pwc-archive/papers-with-abstracts huggingface dataset:
Molecular Insights from Conformational Ensembles via Machine Learning
Authors: Fleetwood O, Kasimova MA, Westerlund AM, Delemotte L
Date: 2020-02-04 00:00:00
Proceeding: Biophys Journal 2020 2
Tasks: BIG-bench Machine Learning, Dimensionality Reduction, Physical Simulations

Biomolecular simulations are intrinsically high dimensional and generate noisy data sets of ever-increasing size. Extracting important features from the data is crucial for understanding the biophysical properties of molecular processes, but remains a big challenge. Machine learning (ML) provides powerful dimensionality reduction tools. However, such methods are often criticized as resembling black boxes with limited human-interpretable insight. We use methods from supervised and unsupervised ML to efficiently create interpretable maps of important features from molecular simulations. We benchmark the performance of several methods, including neural networks, random forests, and principal component analysis, using a toy model with properties reminiscent of macromolecular behavior. We then analyze three diverse biological processes: conformational changes within the soluble protein calmodulin, ligand binding to a G protein-coupled receptor, and activation of an ion channel voltage-sensor domain, unraveling features critical for signal transduction, ligand binding, and voltage sensing. This work demonstrates the usefulness of ML in understanding biomolecular states and demystifying complex simulations.
Adversarial Attack on Large Scale Graph
Authors: Jintang Li, Tao Xie, Liang Chen, Fenfang Xie, Xiangnan He, Zibin Zheng
Date: 2020-09-08 00:00:00
Tasks: Adversarial Attack

Recent studies have shown that graph neural networks (GNNs) are vulnerable against perturbations due to lack of robustness and can therefore be easily fooled. Currently, most works on attacking GNNs are mainly using gradient information to guide the attack and achieve outstanding performance. However, the high complexity of time and space makes them unmanageable for large scale graphs and becomes the major bottleneck that prevents the practical usage. We argue that the main reason is that they have to use the whole graph for attacks, resulting in the increasing time and space complexity as the data scale grows. In this work, we propose an efficient Simplified Gradient-based Attack (SGA) method to bridge this gap. SGA can cause the GNNs to misclassify specific target nodes through a multi-stage attack framework, which needs only a much smaller subgraph. In addition, we present a practical metric named Degree Assortativity Change (DAC) to measure the impacts of adversarial attacks on graph data. We evaluate our attack method on four real-world graph networks by attacking several commonly used GNNs. The experimental results demonstrate that SGA can achieve significant time and memory efficiency improvements while maintaining competitive attack performance compared to state-of-art attack techniques. Codes are available via: https://github.com/EdisonLeeeee/SGAttack.
Induction and Exploitation of Subgoal Automata for Reinforcement Learning
Authors: Daniel Furelos-Blanco, Mark Law, Anders Jonsson, Krysia Broda, Alessandra Russo
Date: 2020-09-08 00:00:00
Tasks: Inductive logic programming, reinforcement-learning, Reinforcement Learning, Reinforcement Learning (RL)

In this paper we present ISA, an approach for learning and exploiting subgoals in episodic reinforcement learning (RL) tasks. ISA interleaves reinforcement learning with the induction of a subgoal automaton, an automaton whose edges are labeled by the task's subgoals expressed as propositional logic formulas over a set of high-level events. A subgoal automaton also consists of two special states: a state indicating the successful completion of the task, and a state indicating that the task has finished without succeeding. A state-of-the-art inductive logic programming system is used to learn a subgoal automaton that covers the traces of high-level events observed by the RL agent. When the currently exploited automaton does not correctly recognize a trace, the automaton learner induces a new automaton that covers that trace. The interleaving process guarantees the induction of automata with the minimum number of states, and applies a symmetry breaking mechanism to shrink the search space whilst remaining complete. We evaluate ISA in several gridworld and continuous state space problems using different RL algorithms that leverage the automaton structures. We provide an in-depth empirical analysis of the automaton learning performance in terms of the traces, the symmetry breaking and specific restrictions imposed on the final learnable automaton. For each class of RL problem, we show that the learned automata can be successfully exploited to learn policies that reach the goal, achieving an average reward comparable to the case where automata are not learned but handcrafted and given beforehand.
Low-Rank Training of Deep Neural Networks for Emerging Memory Technology
Authors: Albert Gural, Phillip Nadeau, Mehul Tikekar, Boris Murmann
Date: 2020-09-08 00:00:00
Tasks: Computational Efficiency, Decision Making, Federated Learning

