DeepAtom: A Framework for Protein-Ligand Binding Affinity Prediction

The cornerstone of computational drug design is the calculation of binding affinity between two biological counterparts, especially a chemical compound, i.e., a ligand, and a protein. Predicting the strength of protein-ligand binding with reasonable accuracy is critical for drug discovery. In this paper, we propose a data-driven framework named DeepAtom to accurately predict the protein-ligand binding affinity. With 3D Convolutional Neural Network (3D-CNN) architecture, DeepAtom could automatically extract binding related atomic interaction patterns from the voxelized complex structure. Compared with the other CNN based approaches, our light-weight model design effectively improves the model representational capacity, even with the limited available training data. With validation experiments on the PDBbind v.2016 benchmark and the independent Astex Diverse Set, we demonstrate that the less feature engineering dependent DeepAtom approach consistently outperforms the other state-of-the-art scoring methods. We also compile and propose a new benchmark dataset to further improve the model performances. With the new dataset as training input, DeepAtom achieves Pearson's R=0.83 and RMSE=1.23 pK units on the PDBbind v.2016 core set. The promising results demonstrate that DeepAtom models can be potentially adopted in computational drug development protocols such as molecular docking and virtual screening.

Algorithmic Design and Implementation of Unobtrusive Multistatic Serial LiDAR Image

To fully understand interactions between marine hydrokinetic (MHK) equipment and marine animals, a fast and effective monitoring system is required to capture relevant information whenever underwater animals appear. A new automated underwater imaging system composed of LiDAR (Light Detection and Ranging) imaging hardware and a scene understanding software module named Unobtrusive Multistatic Serial LiDAR Imager (UMSLI) to supervise the presence of animals near turbines. UMSLI integrates the front end LiDAR hardware and a series of software modules to achieve image preprocessing, detection, tracking, segmentation and classification in a hierarchical manner.

Comfort-Centered Design of a Lightweight and Backdrivable Knee Exoskeleton

This paper presents design principles for comfort-centered wearable robots and their application in a lightweight and backdrivable knee exoskeleton. The mitigation of discomfort is treated as mechanical design and control issues and three solutions are proposed in this paper: 1) a new wearable structure optimizes the strap attachment configuration and suit layout to ameliorate excessive shear forces of conventional wearable structure design; 2) rolling knee joint and double-hinge mechanisms reduce the misalignment in the sagittal and frontal plane, without increasing the mechanical complexity and inertia, respectively; 3) a low impedance mechanical transmission reduces the reflected inertia and damping of the actuator to human, thus the exoskeleton is highly-backdrivable. Kinematic simulations demonstrate that misalignment between the robot joint and knee joint can be reduced by 74% at maximum knee flexion. In experiments, the exoskeleton in the unpowered mode exhibits 1.03 Nm root mean square (RMS) low resistive torque. The torque control experiments demonstrate 0.31 Nm RMS torque tracking error in three human subjects.

FoldingZero: Protein Folding from Scratch in Hydrophobic-Polar Model

De novo protein structure prediction from amino acid sequence is one of the most challenging problems in computational biology. As one of the extensively explored mathematical models for protein folding, Hydrophobic-Polar (HP) model enables thorough investigation of protein structure formation and evolution. Although HP model discretizes the conformational space and simplifies the folding energy function, it has been proven to be an NP-complete problem. In this paper, we propose a novel protein folding framework FoldingZero, self-folding a de novo protein 2D HP structure from scratch based on deep reinforcement learning. FoldingZero features the coupled approach of a two-head (policy and value heads) deep convolutional neural network (HPNet) and a regularized Upper Confidence Bounds for Trees (R-UCT). It is trained solely by a reinforcement learning algorithm, which improves HPNet and R-UCT iteratively through iterative policy optimization. Without any supervision and domain knowledge, FoldingZero not only achieves comparable results, but also learns the latent folding knowledge to stabilize the structure. Without exponential computation, FoldingZero shows promising potential to be adopted for real-world protein properties prediction.

