OpenRaiser/Intern-Atlas huggingface dataset:
Modeling the Multiple Sclerosis Brain Disease Using Agents: What Works and What Doesn't?
Venue: arXiv cs.MA 2017
Year: 2017

The human brain is one of the most complex living structures in the known Universe. It consists of billions of neurons and synapses. Due to its intrinsic complexity, it can be a formidable task to accurately depict brain's structure and functionality. In the past, numerous studies have been conducted on modeling brain disease, structure, and functionality. Some of these studies have employed Agent-based approaches including multiagent-based simulation models as well as brain complex networks. While these models have all been developed using agent-based computing, however, to our best knowledge, none of them have employed the use of Agent-Oriented Software Engineering (AOSE) methodologies in developing the brain or disease model. This is a problem because without due process, developed models can miss out on important requirements. AOSE has the unique capability of merging concepts from multiagent systems, agent-based modeling, artificial intelligence, besides concepts from distributed systems. AOSE involves the various tested software engineering principles in various phases of the model development ranging from analysis, design, implementation, and testing phases. In this paper, we employ the use of three different AOSE methodologies for modeling the Multiple Sclerosis brain disease namely GAIA, TROPOS, and MASE. After developing the models, we further employ the use of Exploratory Agent-based Modeling (EABM) to develop an actual model replicating previous results as a proof of concept. The key objective of this study is to demonstrate and explore the viability and effectiveness of AOSE methodologies in the development of complex brain structure and cognitive process models. Our key finding include demonstration that AOSE methodologies can be considerably helpful in modeling various living complex systems, in general, and the human brain, in particular.
Power-Traffic Coordinated Operation for Bi-Peak Shaving and Bi-Ramp Smoothing -A Hierarchical Data-Driven Approach
Venue: arXiv cs.SY 2017
Year: 2017

With the rapid adoption of distributed photovoltaics (PVs) in certain regions, issues such as lower net load valley during the day and more steep ramping of the demand after sunset start to challenge normal operations at utility companies. Urban transportation systems also have high peak congestion periods and steep ramping because of traffic patterns. We propose using the emerging electric vehicles (EVs) and the charing/discharging stations (CDSs) to coordinate the operation between power distribution system (PDS) and the urban transportation system (UTS), therefore, the operation challenges in each system can be mitigated by utilizing the flexibility of the other system. We conducted the simulation and numerical analysis using the IEEE 8,500-bus for the PDS and the Sioux Falls system with about 10,000 cars for the UTS. Two systems are simulated jointly to demonstrate the feasibility and effectiveness of the proposed approach.
Shape Complementarity Analysis for Objects of Arbitrary Shape
Venue: arXiv cs.CG 2017
Year: 2017

The basic problem of shape complementarity analysis appears fundamental to applications as diverse as mechanical design, assembly automation, robot motion planning, micro- and nano-fabrication, protein-ligand binding, and rational drug design. However, the current challenge lies in the lack of a general mathematical formulation that applies to objects of arbitrary shape. We propose that a measure of shape complementarity can be obtained from the extent of approximate overlap between shape skeletons. A space-continuous implicit generalization of the skeleton, called the skeletal density function (SDF) is defined over the Euclidean space that contains the individual assembly partners. The SDF shape descriptors capture the essential features that are relevant to proper contact alignment, and are considerably more robust than the conventional explicit skeletal representations. We express the shape complementarity score as a convolution of the individual SDFs. The problem then breaks down to a global optimization of the score over the configuration space of spatial relations, which can be efficiently implemented using fast Fourier transforms (FFTs) on nonequispaced samples. We demonstrate the effectiveness of the scoring approach for several examples from 2D peg-in-hole alignment to more complex 3D examples in mechanical assembly and protein docking. We show that the proposed method is reliable, inherently robust against small perturbations, and effective in steering gradient-based optimization.
On the Simultaneous Minimum Spanning Trees Problem
Venue: arXiv cs.DM 2017
Year: 2017

Simultaneous Embedding with Fixed Edges (SEFE) is a problem where given $k$ planar graphs we ask whether they can be simultaneously embedded so that the embedding of each graph is planar and common edges are drawn the same. Problems of SEFE type have inspired questions of Simultaneous Geometrical Representations and further derivations. Based on this motivation we investigate the generalization of the simultaneous paradigm on the classical combinatorial problem of minimum spanning trees. Given $k$ graphs with weighted edges, such that they have a common intersection, are there minimum spanning trees of the respective graphs such that they agree on the intersection? We show that the unweighted case is polynomial-time solvable while the weighted case is only polynomial-time solvable for $k=2$ and it is NP-complete for $k\geq 3$.
A Short Solution to the Many-Player Silent Duel with Arbitrary Consolation Prize
Venue: arXiv cs.GT 2017
Year: 2017

