pwc-archive/papers-with-abstracts huggingface dataset:
Poly-encoders: Architectures and Pre-training Strategies for Fast and Accurate Multi-sentence Scoring
Authors: Samuel Humeau, Kurt Shuster, Marie-Anne Lachaux, Jason Weston
Date: 2020-01-01 00:00:00
Proceeding: ICLR 2020 1
Tasks: Sentence

The use of deep pre-trained transformers has led to remarkable progress in a number of applications (Devlin et al., 2018). For tasks that make pairwise comparisons between sequences, matching a given input with a corresponding label, two approaches are common: Cross-encoders performing full self-attention over the pair and Bi-encoders encoding the pair separately. The former often performs better, but is too slow for practical use. In this work, we develop a new transformer architecture, the Poly-encoder, that learns global rather than token level self-attention features. We perform a detailed comparison of all three approaches, including what pre-training and fine-tuning strategies work best. We show our models achieve state-of-the-art results on four tasks; that Poly-encoders are faster than Cross-encoders and more accurate than Bi-encoders; and that the best results are obtained by pre-training on large datasets similar to the downstream tasks.
An introductory guide to aligning networks using SANA, the Simulated Annealing Network Aligner
Authors: Wayne B. Hayes
Date: 2019-11-22 00:00:00
Tasks: CPU

Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological {\em networks} holds similar promise. Biological networks generally model interactions between biomolecules such as proteins, genes, metabolites, or mRNAs. There is strong evidence that the network topology -- the "structure" of the network -- is correlated with the functions performed, so that network topology can be used to help predict or understand function. However, unlike sequence comparison and alignment -- which is an essentially solved problem -- network comparison and alignment is an NP-complete problem for which heuristic algorithms must be used. Here we introduce SANA, the {\it Simulated Annealing Network Aligner}. SANA is one of many algorithms proposed for the arena of biological network alignment. In the context of global network alignment, SANA stands out for its speed, memory efficiency, ease-of-use, and flexibility in the arena of producing alignments between 2 or more networks. SANA produces better alignments in minutes on a laptop than most other algorithms can produce in hours or days of CPU time on large server-class machines. We walk the user through how to use SANA for several types of biomolecular networks. Availability: https://github.com/waynebhayes/SANA
Line Hypergraph Convolution Network: Applying Graph Convolution for Hypergraphs
Authors: Sambaran Bandyopadhyay, Kishalay Das, M. Narasimha Murty
Date: 2020-02-09 00:00:00
Tasks: Node Classification, Representation Learning

Network representation learning and node classification in graphs got significant attention due to the invent of different types graph neural networks. Graph convolution network (GCN) is a popular semi-supervised technique which aggregates attributes within the neighborhood of each node. Conventional GCNs can be applied to simple graphs where each edge connects only two nodes. But many modern days applications need to model high order relationships in a graph. Hypergraphs are effective data types to handle such complex relationships. In this paper, we propose a novel technique to apply graph convolution on hypergraphs with variable hyperedge sizes. We use the classical concept of line graph of a hypergraph for the first time in the hypergraph learning literature. Then we propose to use graph convolution on the line graph of a hypergraph. Experimental analysis on multiple real world network datasets shows the merit of our approach compared to state-of-the-arts.
Persistent spectral based machine learning (PerSpect ML) for drug design
Authors: Zhenyu Meng, Kelin Xia
Date: 2020-02-03 00:00:00
Tasks: BIG-bench Machine Learning, Drug Design

