pwc-archive/papers-with-abstracts huggingface dataset:
PolyFold: an interactive visual simulator for distance-based protein folding
Authors: Andrew McGehee, Sutanu Bhattacharya, Rahmatullah Roche, Debswapna Bhattacharya
Date: 2020-02-14 00:00:00
Tasks: Protein Folding, Protein Structure Prediction, Stochastic Optimization

Recent advances in distance-based protein folding have led to a paradigm shift in protein structure prediction. Through sufficiently precise estimation of the inter-residue distance matrix for a protein sequence, it is now feasible to predict the correct folds for new proteins much more accurately than ever before. Despite the exciting progress, a dedicated visualization system that can dynamically capture the distance-based folding process is still lacking. Most molecular visualizers typically provide only a static view of a folded protein conformation, but do not capture the folding process. Even among the selected few graphical interfaces that do adopt a dynamic perspective, none of them are distance-based. Here we present PolyFold, an interactive visual simulator for dynamically capturing the distance-based protein folding process through real-time rendering of a distance matrix and its compatible spatial conformation as it folds in an intuitive and easy-to-use interface. PolyFold integrates highly convergent stochastic optimization algorithms with on-demand customizations and interactive manipulations to maximally satisfy the geometric constraints imposed by a distance matrix. PolyFold is capable of simulating the complex process of protein folding even on modest personal computers, thus making it accessible to the general public for fostering citizen science. Open source code of PolyFold is freely available for download at https://github.com/Bhattacharya-Lab/PolyFold. It is implemented in cross-platform Java and binary executables are available for macOS, Linux, and Windows.
Fine-Grained Visual Classification with Batch Confusion Norm
Authors: Yen-Chi Hsu, Cheng-Yao Hong, Ding-Jie Chen, Ming-Sui Lee, Davi Geiger, Tyng-Luh Liu
Date: 2019-10-28 00:00:00
Proceeding: None 2019 10
Tasks: Classification, Fine-Grained Image Classification, General Classification

We introduce a regularization concept based on the proposed Batch Confusion Norm (BCN) to address Fine-Grained Visual Classification (FGVC). The FGVC problem is notably characterized by its two intriguing properties, significant inter-class similarity and intra-class variations, which cause learning an effective FGVC classifier a challenging task. Inspired by the use of pairwise confusion energy as a regularization mechanism, we develop the BCN technique to improve the FGVC learning by imposing class prediction confusion on each training batch, and consequently alleviate the possible overfitting due to exploring image feature of fine details. In addition, our method is implemented with an attention gated CNN model, boosted by the incorporation of Atrous Spatial Pyramid Pooling (ASPP) to extract discriminative features and proper attentions. To demonstrate the usefulness of our method, we report state-of-the-art results on several benchmark FGVC datasets, along with comprehensive ablation comparisons.
Destruction from sky: Weakly supervised approach for destruction detection in satellite imagery
Authors: Muhammad Usman Ali, Waqas Sultani, Mohsen Ali
Date: 2020-04-01 00:00:00
Proceeding: ISPRS Journal of Photogrammetry and Remote Sensing 2020 4
Tasks: Change Detection

Natural and man-made disasters cause huge damage to built infrastructures and results in loss of human lives. The rehabilitation efforts and rescue operations are hampered by the non-availability of accurate and timely information regarding the location of damaged infrastructure and its extent. In this paper, we model the destruction in satellite imagery using a deep learning model employing a weakly-supervised approach. In stark contrast to previous approaches, instead of solving the problem as change detection (using pre and post-event images), we model to identify destruction itself using a single post-event image. To overcome the challenge of collecting pixel-level ground truth data mostly used during training, we only assume image-level labels, representing either destruction is present (at any location) in a given image or not. The proposed attention-based mechanism learns to identify the image-patches with destruction automatically under the sparsity constraint. Furthermore, to reduce false-positive and improve segmentation quality, a hard negative mining technique has been proposed that results in considerable improvement over baseline. To validate our approach, we have collected a new dataset containing destruction and non-destruction images from Indonesia, Yemen, Japan, and Pakistan. On testing-dataset, we obtained excellent destruction results with pixel-level accuracy of 93% and patch level accuracy of 91%. The source code and dataset will be made publicly available.
BATS: Binary ArchitecTure Search
Authors: Adrian Bulat, Brais Martinez, Georgios Tzimiropoulos
Date: 2020-03-03 00:00:00
Proceeding: ECCV 2020 8
Tasks: Binarization, Classification with Binary Neural Network, Neural Architecture Search

