OpenRaiser/Intern-Atlas huggingface dataset:
MedGAN: Medical Image Translation using GANs
Venue: arXiv cs.CV 2019
Year: 2019

Image-to-image translation is considered a new frontier in the field of medical image analysis, with numerous potential applications. However, a large portion of recent approaches offers individualized solutions based on specialized task-specific architectures or require refinement through non-end-to-end training. In this paper, we propose a new framework, named MedGAN, for medical image-to-image translation which operates on the image level in an end-to-end manner. MedGAN builds upon recent advances in the field of generative adversarial networks (GANs) by merging the adversarial framework with a new combination of non-adversarial losses. We utilize a discriminator network as a trainable feature extractor which penalizes the discrepancy between the translated medical images and the desired modalities. Moreover, style-transfer losses are utilized to match the textures and fine-structures of the desired target images to the translated images. Additionally, we present a new generator architecture, titled CasNet, which enhances the sharpness of the translated medical outputs through progressive refinement via encoder-decoder pairs. Without any application-specific modifications, we apply MedGAN on three different tasks: PET-CT translation, correction of MR motion artefacts and PET image denoising. Perceptual analysis by radiologists and quantitative evaluations illustrate that the MedGAN outperforms other existing translation approaches.
Property Testing for Differential Privacy
Venue: arXiv cs.CR 2019
Year: 2019

We consider the problem of property testing for differential privacy: with black-box access to a purportedly private algorithm, can we verify its privacy guarantees? In particular, we show that any privacy guarantee that can be efficiently verified is also efficiently breakable in the sense that there exist two databases between which we can efficiently distinguish. We give lower bounds on the query complexity of verifying pure differential privacy, approximate differential privacy, random pure differential privacy, and random approximate differential privacy. We also give algorithmic upper bounds. The lower bounds obtained in the work are infeasible for the scale of parameters that are typically considered reasonable in the differential privacy literature, even when we suppose that the verifier has access to an (untrusted) description of the algorithm. A central message of this work is that verifying privacy requires compromise by either the verifier or the algorithm owner. Either the verifier has to be satisfied with a weak privacy guarantee, or the algorithm owner has to compromise on side information or access to the algorithm.
Implicit Policy for Reinforcement Learning
Venue: arXiv cs.LG 2019
Year: 2019

We introduce Implicit Policy, a general class of expressive policies that can flexibly represent complex action distributions in reinforcement learning, with efficient algorithms to compute entropy regularized policy gradients. We empirically show that, despite its simplicity in implementation, entropy regularization combined with a rich policy class can attain desirable properties displayed under maximum entropy reinforcement learning framework, such as robustness and multi-modality.
Adaptive Input Estimation in Linear Dynamical Systems with Applications to Learning-from-Observations
Venue: arXiv cs.LG 2019
Year: 2019

We address the problem of estimating the inputs of a dynamical system from measurements of the system's outputs. To this end, we introduce a novel estimation algorithm that explicitly trades off bias and variance to optimally reduce the overall estimation error. This optimal trade-off is done efficiently and adaptively in every time step. Experimentally, we show that our method often produces estimates with substantially lower error compared to the state-of-the-art. Finally, we consider the more complex \emph{Learning-from-Observations} framework, where an agent should learn a controller from the outputs of an expert's demonstration. We incorporate our estimation algorithm as a building block inside this framework and show that it enables learning controllers successfully.
COUNTDOWN: a Run-time Library for Performance-Neutral Energy Saving in MPI Applications
Venue: arXiv cs.DC 2019
Year: 2019

Power and energy consumption is becoming key challenges to deploy the first exascale supercomputer successfully. Large-scale HPC applications waste a significant amount of power in communication and synchronization-related idle times. However, due to the time scale at which communication happens, transitioning in low power states during communication's idle times may introduce unacceptable overhead in applications' execution time. In this paper, we present COUNTDOWN, a runtime library, supported by a methodology and analysis tool for identifying and automatically reducing the power consumption of the computing elements during communication and synchronization. COUNTDOWN saves energy without imposing significant time-to-completion increase by lowering CPUs power consumption only during idle times for which power state transition overhead are negligible. This is done transparently to the user, without requiring labor-intensive and error-prone application code modifications, nor requiring recompilation of the application. We test our methodology in a production Tier-0 system. For the NAS benchmarks, COUNTDOWN saves between 6% and 50% energy, with a time-to-solution penalty lower than 5%. In a complete production --- Quantum ESPRESSO --- for a 3.5K cores run, COUNTDOWN saves 22.36% energy, with a performance penalty below 3%. Energy saving increases to 37% with a performance penalty of 6.38%, if the application is executed without communication tuning.
Detecting and interpreting myocardial infarction using fully convolutional neural networks
Venue: arXiv cs.CY 2019
Year: 2019