In this paper, we propose persistent spectral based machine learning (PerSpect ML) models for drug design. Persistent spectral models, including persistent spectral graph, persistent spectral simplicial complex and persistent spectral hypergraph, are proposed based on spectral graph theory, spectral simplicial complex theory and spectral hypergraph theory, respectively. Different from all previous spectral models, a filtration process, as proposed in persistent homology, is introduced to generate multiscale spectral models. More specifically, from the filtration process, a series of nested topological representations, i,e., graphs, simplicial complexes, and hypergraphs, can be systematically generated and their spectral information can be obtained. Persistent spectral variables are defined as the function of spectral variables over the filtration value. Mathematically, persistent multiplicity (of zero eigenvalues) is exactly the persistent Betti number (or Betti curve). We consider 11 persistent spectral variables and use them as the feature for machine learning models in protein-ligand binding affinity prediction. We systematically test our models on three most commonly-used databases, including PDBbind-2007, PDBbind-2013 and PDBbind-2016. Our results, for all these databases, are better than all existing models, as far as we know. This demonstrates the great power of our PerSpect ML in molecular data analysis and drug design.
Self-Distillation Amplifies Regularization in Hilbert Space
Authors: Hossein Mobahi, Mehrdad Farajtabar, Peter L. Bartlett
Date: 2020-02-13 00:00:00
Proceeding: NeurIPS 2020 12
Tasks: Knowledge Distillation, L2 Regularization

Knowledge distillation introduced in the deep learning context is a method to transfer knowledge from one architecture to another. In particular, when the architectures are identical, this is called self-distillation. The idea is to feed in predictions of the trained model as new target values for retraining (and iterate this loop possibly a few times). It has been empirically observed that the self-distilled model often achieves higher accuracy on held out data. Why this happens, however, has been a mystery: the self-distillation dynamics does not receive any new information about the task and solely evolves by looping over training. To the best of our knowledge, there is no rigorous understanding of this phenomenon. This work provides the first theoretical analysis of self-distillation. We focus on fitting a nonlinear function to training data, where the model space is Hilbert space and fitting is subject to $\ell_2$ regularization in this function space. We show that self-distillation iterations modify regularization by progressively limiting the number of basis functions that can be used to represent the solution. This implies (as we also verify empirically) that while a few rounds of self-distillation may reduce over-fitting, further rounds may lead to under-fitting and thus worse performance.
Automatically Discovering and Learning New Visual Categories with Ranking Statistics
Authors: Kai Han, Sylvestre-Alvise Rebuffi, Sebastien Ehrhardt, Andrea Vedaldi, Andrew Zisserman
Date: 2020-02-13 00:00:00
Proceeding: ICLR 2020 1
Tasks: Clustering, General Classification, Self-Supervised Learning

We tackle the problem of discovering novel classes in an image collection given labelled examples of other classes. This setting is similar to semi-supervised learning, but significantly harder because there are no labelled examples for the new classes. The challenge, then, is to leverage the information contained in the labelled images in order to learn a general-purpose clustering model and use the latter to identify the new classes in the unlabelled data. In this work we address this problem by combining three ideas: (1) we suggest that the common approach of bootstrapping an image representation using the labeled data only introduces an unwanted bias, and that this can be avoided by using self-supervised learning to train the representation from scratch on the union of labelled and unlabelled data; (2) we use rank statistics to transfer the model's knowledge of the labelled classes to the problem of clustering the unlabelled images; and, (3) we train the data representation by optimizing a joint objective function on the labelled and unlabelled subsets of the data, improving both the supervised classification of the labelled data, and the clustering of the unlabelled data. We evaluate our approach on standard classification benchmarks and outperform current methods for novel category discovery by a significant margin.
Cross-Iteration Batch Normalization
Authors: Zhuliang Yao, Yue Cao, Shuxin Zheng, Gao Huang, Stephen Lin
Date: 2020-02-13 00:00:00
Proceeding: CVPR 2021 1
Tasks: image-classification, Image Classification, object-detection, Object Detection