This paper proposes Binary ArchitecTure Search (BATS), a framework that drastically reduces the accuracy gap between binary neural networks and their real-valued counterparts by means of Neural Architecture Search (NAS). We show that directly applying NAS to the binary domain provides very poor results. To alleviate this, we describe, to our knowledge, for the first time, the 3 key ingredients for successfully applying NAS to the binary domain. Specifically, we (1) introduce and design a novel binary-oriented search space, (2) propose a new mechanism for controlling and stabilising the resulting searched topologies, (3) propose and validate a series of new search strategies for binary networks that lead to faster convergence and lower search times. Experimental results demonstrate the effectiveness of the proposed approach and the necessity of searching in the binary space directly. Moreover, (4) we set a new state-of-the-art for binary neural networks on CIFAR10, CIFAR100 and ImageNet datasets. Code will be made available https://github.com/1adrianb/binary-nas
Hierarchically Decoupled Imitation for Morphological Transfer
Authors: Donald J. Hejna III, Pieter Abbeel, Lerrel Pinto
Date: 2020-03-03 00:00:00

Learning long-range behaviors on complex high-dimensional agents is a fundamental problem in robot learning. For such tasks, we argue that transferring learned information from a morphologically simpler agent can massively improve the sample efficiency of a more complex one. To this end, we propose a hierarchical decoupling of policies into two parts: an independently learned low-level policy and a transferable high-level policy. To remedy poor transfer performance due to mismatch in morphologies, we contribute two key ideas. First, we show that incentivizing a complex agent's low-level to imitate a simpler agent's low-level significantly improves zero-shot high-level transfer. Second, we show that KL-regularized training of the high level stabilizes learning and prevents mode-collapse. Finally, on a suite of publicly released navigation and manipulation environments, we demonstrate the applicability of hierarchical transfer on long-range tasks across morphologies. Our code and videos can be found at https://sites.google.com/berkeley.edu/morphology-transfer.
Model Selection in Contextual Stochastic Bandit Problems
Authors: Aldo Pacchiano, My Phan, Yasin Abbasi-Yadkori, Anup Rao, Julian Zimmert, Tor Lattimore, Csaba Szepesvari
Date: 2020-03-03 00:00:00
Proceeding: NeurIPS 2020 12
Tasks: model, Model Selection, Multi-Armed Bandits

We study bandit model selection in stochastic environments. Our approach relies on a meta-algorithm that selects between candidate base algorithms. We develop a meta-algorithm-base algorithm abstraction that can work with general classes of base algorithms and different type of adversarial meta-algorithms. Our methods rely on a novel and generic smoothing transformation for bandit algorithms that permits us to obtain optimal $O(\sqrt{T})$ model selection guarantees for stochastic contextual bandit problems as long as the optimal base algorithm satisfies a high probability regret guarantee. We show through a lower bound that even when one of the base algorithms has $O(\log T)$ regret, in general it is impossible to get better than $\Omega(\sqrt{T})$ regret in model selection, even asymptotically. Using our techniques, we address model selection in a variety of problems such as misspecified linear contextual bandits, linear bandit with unknown dimension and reinforcement learning with unknown feature maps. Our algorithm requires the knowledge of the optimal base regret to adjust the meta-algorithm learning rate. We show that without such prior knowledge any meta-algorithm can suffer a regret larger than the optimal base regret.
Optimal Contextual Pricing and Extensions
Authors: Allen Liu, Renato Paes Leme, Jon Schneider
Date: 2020-03-03 00:00:00

