pwc-archive/papers-with-abstracts huggingface dataset:
Neural Latent Dependency Model for Sequence Labeling
Authors: Yang Zhou, Yong Jiang, Zechuan Hu, Kewei Tu
Date: 2020-11-10 00:00:00
Tasks: model

Sequence labeling is a fundamental problem in machine learning, natural language processing and many other fields. A classic approach to sequence labeling is linear chain conditional random fields (CRFs). When combined with neural network encoders, they achieve very good performance in many sequence labeling tasks. One limitation of linear chain CRFs is their inability to model long-range dependencies between labels. High order CRFs extend linear chain CRFs by modeling dependencies no longer than their order, but the computational complexity grows exponentially in the order. In this paper, we propose the Neural Latent Dependency Model (NLDM) that models dependencies of arbitrary length between labels with a latent tree structure. We develop an end-to-end training algorithm and a polynomial-time inference algorithm of our model. We evaluate our model on both synthetic and real datasets and show that our model outperforms strong baselines.
A step towards neural genome assembly
Authors: Lovro Vrček, Petar Veličković, Mile Šikić
Date: 2020-11-10 00:00:00
Proceeding: NeurIPS Workshop LMCA 2020 12
Tasks: Graph Representation Learning, Representation Learning

De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a large directed graph with a constraint that an unknown number of nodes and edges should be avoided. However, due to local structures in the graph and biological features, the problem can be reduced to graph simplification, which includes removal of redundant information. Motivated by recent advancements in graph representation learning and neural execution of algorithms, in this work we train the MPNN model with max-aggregator to execute several algorithms for graph simplification. We show that the algorithms were learned successfully and can be scaled to graphs of sizes up to 20 times larger than the ones used in training. We also test on graphs obtained from real-world genomic data---that of a lambda phage and E. coli.
Distributed Learning with Low Communication Cost via Gradient Boosting Untrained Neural Network
Authors: Xiatian Zhang, Xunshi He, Nan Wang, Rong Chen
Date: 2020-11-10 00:00:00
Tasks: Federated Learning

For high-dimensional data, there are huge communication costs for distributed GBDT because the communication volume of GBDT is related to the number of features. To overcome this problem, we propose a novel gradient boosting algorithm, the Gradient Boosting Untrained Neural Network(GBUN). GBUN ensembles the untrained randomly generated neural network that softly distributes data samples to multiple neuron outputs and dramatically reduces the communication costs for distributed learning. To avoid creating huge neural networks for high-dimensional data, we extend Simhash algorithm to mimic forward calculation of the neural network. Our experiments on multiple public datasets show that GBUN is as good as conventional GBDT in terms of prediction accuracy and much better than it in scaling property for distributed learning. Comparing to conventional GBDT varieties, GBUN speeds up the training process up to 13 times on the cluster with 64 machines, and up to 4614 times on the cluster with 100KB/s network bandwidth. Therefore, GBUN is not only an efficient distributed learning algorithm but also has great potentials for federated learning.
Sample Complexity Bounds for Two Timescale Value-based Reinforcement Learning Algorithms
Authors: Tengyu Xu, Yingbin Liang
Date: 2020-11-10 00:00:00
Tasks: reinforcement-learning, Reinforcement Learning (RL), Vocal Bursts Valence Prediction