A well-known issue of Batch Normalization is its significantly reduced effectiveness in the case of small mini-batch sizes. When a mini-batch contains few examples, the statistics upon which the normalization is defined cannot be reliably estimated from it during a training iteration. To address this problem, we present Cross-Iteration Batch Normalization (CBN), in which examples from multiple recent iterations are jointly utilized to enhance estimation quality. A challenge of computing statistics over multiple iterations is that the network activations from different iterations are not comparable to each other due to changes in network weights. We thus compensate for the network weight changes via a proposed technique based on Taylor polynomials, so that the statistics can be accurately estimated and batch normalization can be effectively applied. On object detection and image classification with small mini-batch sizes, CBN is found to outperform the original batch normalization and a direct calculation of statistics over previous iterations without the proposed compensation technique. Code is available at https://github.com/Howal/Cross-iterationBatchNorm .
A Simple Framework for Contrastive Learning of Visual Representations
Authors: Ting Chen, Simon Kornblith, Mohammad Norouzi, Geoffrey Hinton
Date: 2020-02-13 00:00:00
Proceeding: ICML 2020 1
Tasks: Contrastive Learning, Image Classification, Object Recognition, Person Re-Identification, Self-Supervised Image Classification, Self-Supervised Learning, Self-Supervised Person Re-Identification, Semi-Supervised Image Classification

This paper presents SimCLR: a simple framework for contrastive learning of visual representations. We simplify recently proposed contrastive self-supervised learning algorithms without requiring specialized architectures or a memory bank. In order to understand what enables the contrastive prediction tasks to learn useful representations, we systematically study the major components of our framework. We show that (1) composition of data augmentations plays a critical role in defining effective predictive tasks, (2) introducing a learnable nonlinear transformation between the representation and the contrastive loss substantially improves the quality of the learned representations, and (3) contrastive learning benefits from larger batch sizes and more training steps compared to supervised learning. By combining these findings, we are able to considerably outperform previous methods for self-supervised and semi-supervised learning on ImageNet. A linear classifier trained on self-supervised representations learned by SimCLR achieves 76.5% top-1 accuracy, which is a 7% relative improvement over previous state-of-the-art, matching the performance of a supervised ResNet-50. When fine-tuned on only 1% of the labels, we achieve 85.8% top-5 accuracy, outperforming AlexNet with 100X fewer labels.
Simple Interactive Image Segmentation using Label Propagation through kNN graphs
Authors: Fabricio Aparecido Breve
Date: 2020-02-13 00:00:00
Tasks: Image Segmentation, Object, Segmentation, Semantic Segmentation

Many interactive image segmentation techniques are based on semi-supervised learning. The user may label some pixels from each object and the SSL algorithm will propagate the labels from the labeled to the unlabeled pixels, finding object boundaries. This paper proposes a new SSL graph-based interactive image segmentation approach, using undirected and unweighted kNN graphs, from which the unlabeled nodes receive contributions from other nodes (either labeled or unlabeled). It is simpler than many other techniques, but it still achieves significant classification accuracy in the image segmentation task. Computer simulations are performed using some real-world images, extracted from the Microsoft GrabCut dataset. The segmentation results show the effectiveness of the proposed approach.
A Framework for End-to-End Learning on Semantic Tree-Structured Data
Authors: William Woof, Ke Chen
Date: 2020-02-13 00:00:00
Tasks: Reinforcement Learning

While learning models are typically studied for inputs in the form of a fixed dimensional feature vector, real world data is rarely found in this form. In order to meet the basic requirement of traditional learning models, structural data generally have to be converted into fix-length vectors in a handcrafted manner, which is tedious and may even incur information loss. A common form of structured data is what we term "semantic tree-structures", corresponding to data where rich semantic information is encoded in a compositional manner, such as those expressed in JavaScript Object Notation (JSON) and eXtensible Markup Language (XML). For tree-structured data, several learning models have been studied to allow for working directly on raw tree-structure data, However such learning models are limited to either a specific tree-topology or a specific tree-structured data format, e.g., synthetic parse trees. In this paper, we propose a novel framework for end-to-end learning on generic semantic tree-structured data of arbitrary topology and heterogeneous data types, such as data expressed in JSON, XML and so on. Motivated by the works in recursive and recurrent neural networks, we develop exemplar neural implementations of our framework for the JSON format. We evaluate our approach on several UCI benchmark datasets, including ablation and data-efficiency studies, and on a toy reinforcement learning task. Experimental results suggest that our framework yields comparable performance to use of standard models with dedicated feature-vectors in general, and even exceeds baseline performance in cases where compositional nature of the data is particularly important. The source code for a JSON-based implementation of our framework along with experiments can be downloaded at https://github.com/EndingCredits/json2vec.
Sequential Cooperative Bayesian Inference
Authors: Junqi Wang, Pei Wang, Patrick Shafto
Date: 2020-02-13 00:00:00
Proceeding: ICML 2020 1
Tasks: Bayesian Inference

