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In-flight objects capture is extremely challenging. The robot is required to complete trajectory prediction, interception position calculation and motion planning in sequence within tens of milliseconds. As in-flight uneven objects are affected by various kinds of forces, motion prediction is difficult for a time-varying acceleration. In order to compensate the system's non-linearity, we introduce the Neural Acceleration Estimator (NAE) that estimates the varying acceleration by observing a small fragment of previous deflected trajectory. Moreover, end-to-end training with Differantiable Filter (NAE-DF) gives a supervision for measurement uncertainty and further improves the prediction accuracy. Experimental results show that motion prediction with NAE and NAE-DF is superior to other methods and has a good generalization performance on unseen objects. We test our methods on a robot, performing velocity control in real world and respectively achieve 83.3% and 86.7% success rate on a ploy urethane banana and a gourd. We also release an object in-flight dataset containing 1,500 trajectorys for uneven objects.