pwc-archive/papers-with-abstracts huggingface dataset:
Distance-aware Molecule Graph Attention Network for Drug-Target Binding Affinity Prediction
Authors: Jingbo Zhou, Shuangli Li, Liang Huang, Haoyi Xiong, Fan Wang, Tong Xu, Hui Xiong, Dejing Dou
Date: 2020-12-17 00:00:00
Tasks: Drug Discovery, Graph Attention, Knowledge Graphs, Position

Accurately predicting the binding affinity between drugs and proteins is an essential step for computational drug discovery. Since graph neural networks (GNNs) have demonstrated remarkable success in various graph-related tasks, GNNs have been considered as a promising tool to improve the binding affinity prediction in recent years. However, most of the existing GNN architectures can only encode the topological graph structure of drugs and proteins without considering the relative spatial information among their atoms. Whereas, different from other graph datasets such as social networks and commonsense knowledge graphs, the relative spatial position and chemical bonds among atoms have significant impacts on the binding affinity. To this end, in this paper, we propose a diStance-aware Molecule graph Attention Network (S-MAN) tailored to drug-target binding affinity prediction. As a dedicated solution, we first propose a position encoding mechanism to integrate the topological structure and spatial position information into the constructed pocket-ligand graph. Moreover, we propose a novel edge-node hierarchical attentive aggregation structure which has edge-level aggregation and node-level aggregation. The hierarchical attentive aggregation can capture spatial dependencies among atoms, as well as fuse the position-enhanced information with the capability of discriminating multiple spatial relations among atoms. Finally, we conduct extensive experiments on two standard datasets to demonstrate the effectiveness of S-MAN.
Interval propagation through the discrete Fourier transform
Authors: Marco De Angelis, Marco Behrendt, Liam Comerford, Yuanjin Zhang, Michael Beer
Date: 2020-12-17 00:00:00

We present an algorithm for the forward propagation of intervals through the discrete Fourier transform. The algorithm yields best-possible bounds when computing the amplitude of the Fourier transform for real and complex valued sequences. We show that computing the exact bounds of the amplitude can be achieved with an exhaustive examination of all possible corners of the interval domain. However, because the number of corners increases exponentially with the number of intervals, such method is infeasible for large interval signals. We provide an algorithm that does not need such an exhaustive search, and show that the best possible bounds can be obtained propagating complex pairs only from the convex hull of endpoints at each term of the Fourier series. Because the convex hull is always tightly inscribed in the respective rigorous bounding box resulting from interval arithmetic, we conclude that the obtained bounds are guaranteed to enclose the true values.
SAR Image Autofocusing using Wirtinger calculus and Cauchy regularization
Authors: Zi-Yao Zhang, Odysseas Pappas, Alin Achim
Date: 2020-12-17 00:00:00
Tasks: Image Reconstruction

In this paper, an optimization model using Cauchy regularization is proposed for simultaneous SAR image reconstruction and autofocusing. A coordinate descent framework in which the desired image and the phase errors are optimized alternatively is designed to solve the model. For the subproblem of estimating the image, we utilize the techniques of Wirtinger calculus to directly minimize the cost function which involves complex variables. We also utilise a state-of-the-art, sparsity-enforcing Cauchy regularizer. The proposed method is demonstrated to give impressive autofocusing results by conducting experiments on both simulated scene and real SAR image.
End-to-end Deep Object Tracking with Circular Loss Function for Rotated Bounding Box
Authors: Vladislav Belyaev, Aleksandra Malysheva, Aleksei Shpilman
Date: 2020-12-17 00:00:00
Tasks: Autonomous Driving, Deep Learning, Object, Object Tracking, Video Object Tracking