Cooperation is often implicitly assumed when learning from other agents. Cooperation implies that the agent selecting the data, and the agent learning from the data, have the same goal, that the learner infer the intended hypothesis. Recent models in human and machine learning have demonstrated the possibility of cooperation. We seek foundational theoretical results for cooperative inference by Bayesian agents through sequential data. We develop novel approaches analyzing consistency, rate of convergence and stability of Sequential Cooperative Bayesian Inference (SCBI). Our analysis of the effectiveness, sample efficiency and robustness show that cooperation is not only possible in specific instances but theoretically well-founded in general. We discuss implications for human-human and human-machine cooperation.
Generative-based Airway and Vessel Morphology Quantification on Chest CT Images
Authors: Pietro Nardelli, James C. Ross, Raúl San José Estépar
Date: 2020-02-13 00:00:00
Tasks: Computed Tomography (CT), Generative Adversarial Network

Accurately and precisely characterizing the morphology of small pulmonary structures from Computed Tomography (CT) images, such as airways and vessels, is becoming of great importance for diagnosis of pulmonary diseases. The smaller conducting airways are the major site of increased airflow resistance in chronic obstructive pulmonary disease (COPD), while accurately sizing vessels can help identify arterial and venous changes in lung regions that may determine future disorders. However, traditional methods are often limited due to image resolution and artifacts. We propose a Convolutional Neural Regressor (CNR) that provides cross-sectional measurement of airway lumen, airway wall thickness, and vessel radius. CNR is trained with data created by a generative model of synthetic structures which is used in combination with Simulated and Unsupervised Generative Adversarial Network (SimGAN) to create simulated and refined airways and vessels with known ground-truth. For validation, we first use synthetically generated airways and vessels produced by the proposed generative model to compute the relative error and directly evaluate the accuracy of CNR in comparison with traditional methods. Then, in-vivo validation is performed by analyzing the association between the percentage of the predicted forced expiratory volume in one second (FEV1\%) and the value of the Pi10 parameter, two well-known measures of lung function and airway disease, for airways. For vessels, we assess the correlation between our estimate of the small-vessel blood volume and the lungs' diffusing capacity for carbon monoxide (DLCO). The results demonstrate that Convolutional Neural Networks (CNNs) provide a promising direction for accurately measuring vessels and airways on chest CT images with physiological correlates.
BADGR: An Autonomous Self-Supervised Learning-Based Navigation System
Authors: Gregory Kahn, Pieter Abbeel, Sergey Levine
Date: 2020-02-13 00:00:00
Tasks: Navigate, Robot Navigation, Self-Supervised Learning