Two timescale stochastic approximation (SA) has been widely used in value-based reinforcement learning algorithms. In the policy evaluation setting, it can model the linear and nonlinear temporal difference learning with gradient correction (TDC) algorithms as linear SA and nonlinear SA, respectively. In the policy optimization setting, two timescale nonlinear SA can also model the greedy gradient-Q (Greedy-GQ) algorithm. In previous studies, the non-asymptotic analysis of linear TDC and Greedy-GQ has been studied in the Markovian setting, with diminishing or accuracy-dependent stepsize. For the nonlinear TDC algorithm, only the asymptotic convergence has been established. In this paper, we study the non-asymptotic convergence rate of two timescale linear and nonlinear TDC and Greedy-GQ under Markovian sampling and with accuracy-independent constant stepsize. For linear TDC, we provide a novel non-asymptotic analysis and show that it attains an $\epsilon$-accurate solution with the optimal sample complexity of $\mathcal{O}(\epsilon^{-1}\log(1/\epsilon))$ under a constant stepsize. For nonlinear TDC and Greedy-GQ, we show that both algorithms attain $\epsilon$-accurate stationary solution with sample complexity $\mathcal{O}(\epsilon^{-2})$. It is the first non-asymptotic convergence result established for nonlinear TDC under Markovian sampling and our result for Greedy-GQ outperforms the previous result orderwisely by a factor of $\mathcal{O}(\epsilon^{-1}\log(1/\epsilon))$.
Efficient Algorithms for Stochastic Repeated Second-price Auctions
Authors: Juliette Achddou, Olivier Cappé, Aurélien Garivier
Date: 2020-11-10 00:00:00
Tasks: Marketing

Developing efficient sequential bidding strategies for repeated auctions is an important practical challenge in various marketing tasks. In this setting, the bidding agent obtains information, on both the value of the item at sale and the behavior of the other bidders, only when she wins the auction. Standard bandit theory does not apply to this problem due to the presence of action-dependent censoring. In this work, we consider second-price auctions and propose novel, efficient UCB-like algorithms for this task. These algorithms are analyzed in the stochastic setting, assuming regularity of the distribution of the opponents' bids. We provide regret upper bounds that quantify the improvement over the baseline algorithm proposed in the literature. The improvement is particularly significant in cases when the value of the auctioned item is low, yielding a spectacular reduction in the order of the worst-case regret. We further provide the first parametric lower bound for this problem that applies to generic UCB-like strategies. As an alternative, we propose more explainable strategies which are reminiscent of the Explore Then Commit bandit algorithm. We provide a critical analysis of this class of strategies, showing both important advantages and limitations. In particular, we provide a minimax lower bound and propose a nearly minimax-optimal instance of this class.
Efficient and Transferable Adversarial Examples from Bayesian Neural Networks
Authors: Martin Gubri, Maxime Cordy, Mike Papadakis, Yves Le Traon, Koushik Sen
Date: 2020-11-10 00:00:00
Tasks: Adversarial Attack, Bayesian Inference

An established way to improve the transferability of black-box evasion attacks is to craft the adversarial examples on an ensemble-based surrogate to increase diversity. We argue that transferability is fundamentally related to uncertainty. Based on a state-of-the-art Bayesian Deep Learning technique, we propose a new method to efficiently build a surrogate by sampling approximately from the posterior distribution of neural network weights, which represents the belief about the value of each parameter. Our extensive experiments on ImageNet, CIFAR-10 and MNIST show that our approach improves the success rates of four state-of-the-art attacks significantly (up to 83.2 percentage points), in both intra-architecture and inter-architecture transferability. On ImageNet, our approach can reach 94% of success rate while reducing training computations from 11.6 to 2.4 exaflops, compared to an ensemble of independently trained DNNs. Our vanilla surrogate achieves 87.5% of the time higher transferability than three test-time techniques designed for this purpose. Our work demonstrates that the way to train a surrogate has been overlooked, although it is an important element of transfer-based attacks. We are, therefore, the first to review the effectiveness of several training methods in increasing transferability. We provide new directions to better understand the transferability phenomenon and offer a simple but strong baseline for future work.
Higher-Order Spectral Clustering of Directed Graphs
Authors: Steinar Laenen, He Sun
Date: 2020-11-10 00:00:00
Proceeding: NeurIPS 2020 12
Tasks: Clustering, Graph Clustering