The recent success of neural networks for solving difficult decision tasks has incentivized incorporating smart decision making "at the edge." However, this work has traditionally focused on neural network inference, rather than training, due to memory and compute limitations, especially in emerging non-volatile memory systems, where writes are energetically costly and reduce lifespan. Yet, the ability to train at the edge is becoming increasingly important as it enables real-time adaptability to device drift and environmental variation, user customization, and federated learning across devices. In this work, we address two key challenges for training on edge devices with non-volatile memory: low write density and low auxiliary memory. We present a low-rank training scheme that addresses these challenges while maintaining computational efficiency. We then demonstrate the technique on a representative convolutional neural network across several adaptation problems, where it out-performs standard SGD both in accuracy and in number of weight writes.
Convolution Neural Networks for diagnosing colon and lung cancer histopathological images
Authors: Sanidhya Mangal, Aanchal Chaurasia, Ayush Khajanchi
Date: 2020-09-08 00:00:00
Tasks: Diagnostic

Lung and Colon cancer are one of the leading causes of mortality and morbidity in adults. Histopathological diagnosis is one of the key components to discern cancer type. The aim of the present research is to propose a computer aided diagnosis system for diagnosing squamous cell carcinomas and adenocarcinomas of lung as well as adenocarcinomas of colon using convolutional neural networks by evaluating the digital pathology images for these cancers. Hereby, rendering artificial intelligence as useful technology in the near future. A total of 2500 digital images were acquired from LC25000 dataset containing 5000 images for each class. A shallow neural network architecture was used classify the histopathological slides into squamous cell carcinomas, adenocarcinomas and benign for the lung. Similar model was used to classify adenocarcinomas and benign for colon. The diagnostic accuracy of more than 97% and 96% was recorded for lung and colon respectively.
Machine Intelligence for Outcome Predictions of Trauma Patients During Emergency Department Care
Authors: Joshua D. Cardosi, Herman Shen, Jonathan I. Groner, Megan Armstrong, Henry Xiang
Date: 2020-09-08 00:00:00
Tasks: regression, Specificity, Transfer Learning

Trauma mortality results from a multitude of non-linear dependent risk factors including patient demographics, injury characteristics, medical care provided, and characteristics of medical facilities; yet traditional approach attempted to capture these relationships using rigid regression models. We hypothesized that a transfer learning based machine learning algorithm could deeply understand a trauma patient's condition and accurately identify individuals at high risk for mortality without relying on restrictive regression model criteria. Anonymous patient visit data were obtained from years 2007-2014 of the National Trauma Data Bank. Patients with incomplete vitals, unknown outcome, or missing demographics data were excluded. All patient visits occurred in U.S. hospitals, and of the 2,007,485 encounters that were retrospectively examined, 8,198 resulted in mortality (0.4%). The machine intelligence model was evaluated on its sensitivity, specificity, positive and negative predictive value, and Matthews Correlation Coefficient. Our model achieved similar performance in age-specific comparison models and generalized well when applied to all ages simultaneously. While testing for confounding factors, we discovered that excluding fall-related injuries boosted performance for adult trauma patients; however, it reduced performance for children. The machine intelligence model described here demonstrates similar performance to contemporary machine intelligence models without requiring restrictive regression model criteria or extensive medical expertise.
Intraoperative Liver Surface Completion with Graph Convolutional VAE
Authors: Simone Foti, Bongjin Koo, Thomas Dowrick, Joao Ramalhinho, Moustafa Allam, Brian Davidson, Danail Stoyanov, Matthew J. Clarkson
Date: 2020-09-08 00:00:00
Tasks: Data Augmentation