In the contextual pricing problem a seller repeatedly obtains products described by an adversarially chosen feature vector in $\mathbb{R}^d$ and only observes the purchasing decisions of a buyer with a fixed but unknown linear valuation over the products. The regret measures the difference between the revenue the seller could have obtained knowing the buyer valuation and what can be obtained by the learning algorithm. We give a poly-time algorithm for contextual pricing with $O(d \log \log T + d \log d)$ regret which matches the $\Omega(d \log \log T)$ lower bound up to the $d \log d$ additive factor. If we replace pricing loss by the symmetric loss, we obtain an algorithm with nearly optimal regret of $O(d \log d)$ matching the $\Omega(d)$ lower bound up to $\log d$. These algorithms are based on a novel technique of bounding the value of the Steiner polynomial of a convex region at various scales. The Steiner polynomial is a degree $d$ polynomial with intrinsic volumes as the coefficients. We also study a generalized version of contextual search where the hidden linear function over the Euclidean space is replaced by a hidden function $f : \mathcal{X} \rightarrow \mathcal{Y}$ in a certain hypothesis class $\mathcal{H}$. We provide a generic algorithm with $O(d^2)$ regret where $d$ is the covering dimension of this class. This leads in particular to a $\tilde{O}(s^2)$ regret algorithm for linear contextual search if the linear function is guaranteed to be $s$-sparse. Finally we also extend our results to the noisy feedback model, where each round our feedback is flipped with a fixed probability $p < 1/2$.
Robust data encodings for quantum classifiers
Authors: Ryan LaRose, Brian Coyle
Date: 2020-03-03 00:00:00
Tasks: BIG-bench Machine Learning, General Classification, Quantum Machine Learning

Data representation is crucial for the success of machine learning models. In the context of quantum machine learning with near-term quantum computers, equally important considerations of how to efficiently input (encode) data and effectively deal with noise arise. In this work, we study data encodings for binary quantum classification and investigate their properties both with and without noise. For the common classifier we consider, we show that encodings determine the classes of learnable decision boundaries as well as the set of points which retain the same classification in the presence of noise. After defining the notion of a robust data encoding, we prove several results on robustness for different channels, discuss the existence of robust encodings, and prove an upper bound on the number of robust points in terms of fidelities between noisy and noiseless states. Numerical results for several example implementations are provided to reinforce our findings.
Reliable evaluation of adversarial robustness with an ensemble of diverse parameter-free attacks
Authors: Francesco Croce, Matthias Hein
Date: 2020-03-03 00:00:00
Proceeding: ICML 2020 1
Tasks: Adversarial Robustness

The field of defense strategies against adversarial attacks has significantly grown over the last years, but progress is hampered as the evaluation of adversarial defenses is often insufficient and thus gives a wrong impression of robustness. Many promising defenses could be broken later on, making it difficult to identify the state-of-the-art. Frequent pitfalls in the evaluation are improper tuning of hyperparameters of the attacks, gradient obfuscation or masking. In this paper we first propose two extensions of the PGD-attack overcoming failures due to suboptimal step size and problems of the objective function. We then combine our novel attacks with two complementary existing ones to form a parameter-free, computationally affordable and user-independent ensemble of attacks to test adversarial robustness. We apply our ensemble to over 50 models from papers published at recent top machine learning and computer vision venues. In all except one of the cases we achieve lower robust test accuracy than reported in these papers, often by more than $10\%$, identifying several broken defenses.
Automatic Differentiation Variational Inference with Mixtures
Authors: Warren R. Morningstar, Sharad M. Vikram, Cusuh Ham, Andrew Gallagher, Joshua V. Dillon
Date: 2020-03-03 00:00:00
Tasks: Variational Inference