The Power of Complementary Regularizers: Image Recovery via Transform Learning and Low-Rank Modeling

Recent works on adaptive sparse and on low-rank signal modeling have demonstrated their usefulness in various image / video processing applications. Patch-based methods exploit local patch sparsity, whereas other works apply low-rankness of grouped patches to exploit image non-local structures. However, using either approach alone usually limits performance in image reconstruction or recovery applications. In this work, we propose a simultaneous sparsity and low-rank model, dubbed STROLLR, to better represent natural images. In order to fully utilize both the local and non-local image properties, we develop an image restoration framework using a transform learning scheme with joint low-rank regularization. The approach owes some of its computational efficiency and good performance to the use of transform learning for adaptive sparse representation rather than the popular synthesis dictionary learning algorithms, which involve approximation of NP-hard sparse coding and expensive learning steps. We demonstrate the proposed framework in various applications to image denoising, inpainting, and compressed sensing based magnetic resonance imaging. Results show promising performance compared to state-of-the-art competing methods.

Global Geometry of Multichannel Sparse Blind Deconvolution on the Sphere

Multichannel blind deconvolution is the problem of recovering an unknown signal $f$ and multiple unknown channels $x_i$ from convolutional measurements $y_i=x_i \circledast f$ ($i=1,2,\dots,N$). We consider the case where the $x_i$'s are sparse, and convolution with $f$ is invertible. Our nonconvex optimization formulation solves for a filter $h$ on the unit sphere that produces sparse output $y_i\circledast h$. Under some technical assumptions, we show that all local minima of the objective function correspond to the inverse filter of $f$ up to an inherent sign and shift ambiguity, and all saddle points have strictly negative curvatures. This geometric structure allows successful recovery of $f$ and $x_i$ using a simple manifold gradient descent algorithm with random initialization. Our theoretical findings are complemented by numerical experiments, which demonstrate superior performance of the proposed approach over the previous methods.

Blind Gain and Phase Calibration via Sparse Spectral Methods

Blind gain and phase calibration (BGPC) is a bilinear inverse problem involving the determination of unknown gains and phases of the sensing system, and the unknown signal, jointly. BGPC arises in numerous applications, e.g., blind albedo estimation in inverse rendering, synthetic aperture radar autofocus, and sensor array auto-calibration. In some cases, sparse structure in the unknown signal alleviates the ill-posedness of BGPC. Recently there has been renewed interest in solutions to BGPC with careful analysis of error bounds. In this paper, we formulate BGPC as an eigenvalue/eigenvector problem, and propose to solve it via power iteration, or in the sparsity or joint sparsity case, via truncated power iteration. Under certain assumptions, the unknown gains, phases, and the unknown signal can be recovered simultaneously. Numerical experiments show that power iteration algorithms work not only in the regime predicted by our main results, but also in regimes where theoretical analysis is limited. We also show that our power iteration algorithms for BGPC compare favorably with competing algorithms in adversarial conditions, e.g., with noisy measurement or with a bad initial estimate.

Strategically knowing how

In this paper, we propose a single-agent logic of goal-directed knowing how extending the standard epistemic logic of knowing that with a new knowing how operator. The semantics of the new operator is based on the idea that knowing how to achieve $\phi$ means that there exists a (uniform) strategy such that the agent knows that it can make sure $\phi$. We give an intuitive axiomatization of our logic and prove the soundness, completeness, and decidability of the logic. The crucial axioms relating knowing that and knowing how illustrate our understanding of knowing how in this setting. This logic can be used in representing both knowledge-that and knowledge-how.

Joint Dimensionality Reduction for Two Feature Vectors

Many machine learning problems, especially multi-modal learning problems, have two sets of distinct features (e.g., image and text features in news story classification, or neuroimaging data and neurocognitive data in cognitive science research). This paper addresses the joint dimensionality reduction of two feature vectors in supervised learning problems. In particular, we assume a discriminative model where low-dimensional linear embeddings of the two feature vectors are sufficient statistics for predicting a dependent variable. We show that a simple algorithm involving singular value decomposition can accurately estimate the embeddings provided that certain sample complexities are satisfied, without specifying the nonlinear link function (regressor or classifier). The main results establish sample complexities under multiple settings. Sample complexities for different link functions only differ by constant factors.

A Dynamic Epistemic Framework for Conformant Planning

In this paper, we introduce a lightweight dynamic epistemic logical framework for automated planning under initial uncertainty. We reduce plan verification and conformant planning to model checking problems of our logic. We show that the model checking problem of the iteration-free fragment is PSPACE-complete. By using two non-standard (but equivalent) semantics, we give novel model checking algorithms to the full language and the iteration-free language.