The classical constant-sum 'silent duel' game had two antagonistic marksmen walking towards each other. A more friendly formulation has two equally skilled marksmen approaching targets at which they may silently fire at distances of their own choice. The winner, who gets a unit prize, is the marksman who hits his target at the greatest distance; if both miss, they share the prize (each gets a 'consolation prize' of one half). In another formulation, if they both miss they each get zero. More generally we can consider more than two marksmen and an arbitrary consolation prize. This non-constant sum game may be interpreted as a research tournament where the entrant who successfully solves the hardest problem wins the prize. We give the first complete solution to the many-player problem with arbitrary consolation prize: moreover (by taking particular values for the consolation prize), our theorem incorporates various special results in the literature, and our proof is simpler than any of these.
Deep Learning with Permutation-invariant Operator for Multi-instance Histopathology Classification
Venue: arXiv cs.LG 2017
Year: 2017

The computer-aided analysis of medical scans is a longstanding goal in the medical imaging field. Currently, deep learning has became a dominant methodology for supporting pathologists and radiologist. Deep learning algorithms have been successfully applied to digital pathology and radiology, nevertheless, there are still practical issues that prevent these tools to be widely used in practice. The main obstacles are low number of available cases and large size of images (a.k.a. the small n, large p problem in machine learning), and a very limited access to annotation at a pixel level that can lead to severe overfitting and large computational requirements. We propose to handle these issues by introducing a framework that processes a medical image as a collection of small patches using a single, shared neural network. The final diagnosis is provided by combining scores of individual patches using a permutation-invariant operator (combination). In machine learning community such approach is called a multi-instance learning (MIL).
Enabling Embodied Analogies in Intelligent Music Systems
Venue: arXiv cs.HC 2017
Year: 2017

The present methodology is aimed at cross-modal machine learning and uses multidisciplinary tools and methods drawn from a broad range of areas and disciplines, including music, systematic musicology, dance, motion capture, human-computer interaction, computational linguistics and audio signal processing. Main tasks include: (1) adapting wisdom-of-the-crowd approaches to embodiment in music and dance performance to create a dataset of music and music lyrics that covers a variety of emotions, (2) applying audio/language-informed machine learning techniques to that dataset to identify automatically the emotional content of the music and the lyrics, and (3) integrating motion capture data from a Vicon system and dancers performing on that music.
Maximum-width Axis-Parallel Empty Rectangular Annulus
Venue: arXiv cs.CG 2017
Year: 2017

Given a set $P$ of $n$ points on $\mathbb R^{2}$, we address the problem of computing an axis-parallel empty rectangular annulus $A$ of maximum-width such that no point of $P$ lies inside $A$ but all points of $P$ must lie inside, outside and on the boundaries of two parallel rectangles forming the annulus $A$. We propose an $O(n^3)$ time and $O(n)$ space algorithm to solve the problem. In a particular case when the inner rectangle of an axis-parallel empty rectangular annulus reduces to an input point we can solve the problem in $O(n \log n)$ time and $O(n)$ space.
Deep Learning Scaling is Predictable, Empirically
Venue: arXiv cs.LG 2017
Year: 2017

Deep learning (DL) creates impactful advances following a virtuous recipe: model architecture search, creating large training data sets, and scaling computation. It is widely believed that growing training sets and models should improve accuracy and result in better products. As DL application domains grow, we would like a deeper understanding of the relationships between training set size, computational scale, and model accuracy improvements to advance the state-of-the-art. This paper presents a large scale empirical characterization of generalization error and model size growth as training sets grow. We introduce a methodology for this measurement and test four machine learning domains: machine translation, language modeling, image processing, and speech recognition. Our empirical results show power-law generalization error scaling across a breadth of factors, resulting in power-law exponents---the "steepness" of the learning curve---yet to be explained by theoretical work. Further, model improvements only shift the error but do not appear to affect the power-law exponent. We also show that model size scales sublinearly with data size. These scaling relationships have significant implications on deep learning research, practice, and systems. They can assist model debugging, setting accuracy targets, and decisions about data set growth. They can also guide computing system design and underscore the importance of continued computational scaling.
Novel Exploration Techniques (NETs) for Malaria Policy Interventions
Venue: arXiv cs.AI 2017
Year: 2017

The task of decision-making under uncertainty is daunting, especially for problems which have significant complexity. Healthcare policy makers across the globe are facing problems under challenging constraints, with limited tools to help them make data driven decisions. In this work we frame the process of finding an optimal malaria policy as a stochastic multi-armed bandit problem, and implement three agent based strategies to explore the policy space. We apply a Gaussian Process regression to the findings of each agent, both for comparison and to account for stochastic results from simulating the spread of malaria in a fixed population. The generated policy spaces are compared with published results to give a direct reference with human expert decisions for the same simulated population. Our novel approach provides a powerful resource for policy makers, and a platform which can be readily extended to capture future more nuanced policy spaces.
State Estimation For An Agonistic-Antagonistic Muscle System
Venue: arXiv cs.SY 2017
Year: 2017