Clustering is an important topic in algorithms, and has a number of applications in machine learning, computer vision, statistics, and several other research disciplines. Traditional objectives of graph clustering are to find clusters with low conductance. Not only are these objectives just applicable for undirected graphs, they are also incapable to take the relationships between clusters into account, which could be crucial for many applications. To overcome these downsides, we study directed graphs (digraphs) whose clusters exhibit further "structural" information amongst each other. Based on the Hermitian matrix representation of digraphs, we present a nearly-linear time algorithm for digraph clustering, and further show that our proposed algorithm can be implemented in sublinear time under reasonable assumptions. The significance of our theoretical work is demonstrated by extensive experimental results on the UN Comtrade Dataset: the output clustering of our algorithm exhibits not only how the clusters (sets of countries) relate to each other with respect to their import and export records, but also how these clusters evolve over time, in accordance with known facts in international trade.
Two-stage Training of Graph Neural Networks for Graph Classification
Authors: Manh Tuan Do, Noseong Park, Kijung Shin
Date: 2020-11-10 00:00:00
Tasks: Classification, General Classification, Graph Classification, Link Prediction, Node Classification, Triplet, Vocal Bursts Valence Prediction

Graph neural networks (GNNs) have received massive attention in the field of machine learning on graphs. Inspired by the success of neural networks, a line of research has been conducted to train GNNs to deal with various tasks, such as node classification, graph classification, and link prediction. In this work, our task of interest is graph classification. Several GNN models have been proposed and shown great accuracy in this task. However, the question is whether usual training methods fully realize the capacity of the GNN models. In this work, we propose a two-stage training framework based on triplet loss. In the first stage, GNN is trained to map each graph to a Euclidean-space vector so that graphs of the same class are close while those of different classes are mapped far apart. Once graphs are well-separated based on labels, a classifier is trained to distinguish between different classes. This method is generic in the sense that it is compatible with any GNN model. By adapting five GNN models to our method, we demonstrate the consistent improvement in accuracy and utilization of each GNN's allocated capacity over the original training method of each model up to 5.4\% points in 12 datasets.
Feedback-Based Dynamic Feature Selection for Constrained Continuous Data Acquisition
Authors: Alp Sahin, Xiangrui Zeng
Date: 2020-11-10 00:00:00
Tasks: BIG-bench Machine Learning, feature selection

Relevant and high-quality data are critical to successful development of machine learning applications. For machine learning applications on dynamic systems equipped with a large number of sensors, such as connected vehicles and robots, how to find relevant and high-quality data features in an efficient way is a challenging problem. In this work, we address the problem of feature selection in constrained continuous data acquisition. We propose a feedback-based dynamic feature selection algorithm that efficiently decides on the feature set for data collection from a dynamic system in a step-wise manner. We formulate the sequential feature selection procedure as a Markov Decision Process. The machine learning model performance feedback with an exploration component is used as the reward function in an $\epsilon$-greedy action selection. Our evaluation shows that the proposed feedback-based feature selection algorithm has superior performance over constrained baseline methods and matching performance with unconstrained baseline methods.
Biomedical Information Extraction for Disease Gene Prioritization
Authors: Jupinder Parmar, William Koehler, Martin Bringmann, Katharina Sophia Volz, Berk Kapicioglu
Date: 2020-11-10 00:00:00
Tasks: named-entity-recognition, Named Entity Recognition, Named Entity Recognition (NER), NER, Relation Extraction

We introduce a biomedical information extraction (IE) pipeline that extracts biological relationships from text and demonstrate that its components, such as named entity recognition (NER) and relation extraction (RE), outperform state-of-the-art in BioNLP. We apply it to tens of millions of PubMed abstracts to extract protein-protein interactions (PPIs) and augment these extractions to a biomedical knowledge graph that already contains PPIs extracted from STRING, the leading structured PPI database. We show that, despite already containing PPIs from an established structured source, augmenting our own IE-based extractions to the graph allows us to predict novel disease-gene associations with a 20% relative increase in hit@30, an important step towards developing drug targets for uncured diseases.
Dynamic Embeddings for Interaction Prediction
Authors: Zekarias T. Kefato, Sarunas Girdzijauskas, Nasrullah Sheikh, Alberto Montresor
Date: 2020-11-10 00:00:00
Tasks: Prediction, Recommendation Systems

