The generation of small molecule candidate (ligand) binding poses in its target protein pocket is important for computer-aided drug discovery. Typical rigid-body docking methods ignore the pocket flexibility of protein, while the more accurate pose generation using molecular dynamics is hindered by slow protein dynamics. We develop a tiered tensor transform (3T) algorithm to rapidly generate diverse protein-ligand complex conformations for both pose and affinity estimation in drug screening, requiring neither machine learning training nor lengthy dynamics computation, while maintaining both coarse-grain-like coordinated protein dynamics and atomistic-level details of the complex pocket. The 3T conformation structures we generate achieve significantly higher accuracy in active ligand classification than traditional ensemble docking using hundreds of experimental protein conformations. Furthermore, we demonstrate that 3T can be used to explore distant protein-ligand binding poses within the protein pocket. 3T structure transformation is decoupled from the system physics, making future usage in other computational scientific domains possible.
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Ordered sequences of data, specified with a join operation to combine sequences, serve as a foundation for the implementation of parallel functional algorithms. This abstract data type can be elegantly and efficiently implemented using balanced binary trees, where a join operation is provided to combine two trees and rebalance as necessary. In this work, we present a verified implementation and cost analysis of joinable red-black trees in $\textbf{calf}$, a dependent type theory for cost analysis. We implement red-black trees and auxiliary intermediate data structures in such a way that all correctness invariants are intrinsically maintained. Then, we describe and verify precise cost bounds on the operations, making use of the red-black tree invariants. Finally, we implement standard algorithms on sequences using the simple join-based signature and bound their cost in the case that red-black trees are used as the underlying implementation. All proofs are formally mechanized using the embedding of $\textbf{calf}$ in the Agda theorem prover.
The automatic projection filter is a recently developed numerical method for projection filtering that leverages sparse-grid integration and automatic differentiation. However, its accuracy is highly sensitive to the accuracy of the cumulant-generating function computed via the sparse-grid integration, which in turn is also sensitive to the choice of the bijection from the canonical hypercube to the state space. In this paper, we propose two new adaptive parametric bijections for the automatic projection filter. The first bijection relies on the minimization of Kullback--Leibler divergence, whereas the second method employs the sparse-grid Gauss--Hermite quadrature. The two new bijections allow the sparse-grid nodes to adaptively move within the high-density region of the state space, resulting in a substantially improved approximation while using only a small number of quadrature nodes. The practical applicability of the methodology is illustrated in three simulated nonlinear filtering problems.
Following complex instructions in conversational assistants can be quite daunting due to the shorter attention and memory spans when compared to reading the same instructions. Hence, when conversational assistants walk users through the steps of complex tasks, there is a need to structure the task into manageable pieces of information of the right length and complexity. In this paper, we tackle the recipes domain and convert reading structured instructions into conversational structured ones. We annotated the structure of instructions according to a conversational scenario, which provided insights into what is expected in this setting. To computationally model the conversational step's characteristics, we tested various Transformer-based architectures, showing that a token-based approach delivers the best results. A further user study showed that users tend to favor steps of manageable complexity and length, and that the proposed methodology can improve the original web-based instructional text. Specifically, 86% of the evaluated tasks were improved from a conversational suitability point of view.
Exhibiting an explicit Boolean function with a large high-order nonlinearity is an important problem in cryptography, coding theory, and computational complexity. We prove lower bounds on the second-order, third-order, and higher-order nonlinearities of some trace monomial Boolean functions. We prove lower bounds on the second-order nonlinearities of functions $\mathrm{tr}_n(x^7)$ and $\mathrm{tr}_n(x^{2^r+3})$ where $n=2r$. Among all trace monomials, our bounds match the best second-order nonlinearity lower bounds by \cite{Car08} and \cite{YT20} for odd and even $n$ respectively. We prove a lower bound on the third-order nonlinearity for functions $\mathrm{tr}_n(x^{15})$, which is the best third-order nonlinearity lower bound. For any $r$, we prove that the $r$-th order nonlinearity of $\mathrm{tr}_n(x^{2^{r+1}-1})$ is at least $2^{n-1}-2^{(1-2^{-r})n+\frac{r}{2^{r-1}}-1}- O(2^{\frac{n}{2}})$. For $r \ll \log_2 n$, this is the best lower bound among all explicit functions.
