Abstract Objective.This paper presents data-driven solutions to address two challenges in the problem of linking neural data and behavior: (1) unsupervised analysis of behavioral data and automatic label generation from behavioral observations, and (2) extraction of subject-invariant features for the development of generalized neural decoding models. Approach. For behavioral analysis and label generation, an unsupervised method, which employs an autoencoder to transform behavioral data into a cluster-friendly feature space is presented. The model iteratively refines the assigned clusters with soft clustering assignment loss, and gradually improves the learned feature representations. To address subject variability in decoding neural activity, adversarial learning in combination with a long short-term memory-based adversarial variational autoencoder (LSTM-AVAE) model is employed. By using an adversary network to constrain the latent representations, the model captures shared information among subjects’ neural activity, making it proper for cross-subject transfer learning. Main results. The proposed approach is evaluated using cortical recordings of Thy1-GCaMP6s transgenic mice obtained via widefield calcium imaging during a motivational licking behavioral experiment. The results show that the proposed model achieves an accuracy of 89.7% in cross-subject neural decoding, outperforming other well-known autoencoder-based feature learning models. These findings suggest that incorporating an adversary network eliminates subject dependency in representations, leading to improved cross-subject transfer learning performance, while also demonstrating the effectiveness of LSTM-based models in capturing the temporal dependencies within neural data. Significance. Results demonstrate the feasibility of the proposed framework in unsupervised clustering and label generation of behavioral data, as well as achieving high accuracy in cross-subject neural decoding, indicating its potentials for relating neural activity to behavior.