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This paper proposes a novel natural facial expression recognition method that recognizes a sequence of dynamic facial expression images using the differential active appearance model (AAM) and manifold learning as follows. First, the differential-AAM features (DAFs) are computed by the difference of the AAM parameters between an input face image and a reference (neutral expression) face image. Second, manifold learning embeds the DAFs on the smooth and continuous feature space. Third, the input facial expression is recognized through two steps: (1) computing the distances between the input image sequence and gallery image sequences using directed Hausdorff distance (DHD) and (2) selecting the expression by a majority voting of k-nearest neighbors (k-NN) sequences in the gallery. The DAFs are robust and efficient for the facial expression analysis due to the elimination of the inter-person, camera, and illumination variations. Since the DAFs treat the neutral expression image as the reference image, the neutral expression image must be found effectively. This is done via the differential facial expression probability density model (DFEPDM) using the kernel density approximation of the positively directional DAFs changing from neutral to angry (happy, surprised) and negatively directional DAFs changing from angry (happy, surprised) to neutral. Then, a face image is considered to be the neutral expression if it has the maximum DFEPDM in the input sequences. Experimental results show that (1) the DAFs improve the facial expression recognition performance over conventional AAM features by 20% and (2) the sequence-based k-NN classifier provides a 95% facial expression recognition performance on the facial expression database (FED06).