The task object tracking is vital in numerous applications such as autonomous driving, intelligent surveillance, robotics, etc. This task entails the assigning of a bounding box to an object in a video stream, given only the bounding box for that object on the first frame. In 2015, a new type of video object tracking (VOT) dataset was created that introduced rotated bounding boxes as an extension of axis-aligned ones. In this work, we introduce a novel end-to-end deep learning method based on the Transformer Multi-Head Attention architecture. We also present a new type of loss function, which takes into account the bounding box overlap and orientation. Our Deep Object Tracking model with Circular Loss Function (DOTCL) shows an considerable improvement in terms of robustness over current state-of-the-art end-to-end deep learning models. It also outperforms state-of-the-art object tracking methods on VOT2018 dataset in terms of expected average overlap (EAO) metric.
Rank-One Measurements of Low-Rank PSD Matrices Have Small Feasible Sets
Authors: T. Mitchell Roddenberry, Santiago Segarra, Anastasios Kyrillidis
Date: 2020-12-17 00:00:00

We study the role of the constraint set in determining the solution to low-rank, positive semidefinite (PSD) matrix sensing problems. The setting we consider involves rank-one sensing matrices: In particular, given a set of rank-one projections of an approximately low-rank PSD matrix, we characterize the radius of the set of PSD matrices that satisfy the measurements. This result yields a sampling rate to guarantee singleton solution sets when the true matrix is exactly low-rank, such that the choice of the objective function or the algorithm to be used is inconsequential in its recovery. We discuss applications of this contribution and compare it to recent literature regarding implicit regularization for similar problems. We demonstrate practical implications of this result by applying conic projection methods for PSD matrix recovery without incorporating low-rank regularization.
MAGNet: Multi-agent Graph Network for Deep Multi-agent Reinforcement Learning
Authors: Aleksandra Malysheva, Daniel Kudenko, Aleksei Shpilman
Date: 2020-12-17 00:00:00
Tasks: Deep Reinforcement Learning, Multi-agent Reinforcement Learning, reinforcement-learning, Reinforcement Learning, Reinforcement Learning (RL)

Over recent years, deep reinforcement learning has shown strong successes in complex single-agent tasks, and more recently this approach has also been applied to multi-agent domains. In this paper, we propose a novel approach, called MAGNet, to multi-agent reinforcement learning that utilizes a relevance graph representation of the environment obtained by a self-attention mechanism, and a message-generation technique. We applied our MAGnet approach to the synthetic predator-prey multi-agent environment and the Pommerman game and the results show that it significantly outperforms state-of-the-art MARL solutions, including Multi-agent Deep Q-Networks (MADQN), Multi-agent Deep Deterministic Policy Gradient (MADDPG), and QMIX
End-to-End Human Pose and Mesh Reconstruction with Transformers
Authors: Kevin Lin, Lijuan Wang, Zicheng Liu
Date: 2020-12-17 00:00:00
Proceeding: CVPR 2021 1
Tasks: 3D Absolute Human Pose Estimation, 3D Hand Pose Estimation, 3D Human Pose Estimation

We present a new method, called MEsh TRansfOrmer (METRO), to reconstruct 3D human pose and mesh vertices from a single image. Our method uses a transformer encoder to jointly model vertex-vertex and vertex-joint interactions, and outputs 3D joint coordinates and mesh vertices simultaneously. Compared to existing techniques that regress pose and shape parameters, METRO does not rely on any parametric mesh models like SMPL, thus it can be easily extended to other objects such as hands. We further relax the mesh topology and allow the transformer self-attention mechanism to freely attend between any two vertices, making it possible to learn non-local relationships among mesh vertices and joints. With the proposed masked vertex modeling, our method is more robust and effective in handling challenging situations like partial occlusions. METRO generates new state-of-the-art results for human mesh reconstruction on the public Human3.6M and 3DPW datasets. Moreover, we demonstrate the generalizability of METRO to 3D hand reconstruction in the wild, outperforming existing state-of-the-art methods on FreiHAND dataset. Code and pre-trained models are available at https://github.com/microsoft/MeshTransformer.
Game-theoretic Models of Moral and Other-Regarding Agents
Authors: Gabriel Istrate
Date: 2020-12-17 00:00:00
Tasks: Form

