DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function.

Motivation: Predicting protein structures with high accuracy is a critical challenge for the broad community of life sciences and industry. Despite progress made by deep neural networks like AlphaFold2, there is a need for further improvements in the quality of detailed structures, such as side-chains, along with protein backbone structures.

Results: Building upon the successes of AlphaFold2, the modifications we made include changing the losses of side-chain torsion angles and frame aligned point error, adding loss functions for side chain confidence and secondary structure prediction, and replacing template feature generation with a new alignment method based on conditional random fields.

Toward On-line Parameter Estimation of Concentric Tube Robots Using a Mechanics-based Kinematic Model.

Although existing mechanics-based models of concentric tube robots have been experimentally demonstrated to approximate the actual kinematics, determining accurate estimates of model parameters remains difficult due to the complex relationship between the parameters and available measurements. Further, because the mechanics-based models neglect some phenomena like friction, nonlinear elasticity, and cross section deformation, it is also not clear if model error is due to model simplification or to parameter estimation errors. The parameters of the superelastic materials used in these robots can be slowly time-varying, necessitating periodic re-estimation.

A minimum attention control law for ball catching.

Digital implementations of control laws typically involve discretization with respect to both time and space, and a control law that can achieve a task at coarser levels of discretization can be said to require less control attention, and also reduced implementation costs. One means of quantitatively capturing the attention of a control law is to measure the rate of change of the control with respect to changes in state and time. In this paper we present an attention-minimizing control law for ball catching and other target tracking tasks based on Brockett's attention criterion.

Kinematic feedback control laws for generating natural arm movements.

We propose a stochastic optimal feedback control law for generating natural robot arm motions. Our approach, inspired by the minimum variance principle of Harris and Wolpert (1998 Nature 394 780-4) and the optimal feedback control principles put forth by Todorov and Jordan (2002 Nature Neurosci. 5 1226-35) for explaining human movements, differs in two crucial respects: (i) the endpoint variance is minimized in joint space rather than Cartesian hand space, and (ii) we ignore the dynamics and instead consider only the second-order differential kinematics.