Beam selection for joint transmission in cell-free massive multi-input multi-output systems faces the problem of extremely high training overhead and computational complexity. The traffic-aware quality of service additionally complicates the beam selection problem. To address this issue, we propose a traffic-aware hierarchical beam selection scheme performed in a dual timescale. In the long-timescale, the central processing unit collects wide beam responses from base stations (BSs) to predict the power profile in the narrow beam space with a convolutional neural network, based on which the cascaded multiple-BS beam space is carefully pruned. In the short-timescale, we introduce a centralized reinforcement learning (RL) algorithm to maximize the satisfaction rate of delay w.r.t. beam selection within multiple consecutive time slots. Moreover, we put forward three scalable distributed algorithms including hierarchical distributed Lyapunov optimization, fully distributed RL, and centralized training with decentralized execution of RL to achieve better scalability and better tradeoff between the performance and the execution signal overhead. Numerical results demonstrate that the proposed schemes significantly reduce both model training cost and beam training overhead and are easier to meet the user-specific delay requirement, compared to existing methods.
A mainstream type of current self-supervised learning methods pursues a general-purpose representation that can be well transferred to downstream tasks, typically by optimizing on a given pretext task such as instance discrimination. In this work, we argue that existing pretext tasks inevitably introduce biases into the learned representation, which in turn leads to biased transfer performance on various downstream tasks. To cope with this issue, we propose Maximum Entropy Coding (MEC), a more principled objective that explicitly optimizes on the structure of the representation, so that the learned representation is less biased and thus generalizes better to unseen downstream tasks. Inspired by the principle of maximum entropy in information theory, we hypothesize that a generalizable representation should be the one that admits the maximum entropy among all plausible representations. To make the objective end-to-end trainable, we propose to leverage the minimal coding length in lossy data coding as a computationally tractable surrogate for the entropy, and further derive a scalable reformulation of the objective that allows fast computation. Extensive experiments demonstrate that MEC learns a more generalizable representation than previous methods based on specific pretext tasks. It achieves state-of-the-art performance consistently on various downstream tasks, including not only ImageNet linear probe, but also semi-supervised classification, object detection, instance segmentation, and object tracking. Interestingly, we show that existing batch-wise and feature-wise self-supervised objectives could be seen equivalent to low-order approximations of MEC. Code and pre-trained models are available at //github.com/xinliu20/MEC.
The development of autonomous agents which can interact with other agents to accomplish a given task is a core area of research in artificial intelligence and machine learning. Towards this goal, the Autonomous Agents Research Group develops novel machine learning algorithms for autonomous systems control, with a specific focus on deep reinforcement learning and multi-agent reinforcement learning. Research problems include scalable learning of coordinated agent policies and inter-agent communication; reasoning about the behaviours, goals, and composition of other agents from limited observations; and sample-efficient learning based on intrinsic motivation, curriculum learning, causal inference, and representation learning. This article provides a broad overview of the ongoing research portfolio of the group and discusses open problems for future directions.
Embedding entities and relations into a continuous multi-dimensional vector space have become the dominant method for knowledge graph embedding in representation learning. However, most existing models ignore to represent hierarchical knowledge, such as the similarities and dissimilarities of entities in one domain. We proposed to learn a Domain Representations over existing knowledge graph embedding models, such that entities that have similar attributes are organized into the same domain. Such hierarchical knowledge of domains can give further evidence in link prediction. Experimental results show that domain embeddings give a significant improvement over the most recent state-of-art baseline knowledge graph embedding models.
We advocate the use of implicit fields for learning generative models of shapes and introduce an implicit field decoder for shape generation, aimed at improving the visual quality of the generated shapes. An implicit field assigns a value to each point in 3D space, so that a shape can be extracted as an iso-surface. Our implicit field decoder is trained to perform this assignment by means of a binary classifier. Specifically, it takes a point coordinate, along with a feature vector encoding a shape, and outputs a value which indicates whether the point is outside the shape or not. By replacing conventional decoders by our decoder for representation learning and generative modeling of shapes, we demonstrate superior results for tasks such as shape autoencoding, generation, interpolation, and single-view 3D reconstruction, particularly in terms of visual quality.
Deep neural networks (DNNs) have been found to be vulnerable to adversarial examples resulting from adding small-magnitude perturbations to inputs. Such adversarial examples can mislead DNNs to produce adversary-selected results. Different attack strategies have been proposed to generate adversarial examples, but how to produce them with high perceptual quality and more efficiently requires more research efforts. In this paper, we propose AdvGAN to generate adversarial examples with generative adversarial networks (GANs), which can learn and approximate the distribution of original instances. For AdvGAN, once the generator is trained, it can generate adversarial perturbations efficiently for any instance, so as to potentially accelerate adversarial training as defenses. We apply AdvGAN in both semi-whitebox and black-box attack settings. In semi-whitebox attacks, there is no need to access the original target model after the generator is trained, in contrast to traditional white-box attacks. In black-box attacks, we dynamically train a distilled model for the black-box model and optimize the generator accordingly. Adversarial examples generated by AdvGAN on different target models have high attack success rate under state-of-the-art defenses compared to other attacks. Our attack has placed the first with 92.76% accuracy on a public MNIST black-box attack challenge.
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