In this work we propose a method based on geometric deep learning to predict the complete surface of the liver, given a partial point cloud of the organ obtained during the surgical laparoscopic procedure. We introduce a new data augmentation technique that randomly perturbs shapes in their frequency domain to compensate the limited size of our dataset. The core of our method is a variational autoencoder (VAE) that is trained to learn a latent space for complete shapes of the liver. At inference time, the generative part of the model is embedded in an optimisation procedure where the latent representation is iteratively updated to generate a model that matches the intraoperative partial point cloud. The effect of this optimisation is a progressive non-rigid deformation of the initially generated shape. Our method is qualitatively evaluated on real data and quantitatively evaluated on synthetic data. We compared with a state-of-the-art rigid registration algorithm, that our method outperformed in visible areas.
Contraction $\mathcal{L}_1$-Adaptive Control using Gaussian Processes
Authors: Aditya Gahlawat, Arun Lakshmanan, Lin Song, Andrew Patterson, Zhuohuan Wu, Naira Hovakimyan, Evangelos Theodorou
Date: 2020-09-08 00:00:00
Tasks: Gaussian Processes

We present $\mathcal{CL}_1$-$\mathcal{GP}$, a control framework that enables safe simultaneous learning and control for systems subject to uncertainties. The two main constituents are contraction theory-based $\mathcal{L}_1$ ($\mathcal{CL}_1$) control and Bayesian learning in the form of Gaussian process (GP) regression. The $\mathcal{CL}_1$ controller ensures that control objectives are met while providing safety certificates. Furthermore, $\mathcal{CL}_1$-$\mathcal{GP}$ incorporates any available data into a GP model of uncertainties, which improves performance and enables the motion planner to achieve optimality safely. This way, the safe operation of the system is always guaranteed, even during the learning transients. We provide a few illustrative examples for the safe learning and control of planar quadrotor systems in a variety of environments.
TanhSoft -- a family of activation functions combining Tanh and Softplus
Authors: Koushik Biswas, Sandeep Kumar, Shilpak Banerjee, Ashish Kumar Pandey
Date: 2020-09-08 00:00:00
Tasks: General Classification, Image Classification

Deep learning at its core, contains functions that are composition of a linear transformation with a non-linear function known as activation function. In past few years, there is an increasing interest in construction of novel activation functions resulting in better learning. In this work, we propose a family of novel activation functions, namely TanhSoft, with four undetermined hyper-parameters of the form tanh({\alpha}x+{\beta}e^{{\gamma}x})ln({\delta}+e^x) and tune these hyper-parameters to obtain activation functions which are shown to outperform several well known activation functions. For instance, replacing ReLU with xtanh(0.6e^x)improves top-1 classification accuracy on CIFAR-10 by 0.46% for DenseNet-169 and 0.7% for Inception-v3 while with tanh(0.87x)ln(1 +e^x) top-1 classification accuracy on CIFAR-100 improves by 1.24% for DenseNet-169 and 2.57% for SimpleNet model.
Trajectory Based Podcast Recommendation
Authors: Greg Benton, Ghazal Fazelnia, Alice Wang, Ben Carterette
Date: 2020-09-08 00:00:00
Tasks: Collaborative Filtering

Podcast recommendation is a growing area of research that presents new challenges and opportunities. Individuals interact with podcasts in a way that is distinct from most other media; and primary to our concerns is distinct from music consumption. We show that successful and consistent recommendations can be made by viewing users as moving through the podcast library sequentially. Recommendations for future podcasts are then made using the trajectory taken from their sequential behavior. Our experiments provide evidence that user behavior is confined to local trends, and that listening patterns tend to be found over short sequences of similar types of shows. Ultimately, our approach gives a450%increase in effectiveness over a collaborative filtering baseline.
Nonlinear computations in spiking neural networks through multiplicative synapses
Authors: Michele Nardin, James W Phillips, William F. Podlaski, Sander W Keemink
Date: 2020-09-08 00:00:00