We investigate Kantian equilibria in finite normal form games, a class of non-Nashian, morally motivated courses of action that was recently proposed in the economics literature. We highlight a number of problems with such equilibria, including computational intractability, a high price of miscoordination, and expensive/problematic extension to general normal form games. We point out that such a proper generalization will likely involve the concept of program equilibrium. Finally we propose some general, intuitive, computationally tractable, other-regarding equilibria related to Kantian equilibria, as well as a class of courses of action that interpolates between purely self-regarding and Kantian behavior.
Describing the Structural Phenotype of the Glaucomatous Optic Nerve Head Using Artificial Intelligence
Authors: Satish K. Panda, Haris Cheong, Tin A. Tun, Sripad K. Devella, Ramaswami Krishnadas, Martin L. Buist, Shamira Perera, Ching-Yu Cheng, Tin Aung, Alexandre H. Thiéry, Michaël J. A. Girard
Date: 2020-12-17 00:00:00
Tasks: Diagnostic, Prognosis, Specificity

The optic nerve head (ONH) typically experiences complex neural- and connective-tissue structural changes with the development and progression of glaucoma, and monitoring these changes could be critical for improved diagnosis and prognosis in the glaucoma clinic. The gold-standard technique to assess structural changes of the ONH clinically is optical coherence tomography (OCT). However, OCT is limited to the measurement of a few hand-engineered parameters, such as the thickness of the retinal nerve fiber layer (RNFL), and has not yet been qualified as a stand-alone device for glaucoma diagnosis and prognosis applications. We argue this is because the vast amount of information available in a 3D OCT scan of the ONH has not been fully exploited. In this study we propose a deep learning approach that can: \textbf{(1)} fully exploit information from an OCT scan of the ONH; \textbf{(2)} describe the structural phenotype of the glaucomatous ONH; and that can \textbf{(3)} be used as a robust glaucoma diagnosis tool. Specifically, the structural features identified by our algorithm were found to be related to clinical observations of glaucoma. The diagnostic accuracy from these structural features was $92.0 \pm 2.3 \%$ with a sensitivity of $90.0 \pm 2.4 \% $ (at $95 \%$ specificity). By changing their magnitudes in steps, we were able to reveal how the morphology of the ONH changes as one transitions from a `non-glaucoma' to a `glaucoma' condition. We believe our work may have strong clinical implication for our understanding of glaucoma pathogenesis, and could be improved in the future to also predict future loss of vision.
On the performance of deep learning for numerical optimization: an application to protein structure prediction
Authors: Hojjat Rakhshani, Lhassane Idoumghar, Soheila Ghambari, Julien Lepagnot, Mathieu Brévilliers
Date: 2020-12-17 00:00:00
Tasks: global-optimization, GPU, Neural Architecture Search, Protein Structure Prediction

Deep neural networks have recently drawn considerable attention to build and evaluate artificial learning models for perceptual tasks. Here, we present a study on the performance of the deep learning models to deal with global optimization problems. The proposed approach adopts the idea of the neural architecture search (NAS) to generate efficient neural networks for solving the problem at hand. The space of network architectures is represented using a directed acyclic graph and the goal is to find the best architecture to optimize the objective function for a new, previously unknown task. Different from proposing very large networks with GPU computational burden and long training time, we focus on searching for lightweight implementations to find the best architecture. The performance of NAS is first analyzed through empirical experiments on CEC 2017 benchmark suite. Thereafter, it is applied to a set of protein structure prediction (PSP) problems. The experiments reveal that the generated learning models can achieve competitive results when compared to hand-designed algorithms; given enough computational budget
Model-free and Bayesian Ensembling Model-based Deep Reinforcement Learning for Particle Accelerator Control Demonstrated on the FERMI FEL
Authors: Simon Hirlaender, Niky Bruchon
Date: 2020-12-17 00:00:00
Tasks: Deep Reinforcement Learning, model, Policy Gradient Methods, Q-Learning, reinforcement-learning, Reinforcement Learning, Reinforcement Learning (RL)