Mobile robot navigation is typically regarded as a geometric problem, in which the robot's objective is to perceive the geometry of the environment in order to plan collision-free paths towards a desired goal. However, a purely geometric view of the world can can be insufficient for many navigation problems. For example, a robot navigating based on geometry may avoid a field of tall grass because it believes it is untraversable, and will therefore fail to reach its desired goal. In this work, we investigate how to move beyond these purely geometric-based approaches using a method that learns about physical navigational affordances from experience. Our approach, which we call BADGR, is an end-to-end learning-based mobile robot navigation system that can be trained with self-supervised off-policy data gathered in real-world environments, without any simulation or human supervision. BADGR can navigate in real-world urban and off-road environments with geometrically distracting obstacles. It can also incorporate terrain preferences, generalize to novel environments, and continue to improve autonomously by gathering more data. Videos, code, and other supplemental material are available on our website https://sites.google.com/view/badgr
Neuromorphologicaly-preserving Volumetric data encoding using VQ-VAE
Authors: Petru-Daniel Tudosiu, Thomas Varsavsky, Richard Shaw, Mark Graham, Parashkev Nachev, Sebastien Ourselin, Carole H. Sudre, M. Jorge Cardoso
Date: 2020-02-13 00:00:00
Proceeding: MIDL 2019 7

The increasing efficiency and compactness of deep learning architectures, together with hardware improvements, have enabled the complex and high-dimensional modelling of medical volumetric data at higher resolutions. Recently, Vector-Quantised Variational Autoencoders (VQ-VAE) have been proposed as an efficient generative unsupervised learning approach that can encode images to a small percentage of their initial size, while preserving their decoded fidelity. Here, we show a VQ-VAE inspired network can efficiently encode a full-resolution 3D brain volume, compressing the data to $0.825\%$ of the original size while maintaining image fidelity, and significantly outperforming the previous state-of-the-art. We then demonstrate that VQ-VAE decoded images preserve the morphological characteristics of the original data through voxel-based morphology and segmentation experiments. Lastly, we show that such models can be pre-trained and then fine-tuned on different datasets without the introduction of bias.
Classifying the classifier: dissecting the weight space of neural networks
Authors: Gabriel Eilertsen, Daniel Jönsson, Timo Ropinski, Jonas Unger, Anders Ynnerman
Date: 2020-02-13 00:00:00
Tasks: 16k

This paper presents an empirical study on the weights of neural networks, where we interpret each model as a point in a high-dimensional space -- the neural weight space. To explore the complex structure of this space, we sample from a diverse selection of training variations (dataset, optimization procedure, architecture, etc.) of neural network classifiers, and train a large number of models to represent the weight space. Then, we use a machine learning approach for analyzing and extracting information from this space. Most centrally, we train a number of novel deep meta-classifiers with the objective of classifying different properties of the training setup by identifying their footprints in the weight space. Thus, the meta-classifiers probe for patterns induced by hyper-parameters, so that we can quantify how much, where, and when these are encoded through the optimization process. This provides a novel and complementary view for explainable AI, and we show how meta-classifiers can reveal a great deal of information about the training setup and optimization, by only considering a small subset of randomly selected consecutive weights. To promote further research on the weight space, we release the neural weight space (NWS) dataset -- a collection of 320K weight snapshots from 16K individually trained deep neural networks.
Tree-SNE: Hierarchical Clustering and Visualization Using t-SNE
Authors: Isaac Robinson, Emma Pierce-Hoffman
Date: 2020-02-13 00:00:00
Tasks: Clustering, Image Clustering

t-SNE and hierarchical clustering are popular methods of exploratory data analysis, particularly in biology. Building on recent advances in speeding up t-SNE and obtaining finer-grained structure, we combine the two to create tree-SNE, a hierarchical clustering and visualization algorithm based on stacked one-dimensional t-SNE embeddings. We also introduce alpha-clustering, which recommends the optimal cluster assignment, without foreknowledge of the number of clusters, based off of the cluster stability across multiple scales. We demonstrate the effectiveness of tree-SNE and alpha-clustering on images of handwritten digits, mass cytometry (CyTOF) data from blood cells, and single-cell RNA-sequencing (scRNA-seq) data from retinal cells. Furthermore, to demonstrate the validity of the visualization, we use alpha-clustering to obtain unsupervised clustering results competitive with the state of the art on several image data sets. Software is available at https://github.com/isaacrob/treesne.