The brain efficiently performs nonlinear computations through its intricate networks of spiking neurons, but how this is done remains elusive. While nonlinear computations can be implemented successfully in spiking neural networks, this requires supervised training and the resulting connectivity can be hard to interpret. In contrast, the required connectivity for any computation in the form of a linear dynamical system can be directly derived and understood with the spike coding network (SCN) framework. These networks also have biologically realistic activity patterns and are highly robust to cell death. Here we extend the SCN framework to directly implement any polynomial dynamical system, without the need for training. This results in networks requiring a mix of synapse types (fast, slow, and multiplicative), which we term multiplicative spike coding networks (mSCNs). Using mSCNs, we demonstrate how to directly derive the required connectivity for several nonlinear dynamical systems. We also show how to carry out higher-order polynomials with coupled networks that use only pair-wise multiplicative synapses, and provide expected numbers of connections for each synapse type. Overall, our work demonstrates a novel method for implementing nonlinear computations in spiking neural networks, while keeping the attractive features of standard SCNs (robustness, realistic activity patterns, and interpretable connectivity). Finally, we discuss the biological plausibility of our approach, and how the high accuracy and robustness of the approach may be of interest for neuromorphic computing.
Referenced Thermodynamic Integration for Bayesian Model Selection: Application to COVID-19 Model Selection
Authors: Iwona Hawryluk, Swapnil Mishra, Seth Flaxman, Samir Bhatt, Thomas A. Mellan
Date: 2020-09-08 00:00:00
Tasks: Benchmarking, Epidemiology, model, Model Selection

Model selection is a fundamental part of the applied Bayesian statistical methodology. Metrics such as the Akaike Information Criterion are commonly used in practice to select models but do not incorporate the uncertainty of the models' parameters and can give misleading choices. One approach that uses the full posterior distribution is to compute the ratio of two models' normalising constants, known as the Bayes factor. Often in realistic problems, this involves the integration of analytically intractable, high-dimensional distributions, and therefore requires the use of stochastic methods such as thermodynamic integration (TI). In this paper we apply a variation of the TI method, referred to as referenced TI, which computes a single model's normalising constant in an efficient way by using a judiciously chosen reference density. The advantages of the approach and theoretical considerations are set out, along with explicit pedagogical 1 and 2D examples. Benchmarking is presented with comparable methods and we find favourable convergence performance. The approach is shown to be useful in practice when applied to a real problem - to perform model selection for a semi-mechanistic hierarchical Bayesian model of COVID-19 transmission in South Korea involving the integration of a 200D density.
LynyrdSkynyrd at WNUT-2020 Task 2: Semi-Supervised Learning for Identification of Informative COVID-19 English Tweets
Authors: Abhilasha Sancheti, Kushal Chawla, Gaurav Verma
Date: 2020-09-08 00:00:00
Proceeding: EMNLP (WNUT) 2020 11
Tasks: BIG-bench Machine Learning, Task 2

We describe our system for WNUT-2020 shared task on the identification of informative COVID-19 English tweets. Our system is an ensemble of various machine learning methods, leveraging both traditional feature-based classifiers as well as recent advances in pre-trained language models that help in capturing the syntactic, semantic, and contextual features from the tweets. We further employ pseudo-labelling to incorporate the unlabelled Twitter data released on the pandemic. Our best performing model achieves an F1-score of 0.9179 on the provided validation set and 0.8805 on the blind test-set.
Graph neural networks-based Scheduler for Production planning problems using Reinforcement Learning
Authors: Mohammed Sharafath Abdul Hameed, Andreas Schwung
Date: 2020-09-08 00:00:00
Tasks: Distributed Optimization, Graph Neural Network, Job Shop Scheduling, reinforcement-learning, Reinforcement Learning (RL), Scheduling