Objective: We aim to provide an algorithm for the detection of myocardial infarction that operates directly on ECG data without any preprocessing and to investigate its decision criteria. Approach: We train an ensemble of fully convolutional neural networks on the PTB ECG dataset and apply state-of-the-art attribution methods. Main results: Our classifier reaches 93.3% sensitivity and 89.7% specificity evaluated using 10-fold cross-validation with sampling based on patients. The presented method outperforms state-of-the-art approaches and reaches the performance level of human cardiologists for detection of myocardial infarction. We are able to discriminate channel-specific regions that contribute most significantly to the neural network's decision. Interestingly, the network's decision is influenced by signs also recognized by human cardiologists as indicative of myocardial infarction. Significance: Our results demonstrate the high prospects of algorithmic ECG analysis for future clinical applications considering both its quantitative performance as well as the possibility of assessing decision criteria on a per-example basis, which enhances the comprehensibility of the approach.
Countdown Regression: Sharp and Calibrated Survival Predictions
Venue: arXiv cs.LG 2019
Year: 2019

Probabilistic survival predictions from models trained with Maximum Likelihood Estimation (MLE) can have high, and sometimes unacceptably high variance. The field of meteorology, where the paradigm of maximizing sharpness subject to calibration is popular, has addressed this problem by using scoring rules beyond MLE, such as the Continuous Ranked Probability Score (CRPS). In this paper we present the \emph{Survival-CRPS}, a generalization of the CRPS to the survival prediction setting, with right-censored and interval-censored variants. We evaluate our ideas on the mortality prediction task using two different Electronic Health Record (EHR) data sets (STARR and MIMIC-III) covering millions of patients, with suitable deep neural network architectures: a Recurrent Neural Network (RNN) for STARR and a Fully Connected Network (FCN) for MIMIC-III. We compare results between the two scoring rules while keeping the network architecture and data fixed, and show that models trained with Survival-CRPS result in sharper predictive distributions compared to those trained by MLE, while still maintaining calibration.
Simulation Study on a New Peer Review Approach
Venue: arXiv cs.DL 2019
Year: 2019

The increasing volume of scientific publications and grant proposals has generated an unprecedentedly high workload to scientific communities. Consequently, review quality has been decreasing and review outcomes have become less correlated with the real merits of the papers and proposals. A novel distributed peer review (DPR) approach has recently been proposed to address these issues. The new approach assigns principal investigators (PIs) who submitted proposals (or papers) to the same program as reviewers. Each PI reviews and ranks a small number (such as seven) of other PIs' proposals. The individual rankings are then used to estimate a global ranking of all proposals using the Modified Borda Count (MBC). In this study, we perform simulation studies to investigate several parameters important for the decision making when adopting this new approach. We also propose a new method called Concordance Index-based Global Ranking (CIGR) to estimate global ranking from individual rankings. An efficient simulated annealing algorithm is designed to search the optimal Concordance Index (CI). Moreover, we design a new balanced review assignment procedure, which can result in significantly better performance for both MBC and CIGR methods. We found that CIGR performs better than MBC when the review quality is relatively high. As review quality and review difficulty are tightly correlated, we constructed a boundary in the space of review quality vs review difficulty that separates the CIGR-superior and MBC-superior regions. Finally, we propose a multi-stage DPR strategy based on CIGR, which has the potential to substantially improve the overall review performance while reducing the review workload.
Aggregation-Based Certificate Transparency Gossip
Venue: arXiv cs.CR 2019
Year: 2019

Certificate Transparency (CT) requires that every CA-issued TLS certificate must be publicly logged. While a CT log need not be trusted in theory, it relies on the assumption that every client observes and cryptographically verifies the same log. As such, some form of gossip mechanism is needed in practice. Despite CT being adopted by several major browser vendors, no gossip mechanism is widely deployed. We suggest an aggregation-based gossip mechanism that passively observes cryptographic material that CT logs emit in plaintext, aggregating at packet processors (such as routers and switches) to periodically verify log consistency off-path. In other words, gossip is provided as-a-service by the network. Based on 20 days of RIPE Atlas measurements that represent clients from 3500 autonomous systems and 40% of the IPv4 space, our proposal can be deployed incrementally for a realistic threat model with significant protection against split-viewing CT logs. We also show that aggregation-based gossip can be implemented for a variety of packet processors using P4 and XDP, running at 10 Gbps line-speed.
Linear-Time Online Algorithm Inferring the Shortest Path from a Walk
Venue: arXiv cs.DS 2019
Year: 2019

We consider the problem of inferring an edge-labeled graph from the sequence of edge labels seen in a walk of that graph. It has been known that this problem is solvable in $O(n \log n)$ time when the targets are path or cycle graphs. This paper presents an online algorithm for the problem of this restricted case that runs in $O(n)$ time, based on Manacher's algorithm for computing all the maximal palindromes in a string.
Learning Existing Social Conventions via Observationally Augmented Self-Play
Venue: arXiv cs.AI 2019
Year: 2019

