, which cannot be accurately modeled by a linear function. To model the nonlinear relationship between input and output we propose a new conditional probabilistic graphical model, Conditional Neural Fields (CNF), for sequence labeling. CNF extends CRF by adding one (or possibly more) middle layer between input and output. The middle layer consists of a number of gate functions, each acting as a local neuron or feature extractor to capture the nonlinear relationship between input and output. Therefore, conceptually CNF is much more expressive than CRF. Experiments on two widely-used benchmarks indicate that CNF performs significantly better than a number of popular methods. In particular, CNF is the best among approximately 10 machine learning methods for protein secondary structure prediction and also among a few of the best methods for handwriting recognition. 1