Automatic Differentiation Variational Inference (ADVI) is a useful tool for efficiently learning probabilistic models in machine learning. Generally approximate posteriors learned by ADVI are forced to be unimodal in order to facilitate use of the reparameterization trick. In this paper, we show how stratified sampling may be used to enable mixture distributions as the approximate posterior, and derive a new lower bound on the evidence analogous to the importance weighted autoencoder (IWAE). We show that this "SIWAE" is a tighter bound than both IWAE and the traditional ELBO, both of which are special instances of this bound. We verify empirically that the traditional ELBO objective disfavors the presence of multimodal posterior distributions and may therefore not be able to fully capture structure in the latent space. Our experiments show that using the SIWAE objective allows the encoder to learn more complex distributions which regularly contain multimodality, resulting in higher accuracy and better calibration in the presence of incomplete, limited, or corrupted data.
Hybrid Generative-Retrieval Transformers for Dialogue Domain Adaptation
Authors: Igor Shalyminov, Alessandro Sordoni, Adam Atkinson, Hannes Schulz
Date: 2020-03-03 00:00:00
Tasks: Domain Adaptation, Response Generation, Retrieval

Domain adaptation has recently become a key problem in dialogue systems research. Deep learning, while being the preferred technique for modeling such systems, works best given massive training data. However, in the real-world scenario, such resources aren't available for every new domain, so the ability to train with a few dialogue examples can be considered essential. Pre-training on large data sources and adapting to the target data has become the standard method for few-shot problems within the deep learning framework. In this paper, we present the winning entry at the fast domain adaptation task of DSTC8, a hybrid generative-retrieval model based on GPT-2 fine-tuned to the multi-domain MetaLWOz dataset. Robust and diverse in response generation, our model uses retrieval logic as a fallback, being SoTA on MetaLWOz in human evaluation (>4% improvement over the 2nd place system) and attaining competitive generalization performance in adaptation to the unseen MultiWOZ dataset.
EXPLAIN-IT: Towards Explainable AI for Unsupervised Network Traffic Analysis
Authors: Andrea Morichetta, Pedro Casas, Marco Mellia
Date: 2020-03-03 00:00:00
Tasks: Clustering, Explainable artificial intelligence

The application of unsupervised learning approaches, and in particular of clustering techniques, represents a powerful exploration means for the analysis of network measurements. Discovering underlying data characteristics, grouping similar measurements together, and identifying eventual patterns of interest are some of the applications which can be tackled through clustering. Being unsupervised, clustering does not always provide precise and clear insight into the produced output, especially when the input data structure and distribution are complex and difficult to grasp. In this paper we introduce EXPLAIN-IT, a methodology which deals with unlabeled data, creates meaningful clusters, and suggests an explanation to the clustering results for the end-user. EXPLAIN-IT relies on a novel explainable Artificial Intelligence (AI) approach, which allows to understand the reasons leading to a particular decision of a supervised learning-based model, additionally extending its application to the unsupervised learning domain. We apply EXPLAIN-IT to the problem of YouTube video quality classification under encrypted traffic scenarios, showing promising results.
Model Assertions for Monitoring and Improving ML Models
Authors: Daniel Kang, Deepti Raghavan, Peter Bailis, Matei Zaharia
Date: 2020-03-03 00:00:00
Tasks: Active Learning, model

ML models are increasingly deployed in settings with real world interactions such as vehicles, but unfortunately, these models can fail in systematic ways. To prevent errors, ML engineering teams monitor and continuously improve these models. We propose a new abstraction, model assertions, that adapts the classical use of program assertions as a way to monitor and improve ML models. Model assertions are arbitrary functions over a model's input and output that indicate when errors may be occurring, e.g., a function that triggers if an object rapidly changes its class in a video. We propose methods of using model assertions at all stages of ML system deployment, including runtime monitoring, validating labels, and continuously improving ML models. For runtime monitoring, we show that model assertions can find high confidence errors, where a model returns the wrong output with high confidence, which uncertainty-based monitoring techniques would not detect. For training, we propose two methods of using model assertions. First, we propose a bandit-based active learning algorithm that can sample from data flagged by assertions and show that it can reduce labeling costs by up to 40% over traditional uncertainty-based methods. Second, we propose an API for generating "consistency assertions" (e.g., the class change example) and weak labels for inputs where the consistency assertions fail, and show that these weak labels can improve relative model quality by up to 46%. We evaluate model assertions on four real-world tasks with video, LIDAR, and ECG data.
Discriminative Multi-level Reconstruction under Compact Latent Space for One-Class Novelty Detection
Authors: Jaewoo Park, Yoon Gyo Jung, Andrew Beng Jin Teoh
Date: 2020-03-03 00:00:00
Tasks: Novelty Detection