Reinforcement learning holds tremendous promise in accelerator controls. The primary goal of this paper is to show how this approach can be utilised on an operational level on accelerator physics problems. Despite the success of model-free reinforcement learning in several domains, sample-efficiency still is a bottle-neck, which might be encompassed by model-based methods. We compare well-suited purely model-based to model-free reinforcement learning applied to the intensity optimisation on the FERMI FEL system. We find that the model-based approach demonstrates higher representational power and sample-efficiency, while the asymptotic performance of the model-free method is slightly superior. The model-based algorithm is implemented in a DYNA-style using an uncertainty aware model, and the model-free algorithm is based on tailored deep Q-learning. In both cases, the algorithms were implemented in a way, which presents increased noise robustness as omnipresent in accelerator control problems. Code is released in https://github.com/MathPhysSim/FERMI_RL_Paper.
Continuous Speech Separation Using Speaker Inventory for Long Multi-talker Recording
Authors: Cong Han, Yi Luo, Chenda Li, Tianyan Zhou, Keisuke Kinoshita, Shinji Watanabe, Marc Delcroix, Hakan Erdogan, John R. Hershey, Nima Mesgarani, Zhuo Chen
Date: 2020-12-17 00:00:00
Tasks: Clustering, Speech Separation

Leveraging additional speaker information to facilitate speech separation has received increasing attention in recent years. Recent research includes extracting target speech by using the target speaker's voice snippet and jointly separating all participating speakers by using a pool of additional speaker signals, which is known as speech separation using speaker inventory (SSUSI). However, all these systems ideally assume that the pre-enrolled speaker signals are available and are only evaluated on simple data configurations. In realistic multi-talker conversations, the speech signal contains a large proportion of non-overlapped regions, where we can derive robust speaker embedding of individual talkers. In this work, we adopt the SSUSI model in long recordings and propose a self-informed, clustering-based inventory forming scheme for long recording, where the speaker inventory is fully built from the input signal without the need for external speaker signals. Experiment results on simulated noisy reverberant long recording datasets show that the proposed method can significantly improve the separation performance across various conditions.
Near-Optimal Statistical Query Hardness of Learning Halfspaces with Massart Noise
Authors: Ilias Diakonikolas, Daniel M. Kane
Date: 2020-12-17 00:00:00
Tasks: Learning Theory, PAC learning

We study the problem of PAC learning halfspaces with Massart noise. Given labeled samples $(x, y)$ from a distribution $D$ on $\mathbb{R}^{d} \times \{ \pm 1\}$ such that the marginal $D_x$ on the examples is arbitrary and the label $y$ of example $x$ is generated from the target halfspace corrupted by a Massart adversary with flipping probability $\eta(x) \leq \eta \leq 1/2$, the goal is to compute a hypothesis with small misclassification error. The best known $\mathrm{poly}(d, 1/\epsilon)$-time algorithms for this problem achieve error of $\eta+\epsilon$, which can be far from the optimal bound of $\mathrm{OPT}+\epsilon$, where $\mathrm{OPT} = \mathbf{E}_{x \sim D_x} [\eta(x)]$. While it is known that achieving $\mathrm{OPT}+o(1)$ error requires super-polynomial time in the Statistical Query model, a large gap remains between known upper and lower bounds. In this work, we essentially characterize the efficient learnability of Massart halfspaces in the Statistical Query (SQ) model. Specifically, we show that no efficient SQ algorithm for learning Massart halfspaces on $\mathbb{R}^d$ can achieve error better than $\Omega(\eta)$, even if $\mathrm{OPT} = 2^{-\log^{c} (d)}$, for any universal constant $c \in (0, 1)$. Furthermore, when the noise upper bound $\eta$ is close to $1/2$, our error lower bound becomes $\eta - o_{\eta}(1)$, where the $o_{\eta}(1)$ term goes to $0$ when $\eta$ approaches $1/2$. Our results provide strong evidence that known learning algorithms for Massart halfspaces are nearly best possible, thereby resolving a longstanding open problem in learning theory.
Image-Based Jet Analysis
Authors: Michael Kagan
Date: 2020-12-17 00:00:00
Tasks: Anomaly Detection, General Classification