In recommender systems (RSs), predicting the next item that a user interacts with is critical for user retention. While the last decade has seen an explosion of RSs aimed at identifying relevant items that match user preferences, there is still a range of aspects that could be considered to further improve their performance. For example, often RSs are centered around the user, who is modeled using her recent sequence of activities. Recent studies, however, have shown the effectiveness of modeling the mutual interactions between users and items using separate user and item embeddings. Building on the success of these studies, we propose a novel method called DeePRed that addresses some of their limitations. In particular, we avoid recursive and costly interactions between consecutive short-term embeddings by using long-term (stationary) embeddings as a proxy. This enable us to train DeePRed using simple mini-batches without the overhead of specialized mini-batches proposed in previous studies. Moreover, DeePRed's effectiveness comes from the aforementioned design and a multi-way attention mechanism that inspects user-item compatibility. Experiments show that DeePRed outperforms the best state-of-the-art approach by at least 14% on next item prediction task, while gaining more than an order of magnitude speedup over the best performing baselines. Although this study is mainly concerned with temporal interaction networks, we also show the power and flexibility of DeePRed by adapting it to the case of static interaction networks, substituting the short- and long-term aspects with local and global ones.
A Variational Infinite Mixture for Probabilistic Inverse Dynamics Learning
Authors: Hany Abdulsamad, Peter Nickl, Pascal Klink, Jan Peters
Date: 2020-11-10 00:00:00
Tasks: Computational Efficiency

Probabilistic regression techniques in control and robotics applications have to fulfill different criteria of data-driven adaptability, computational efficiency, scalability to high dimensions, and the capacity to deal with different modalities in the data. Classical regressors usually fulfill only a subset of these properties. In this work, we extend seminal work on Bayesian nonparametric mixtures and derive an efficient variational Bayes inference technique for infinite mixtures of probabilistic local polynomial models with well-calibrated certainty quantification. We highlight the model's power in combining data-driven complexity adaptation, fast prediction and the ability to deal with discontinuous functions and heteroscedastic noise. We benchmark this technique on a range of large real inverse dynamics datasets, showing that the infinite mixture formulation is competitive with classical Local Learning methods and regularizes model complexity by adapting the number of components based on data and without relying on heuristics. Moreover, to showcase the practicality of the approach, we use the learned models for online inverse dynamics control of a Barrett-WAM manipulator, significantly improving the trajectory tracking performance.
Explainable Knowledge Tracing Models for Big Data: Is Ensembling an Answer?
Authors: Tirth Shah, Lukas Olson, Aditya Sharma, Nirmal Patel
Date: 2020-11-10 00:00:00
Tasks: Knowledge Tracing

In this paper, we describe our Knowledge Tracing model for the 2020 NeurIPS Education Challenge. We used a combination of 22 models to predict whether the students will answer a given question correctly or not. Our combination of different approaches allowed us to get an accuracy higher than any of the individual models, and the variation of our model types gave our solution better explainability, more alignment with learning science theories, and high predictive power.
Topological Regularization via Persistence-Sensitive Optimization
Authors: Arnur Nigmetov, Aditi S. Krishnapriyan, Nicole Sanderson, Dmitriy Morozov
Date: 2020-11-10 00:00:00

Optimization, a key tool in machine learning and statistics, relies on regularization to reduce overfitting. Traditional regularization methods control a norm of the solution to ensure its smoothness. Recently, topological methods have emerged as a way to provide a more precise and expressive control over the solution, relying on persistent homology to quantify and reduce its roughness. All such existing techniques back-propagate gradients through the persistence diagram, which is a summary of the topological features of a function. Their downside is that they provide information only at the critical points of the function. We propose a method that instead builds on persistence-sensitive simplification and translates the required changes to the persistence diagram into changes on large subsets of the domain, including both critical and regular points. This approach enables a faster and more precise topological regularization, the benefits of which we illustrate with experimental evidence.
Node Attribute Completion in Knowledge Graphs with Multi-Relational Propagation
Authors: Eda Bayram, Alberto Garcia-Duran, Robert West
Date: 2020-11-10 00:00:00
Tasks: Attribute, Knowledge Graph Completion, Knowledge Graphs, Link Prediction, regression