In one-class novelty detection, a model learns solely on the in-class data to single out out-class instances. Autoencoder (AE) variants aim to compactly model the in-class data to reconstruct it exclusively, thus differentiating the in-class from out-class by the reconstruction error. However, compact modeling in an improper way might collapse the latent representations of the in-class data and thus their reconstruction, which would lead to performance deterioration. Moreover, to properly measure the reconstruction error of high-dimensional data, a metric is required that captures high-level semantics of the data. To this end, we propose Discriminative Compact AE (DCAE) that learns both compact and collapse-free latent representations of the in-class data, thereby reconstructing them both finely and exclusively. In DCAE, (a) we force a compact latent space to bijectively represent the in-class data by reconstructing them through internal discriminative layers of generative adversarial nets. (b) Based on the deep encoder's vulnerability to open set risk, out-class instances are encoded into the same compact latent space and reconstructed poorly without sacrificing the quality of in-class data reconstruction. (c) In inference, the reconstruction error is measured by a novel metric that computes the dissimilarity between a query and its reconstruction based on the class semantics captured by the internal discriminator. Extensive experiments on public image datasets validate the effectiveness of our proposed model on both novelty and adversarial example detection, delivering state-of-the-art performance.
Holistically-Attracted Wireframe Parsing
Authors: Nan Xue, Tianfu Wu, Song Bai, Fu-Dong Wang, Gui-Song Xia, Liangpei Zhang, Philip H. S. Torr
Date: 2020-03-03 00:00:00
Proceeding: CVPR 2020 6
Tasks: GPU, Line Segment Detection, Wireframe Parsing

This paper presents a fast and parsimonious parsing method to accurately and robustly detect a vectorized wireframe in an input image with a single forward pass. The proposed method is end-to-end trainable, consisting of three components: (i) line segment and junction proposal generation, (ii) line segment and junction matching, and (iii) line segment and junction verification. For computing line segment proposals, a novel exact dual representation is proposed which exploits a parsimonious geometric reparameterization for line segments and forms a holistic 4-dimensional attraction field map for an input image. Junctions can be treated as the "basins" in the attraction field. The proposed method is thus called Holistically-Attracted Wireframe Parser (HAWP). In experiments, the proposed method is tested on two benchmarks, the Wireframe dataset, and the YorkUrban dataset. On both benchmarks, it obtains state-of-the-art performance in terms of accuracy and efficiency. For example, on the Wireframe dataset, compared to the previous state-of-the-art method L-CNN, it improves the challenging mean structural average precision (msAP) by a large margin ($2.8\%$ absolute improvements) and achieves 29.5 FPS on single GPU ($89\%$ relative improvement). A systematic ablation study is performed to further justify the proposed method.
Unsupervised Learning of Intrinsic Structural Representation Points
Authors: Nenglun Chen, Lingjie Liu, Zhiming Cui, Runnan Chen, Duygu Ceylan, Changhe Tu, Wenping Wang
Date: 2020-03-03 00:00:00
Proceeding: CVPR 2020 6

Learning structures of 3D shapes is a fundamental problem in the field of computer graphics and geometry processing. We present a simple yet interpretable unsupervised method for learning a new structural representation in the form of 3D structure points. The 3D structure points produced by our method encode the shape structure intrinsically and exhibit semantic consistency across all the shape instances with similar structures. This is a challenging goal that has not fully been achieved by other methods. Specifically, our method takes a 3D point cloud as input and encodes it as a set of local features. The local features are then passed through a novel point integration module to produce a set of 3D structure points. The chamfer distance is used as reconstruction loss to ensure the structure points lie close to the input point cloud. Extensive experiments have shown that our method outperforms the state-of-the-art on the semantic shape correspondence task and achieves comparable performance with the state-of-the-art on the segmentation label transfer task. Moreover, the PCA based shape embedding built upon consistent structure points demonstrates good performance in preserving the shape structures. Code is available at https://github.com/NolenChen/3DStructurePoints