Reinforcement learning (RL) is increasingly adopted in job shop scheduling problems (JSSP). But RL for JSSP is usually done using a vectorized representation of machine features as the state space. It has three major problems: (1) the relationship between the machine units and the job sequence is not fully captured, (2) exponential increase in the size of the state space with increasing machines/jobs, and (3) the generalization of the agent to unseen scenarios. We present a novel framework - GraSP-RL, GRAph neural network-based Scheduler for Production planning problems using Reinforcement Learning. It represents JSSP as a graph and trains the RL agent using features extracted using a graph neural network (GNN). While the graph is itself in the non-euclidean space, the features extracted using the GNNs provide a rich encoding of the current production state in the euclidean space, which is then used by the RL agent to select the next job. Further, we cast the scheduling problem as a decentralized optimization problem in which the learning agent is assigned to all the production units and the agent learns asynchronously from the data collected on all the production units. The GraSP-RL is then applied to a complex injection molding production environment with 30 jobs and 4 machines. The task is to minimize the makespan of the production plan. The schedule planned by GraSP-RL is then compared and analyzed with a priority dispatch rule algorithm like first-in-first-out (FIFO) and metaheuristics like tabu search (TS) and genetic algorithm (GA). The proposed GraSP-RL outperforms the FIFO, TS, and GA for the trained task of planning 30 jobs in JSSP. We further test the generalization capability of the trained agent on two different problem classes: Open shop system (OSS) and Reactive JSSP (RJSSP) where our method produces results better than FIFO and comparable results to TS and GA.
Refined approachability algorithms and application to regret minimization with global costs
Authors: Joon Kwon
Date: 2020-09-08 00:00:00

Blackwell's approachability is a framework where two players, the Decision Maker and the Environment, play a repeated game with vector-valued payoffs. The goal of the Decision Maker is to make the average payoff converge to a given set called the target. When this is indeed possible, simple algorithms which guarantee the convergence are known. This abstract tool was successfully used for the construction of optimal strategies in various repeated games, but also found several applications in online learning. By extending an approach proposed by (Abernethy et al., 2011), we construct and analyze a class of Follow the Regularized Leader algorithms (FTRL) for Blackwell's approachability which are able to minimize not only the Euclidean distance to the target set (as it is often the case in the context of Blackwell's approachability) but a wide range of distance-like quantities. This flexibility enables us to apply these algorithms to closely minimize the quantity of interest in various online learning problems. In particular, for regret minimization with $\ell_p$ global costs, we obtain the first bounds with explicit dependence in $p$ and the dimension $d$.
Optimal training of integer-valued neural networks with mixed integer programming
Authors: Tómas Thorbjarnarson, Neil Yorke-Smith
Date: 2020-09-08 00:00:00

Recent work has shown potential in using Mixed Integer Programming (MIP) solvers to optimize certain aspects of neural networks (NNs). However the intriguing approach of training NNs with MIP solvers is under-explored. State-of-the-art-methods to train NNs are typically gradient-based and require significant data, computation on GPUs, and extensive hyper-parameter tuning. In contrast, training with MIP solvers does not require GPUs or heavy hyper-parameter tuning, but currently cannot handle anything but small amounts of data. This article builds on recent advances that train binarized NNs using MIP solvers. We go beyond current work by formulating new MIP models which improve training efficiency and which can train the important class of integer-valued neural networks (INNs). We provide two novel methods to further the potential significance of using MIP to train NNs. The first method optimizes the number of neurons in the NN while training. This reduces the need for deciding on network architecture before training. The second method addresses the amount of training data which MIP can feasibly handle: we provide a batch training method that dramatically increases the amount of data that MIP solvers can use to train. We thus provide a promising step towards using much more data than before when training NNs using MIP models. Experimental results on two real-world data-limited datasets demonstrate that our approach strongly outperforms the previous state of the art in training NN with MIP, in terms of accuracy, training time and amount of data. Our methodology is proficient at training NNs when minimal training data is available, and at training with minimal memory requirements -- which is potentially valuable for deploying to low-memory devices.