In order for artificial agents to coordinate effectively with people, they must act consistently with existing conventions (e.g. how to navigate in traffic, which language to speak, or how to coordinate with teammates). A group's conventions can be viewed as a choice of equilibrium in a coordination game. We consider the problem of an agent learning a policy for a coordination game in a simulated environment and then using this policy when it enters an existing group. When there are multiple possible conventions we show that learning a policy via multi-agent reinforcement learning (MARL) is likely to find policies which achieve high payoffs at training time but fail to coordinate with the real group into which the agent enters. We assume access to a small number of samples of behavior from the true convention and show that we can augment the MARL objective to help it find policies consistent with the real group's convention. In three environments from the literature - traffic, communication, and team coordination - we observe that augmenting MARL with a small amount of imitation learning greatly increases the probability that the strategy found by MARL fits well with the existing social convention. We show that this works even in an environment where standard training methods very rarely find the true convention of the agent's partners.
On the Benefits of Network-level Cooperation in IoT Networks with Aggregators
Venue: arXiv cs.IT 2019
Year: 2019

In this work, we consider a random access Internet of Things IoT wireless network assisted by two aggregators collecting information from two disjoint groups of sensors. The nodes and the aggregators are transmitting in a random access manner under slotted time, the aggregators perform network-level cooperation for the data collection. The aggregators are equipped with queues to store data packets that are transmitted by the network nodes and relaying them to the destination node. We characterize the throughput performance of the IoT network and we obtain the stability conditions for the queues at the aggregators. We apply the theory of boundary value problems to analyze the delay performance. Our results show that the presence of the aggregators provides significant gains in the IoT network performance, in addition, we provide useful insights regarding the scalability of the IoT network.
3D RoI-aware U-Net for Accurate and Efficient Colorectal Tumor Segmentation
Venue: arXiv cs.CV 2019
Year: 2019

Segmentation of colorectal cancerous regions from 3D Magnetic Resonance (MR) images is a crucial procedure for radiotherapy which conventionally requires accurate delineation of tumour boundaries at an expense of labor, time and reproducibility. While deep learning based methods serve good baselines in 3D image segmentation tasks, small applicable patch size limits effective receptive field and degrades segmentation performance. In addition, Regions of interest (RoIs) localization from large whole volume 3D images serves as a preceding operation that brings about multiple benefits in terms of speed, target completeness, reduction of false positives. Distinct from sliding window or non-joint localization-segmentation based models, we propose a novel multitask framework referred to as 3D RoI-aware U-Net (3D RU-Net), for RoI localization and in-region segmentation where the two tasks share one backbone encoder network. With the region proposals from the encoder, we crop multi-level RoI in-region features from the encoder to form a GPU memory-efficient decoder for detailpreserving segmentation and therefore enlarged applicable volume size and effective receptive field. To effectively train the model, we designed a Dice formulated loss function for the global-to-local multi-task learning procedure. Based on the efficiency gains, we went on to ensemble models with different receptive fields to achieve even higher performance costing minor extra computational expensiveness. Extensive experiments were conducted on 64 cancerous cases with a four-fold cross-validation, and the results showed significant superiority in terms of accuracy and efficiency over conventional frameworks. In conclusion, the proposed method has a huge potential for extension to other 3D object segmentation tasks from medical images due to its inherent generalizability. The code for the proposed method is publicly available.
Deep learning in business analytics and operations research: Models, applications and managerial implications
Venue: arXiv cs.LG 2019
Year: 2019

Business analytics refers to methods and practices that create value through data for individuals, firms, and organizations. This field is currently experiencing a radical shift due to the advent of deep learning: deep neural networks promise improvements in prediction performance as compared to models from traditional machine learning. However, our research into the existing body of literature reveals a scarcity of research works utilizing deep learning in our discipline. Accordingly, the objectives of this overview article are as follows: (1) we review research on deep learning for business analytics from an operational point of view. (2) We motivate why researchers and practitioners from business analytics should utilize deep neural networks and review potential use cases, necessary requirements, and benefits. (3) We investigate the added value to operations research in different case studies with real data from entrepreneurial undertakings. All such cases demonstrate improvements in operational performance over traditional machine learning and thus direct value gains. (4) We provide guidelines and implications for researchers, managers and practitioners in operations research who want to advance their capabilities for business analytics with regard to deep learning. (5) Our computational experiments find that default, out-of-the-box architectures are often suboptimal and thus highlight the value of customized architectures by proposing a novel deep-embedded network.
Divergence and unique solution of equations
Venue: arXiv cs.LO 2019
Year: 2019