Image-based jet analysis is built upon the jet image representation of jets that enables a direct connection between high energy physics and the fields of computer vision and deep learning. Through this connection, a wide array of new jet analysis techniques have emerged. In this text, we survey jet image based classification models, built primarily on the use of convolutional neural networks, examine the methods to understand what these models have learned and what is their sensitivity to uncertainties, and review the recent successes in moving these models from phenomenological studies to real world application on experiments at the LHC. Beyond jet classification, several other applications of jet image based techniques, including energy estimation, pileup noise reduction, data generation, and anomaly detection, are discussed.
The Meccano of life
Authors: Pierre Zofel
Date: 2008-08-13 00:00:00

This article is interested in the origin of the genetic code, it puts forward a scenario of a simultaneous selection of the bases and amino acids and setting up of a correlation between them. Each amino acid is associated with a pair of its own kind, called the binding pair and each binding pair is associated with the codon(s) corresponding to the same amino acid. An explanation is also proposed about the origin of the start and stop codons.
Deep Molecular Dreaming: Inverse machine learning for de-novo molecular design and interpretability with surjective representations
Authors: Cynthia Shen, Mario Krenn, Sagi Eppel, Alan Aspuru-Guzik
Date: 2020-12-17 00:00:00
Tasks: BIG-bench Machine Learning

Computer-based de-novo design of functional molecules is one of the most prominent challenges in cheminformatics today. As a result, generative and evolutionary inverse designs from the field of artificial intelligence have emerged at a rapid pace, with aims to optimize molecules for a particular chemical property. These models 'indirectly' explore the chemical space; by learning latent spaces, policies, distributions or by applying mutations on populations of molecules. However, the recent development of the SELFIES string representation of molecules, a surjective alternative to SMILES, have made possible other potential techniques. Based on SELFIES, we therefore propose PASITHEA, a direct gradient-based molecule optimization that applies inceptionism techniques from computer vision. PASITHEA exploits the use of gradients by directly reversing the learning process of a neural network, which is trained to predict real-valued chemical properties. Effectively, this forms an inverse regression model, which is capable of generating molecular variants optimized for a certain property. Although our results are preliminary, we observe a shift in distribution of a chosen property during inverse-training, a clear indication of PASITHEA's viability. A striking property of inceptionism is that we can directly probe the model's understanding of the chemical space it was trained on. We expect that extending PASITHEA to larger datasets, molecules and more complex properties will lead to advances in the design of new functional molecules as well as the interpretation and explanation of machine learning models.
On Exploiting Hitting Sets for Model Reconciliation
Authors: Stylianos Loukas Vasileiou, Alessandro Previti, William Yeoh
Date: 2020-12-16 00:00:00
Tasks: model

In human-aware planning, a planning agent may need to provide an explanation to a human user on why its plan is optimal. A popular approach to do this is called model reconciliation, where the agent tries to reconcile the differences in its model and the human's model such that the plan is also optimal in the human's model. In this paper, we present a logic-based framework for model reconciliation that extends beyond the realm of planning. More specifically, given a knowledge base $KB_1$ entailing a formula $\varphi$ and a second knowledge base $KB_2$ not entailing it, model reconciliation seeks an explanation, in the form of a cardinality-minimal subset of $KB_1$, whose integration into $KB_2$ makes the entailment possible. Our approach, based on ideas originating in the context of analysis of inconsistencies, exploits the existing hitting set duality between minimal correction sets (MCSes) and minimal unsatisfiable sets (MUSes) in order to identify an appropriate explanation. However, differently from those works targeting inconsistent formulas, which assume a single knowledge base, MCSes and MUSes are computed over two distinct knowledge bases. We conclude our paper with an empirical evaluation of the newly introduced approach on planning instances, where we show how it outperforms an existing state-of-the-art solver, and generic non-planning instances from recent SAT competitions, for which no other solver exists.