The existing literature on knowledge graph completion mostly focuses on the link prediction task. However, knowledge graphs have an additional incompleteness problem: their nodes possess numerical attributes, whose values are often missing. Our approach, denoted as MrAP, imputes the values of missing attributes by propagating information across the multi-relational structure of a knowledge graph. It employs regression functions for predicting one node attribute from another depending on the relationship between the nodes and the type of the attributes. The propagation mechanism operates iteratively in a message passing scheme that collects the predictions at every iteration and updates the value of the node attributes. Experiments over two benchmark datasets show the effectiveness of our approach.
Discovering Synergistic Drug Combinations for COVID with Biological Bottleneck Models
Authors: Wengong Jin, Regina Barzilay, Tommi Jaakkola
Date: 2020-11-09 00:00:00

Drug combinations play an important role in therapeutics due to its better efficacy and reduced toxicity. Recent approaches have applied machine learning to identify synergistic combinations for cancer, but they are not applicable to new diseases with limited combination data. Given that drug synergy is closely tied to biological targets, we propose a \emph{biological bottleneck} model that jointly learns drug-target interaction and synergy. The model consists of two parts: a drug-target interaction and target-disease association module. This design enables the model to \emph{explain} how a biological target affects drug synergy. By utilizing additional biological information, our model achieves 0.78 test AUC in drug synergy prediction using only 90 COVID drug combinations for training. We experimentally tested the model predictions in the U.S. National Center for Advancing Translational Sciences (NCATS) facilities and discovered two novel drug combinations (Remdesivir + Reserpine and Remdesivir + IQ-1S) with strong synergy in vitro.
Thompson sampling for linear quadratic mean-field teams
Authors: Mukul Gagrani, Sagar Sudhakara, Aditya Mahajan, Ashutosh Nayyar, Yi Ouyang
Date: 2020-11-09 00:00:00
Tasks: Thompson Sampling

We consider optimal control of an unknown multi-agent linear quadratic (LQ) system where the dynamics and the cost are coupled across the agents through the mean-field (i.e., empirical mean) of the states and controls. Directly using single-agent LQ learning algorithms in such models results in regret which increases polynomially with the number of agents. We propose a new Thompson sampling based learning algorithm which exploits the structure of the system model and show that the expected Bayesian regret of our proposed algorithm for a system with agents of $|M|$ different types at time horizon $T$ is $\tilde{\mathcal{O}} \big( |M|^{1.5} \sqrt{T} \big)$ irrespective of the total number of agents, where the $\tilde{\mathcal{O}}$ notation hides logarithmic factors in $T$. We present detailed numerical experiments to illustrate the salient features of the proposed algorithm.
F-FADE: Frequency Factorization for Anomaly Detection in Edge Streams
Authors: Yen-Yu Chang, Pan Li, Rok Sosic, M. H. Afifi, Marco Schweighauser, Jure Leskovec
Date: 2020-11-09 00:00:00
Tasks: Anomaly Detection, Anomaly Detection in Edge Streams

Edge streams are commonly used to capture interactions in dynamic networks, such as email, social, or computer networks. The problem of detecting anomalies or rare events in edge streams has a wide range of applications. However, it presents many challenges due to lack of labels, a highly dynamic nature of interactions, and the entanglement of temporal and structural changes in the network. Current methods are limited in their ability to address the above challenges and to efficiently process a large number of interactions. Here, we propose F-FADE, a new approach for detection of anomalies in edge streams, which uses a novel frequency-factorization technique to efficiently model the time-evolving distributions of frequencies of interactions between node-pairs. The anomalies are then determined based on the likelihood of the observed frequency of each incoming interaction. F-FADE is able to handle in an online streaming setting a broad variety of anomalies with temporal and structural changes, while requiring only constant memory. Our experiments on one synthetic and six real-world dynamic networks show that F-FADE achieves state of the art performance and may detect anomalies that previous methods are unable to find.