We study proof techniques for bisimilarity based on unique solution of equations. We draw inspiration from a result by Roscoe in the denotational setting of CSP and for failure semantics, essentially stating that an equation (or a system of equations) whose infinite unfolding never produces a divergence has the unique-solution property. We transport this result onto the operational setting of CCS and for bisimilarity. We then exploit the operational approach to: refine the theorem, distinguishing between different forms of divergence; derive an abstract formulation of the theorems, on generic LTSs; adapt the theorems to other equivalences such as trace equivalence, and to preorders such as trace inclusion. We compare the resulting techniques to enhancements of the bisimulation proof method (the `up-to techniques'). Finally, we study the theorems in name-passing calculi such as the asynchronous $π$-calculus, and use them to revisit the completeness part of the proof of full abstraction of Milner's encoding of the $λ$-calculus into the $π$-calculus for Lévy-Longo Trees.
TextWorld: A Learning Environment for Text-based Games
Venue: arXiv cs.LG 2019
Year: 2019

We introduce TextWorld, a sandbox learning environment for the training and evaluation of RL agents on text-based games. TextWorld is a Python library that handles interactive play-through of text games, as well as backend functions like state tracking and reward assignment. It comes with a curated list of games whose features and challenges we have analyzed. More significantly, it enables users to handcraft or automatically generate new games. Its generative mechanisms give precise control over the difficulty, scope, and language of constructed games, and can be used to relax challenges inherent to commercial text games like partial observability and sparse rewards. By generating sets of varied but similar games, TextWorld can also be used to study generalization and transfer learning. We cast text-based games in the Reinforcement Learning formalism, use our framework to develop a set of benchmark games, and evaluate several baseline agents on this set and the curated list.
Probabilistic Databases with an Infinite Open-World Assumption
Venue: arXiv cs.DB 2019
Year: 2019

Probabilistic databases (PDBs) introduce uncertainty into relational databases by specifying probabilities for several possible instances. Traditionally, they are finite probability spaces over database instances. Such finite PDBs inherently make a closed-world assumption: non-occurring facts are assumed to be impossible, rather than just unlikely. As convincingly argued by Ceylan et al. (KR '16), this results in implausibilities and clashes with intuition. An open-world assumption, where facts not explicitly listed may have a small positive probability can yield more reasonable results. The corresponding open-world model of Ceylan et al., however, assumes that all entities in the PDB come from a fixed finite universe. In this work, we take one further step and propose a model of "truly" open-world PDBs with an infinite universe. This is natural when we consider entities from typical domains such as integers, real numbers, or strings. While the probability space might become infinitely large, all instances of a PDB remain finite. We provide a sound mathematical framework for infinite PDBs generalizing the existing theory of finite PDBs. Our main results are concerned with countable, tuple-independent PDBs; we present a generic construction showing that such PDBs exist in the infinite and provide a characterization of their existence. This construction can be used to give an open-world semantics to finite PDBs. The construction can also be extended to so-called block-independent-disjoint probabilistic databases. Algorithmic questions are not the focus of this paper, but we show how query evaluation algorithms can be lifted from finite PDBs to perform approximate evaluation (with an arbitrarily small additive approximation error) in countably infinite tuple-independent PDBs.
Adaptation to Easy Data in Prediction with Limited Advice
Venue: arXiv cs.LG 2019
Year: 2019

We derive an online learning algorithm with improved regret guarantees for `easy' loss sequences. We consider two types of `easiness': (a) stochastic loss sequences and (b) adversarial loss sequences with small effective range of the losses. While a number of algorithms have been proposed for exploiting small effective range in the full information setting, Gerchinovitz and Lattimore [2016] have shown the impossibility of regret scaling with the effective range of the losses in the bandit setting. We show that just one additional observation per round is sufficient to circumvent the impossibility result. The proposed Second Order Difference Adjustments (SODA) algorithm requires no prior knowledge of the effective range of the losses, $\varepsilon$, and achieves an $O(\varepsilon \sqrt{KT \ln K}) + \tilde{O}(\varepsilon K \sqrt[4]{T})$ expected regret guarantee, where $T$ is the time horizon and $K$ is the number of actions. The scaling with the effective loss range is achieved under significantly weaker assumptions than those made by Cesa-Bianchi and Shamir [2018] in an earlier attempt to circumvent the impossibility result. We also provide a regret lower bound of $Ω(\varepsilon\sqrt{T K})$, which almost matches the upper bound. In addition, we show that in the stochastic setting SODA achieves an $O\left(\sum_{a:Δ_a>0} \frac{K^3 \varepsilon^2}{Δ_a}\right)$ pseudo-regret bound that holds simultaneously with the adversarial regret guarantee. In other words, SODA is safe against an unrestricted oblivious adversary and provides improved regret guarantees for at least two different types of `easiness' simultaneously.