Research on assistive technology, rehabilitation, and prosthesis requires the understanding of human machine interaction, in which human muscular properties play a pivotal role. This paper studies a nonlinear agonistic-antagonistic muscle system based on the Hill muscle model. To investigate the characteristics of the muscle model, the problem of estimating the state variables and activation signals of the dual muscle system is considered. In this work, parameter uncertainty and unknown inputs are taken into account for the estimation problem. Three observers are presented: a high gain observer, a sliding mode observer, and an adaptive sliding mode observer. Theoretical analysis shows the convergence of the three observers. To facilitate numerical simulations, a backstepping controller is employed to drive the muscle system to track a desired trajectory. Numerical simulations reveal that the three observers are comparable and provide reliable estimates in noise free and noisy cases. The proposed schemes may serve as frameworks for estimation of complex multi-muscle systems, which could lead to intelligent exercise machines for adaptive training and rehabilitation, and adaptive prosthetics and exoskeletons.
Explainable AI: Beware of Inmates Running the Asylum Or: How I Learnt to Stop Worrying and Love the Social and Behavioural Sciences
Venue: arXiv cs.AI 2017
Year: 2017

In his seminal book `The Inmates are Running the Asylum: Why High-Tech Products Drive Us Crazy And How To Restore The Sanity' [2004, Sams Indianapolis, IN, USA], Alan Cooper argues that a major reason why software is often poorly designed (from a user perspective) is that programmers are in charge of design decisions, rather than interaction designers. As a result, programmers design software for themselves, rather than for their target audience, a phenomenon he refers to as the `inmates running the asylum'. This paper argues that explainable AI risks a similar fate. While the re-emergence of explainable AI is positive, this paper argues most of us as AI researchers are building explanatory agents for ourselves, rather than for the intended users. But explainable AI is more likely to succeed if researchers and practitioners understand, adopt, implement, and improve models from the vast and valuable bodies of research in philosophy, psychology, and cognitive science, and if evaluation of these models is focused more on people than on technology. From a light scan of literature, we demonstrate that there is considerable scope to infuse more results from the social and behavioural sciences into explainable AI, and present some key results from these fields that are relevant to explainable AI.
Recurrent Neural Network Language Models for Open Vocabulary Event-Level Cyber Anomaly Detection
Venue: arXiv cs.NE 2017
Year: 2017

Automated analysis methods are crucial aids for monitoring and defending a network to protect the sensitive or confidential data it hosts. This work introduces a flexible, powerful, and unsupervised approach to detecting anomalous behavior in computer and network logs, one that largely eliminates domain-dependent feature engineering employed by existing methods. By treating system logs as threads of interleaved "sentences" (event log lines) to train online unsupervised neural network language models, our approach provides an adaptive model of normal network behavior. We compare the effectiveness of both standard and bidirectional recurrent neural network language models at detecting malicious activity within network log data. Extending these models, we introduce a tiered recurrent architecture, which provides context by modeling sequences of users' actions over time. Compared to Isolation Forest and Principal Components Analysis, two popular anomaly detection algorithms, we observe superior performance on the Los Alamos National Laboratory Cyber Security dataset. For log-line-level red team detection, our best performing character-based model provides test set area under the receiver operator characteristic curve of 0.98, demonstrating the strong fine-grained anomaly detection performance of this approach on open vocabulary logging sources.
HySIA: Tool for Simulating and Monitoring Hybrid Automata Based on Interval Analysis
Venue: arXiv cs.LO 2017
Year: 2017

We present HySIA: a reliable runtime verification tool for nonlinear hybrid automata (HA) and signal temporal logic (STL) properties. HySIA simulates an HA with interval analysis techniques so that a trajectory is enclosed sharply within a set of intervals. Then, HySIA computes whether the simulated trajectory satisfies a given STL property; the computation is performed again with interval analysis to achieve reliability. Simulation and verification using HySIA are demonstrated through several example HA and STL formulas.
Toward Reliable and Rapid Elasticity for Streaming Dataflows on Clouds
Venue: arXiv cs.DC 2017
Year: 2017

The pervasive availability of streaming data is driving interest in distributed Fast Data platforms for streaming applications. Such latency-sensitive applications need to respond to dynamism in the input rates and task behavior using scale-in and -out on elastic Cloud resources. Platforms like Apache Storm do not provide robust capabilities for responding to such dynamism and for rapid task migration across VMs. We propose several dataflow checkpoint and migration approaches that allow a running streaming dataflow to migrate, without any loss of in-flight messages or their internal tasks states, while reducing the time to recover and stabilize. We implement and evaluate these migration strategies on Apache Storm using micro and application dataflows for scaling in and out on up to 2-21 Azure VMs. Our results show that we can migrate dataflows of large sizes within 50 sec, in comparison to Storm's default approach that takes over $100~sec$. We also find that our approaches stabilize the application much earlier and there is no failure and re-processing of messages.
DR-Net: Transmission Steered Single Image Dehazing Network with Weakly Supervised Refinement
Venue: arXiv cs.CV 2017
Year: 2017

Despite the recent progress in image dehazing, several problems remain largely unsolved such as robustness for varying scenes, the visual quality of reconstructed images, and effectiveness and flexibility for applications. To tackle these problems, we propose a new deep network architecture for single image dehazing called DR-Net. Our model consists of three main subnetworks: a transmission prediction network that predicts transmission map for the input image, a haze removal network that reconstructs latent image steered by the transmission map, and a refinement network that enhances the details and color properties of the dehazed result via weakly supervised learning. Compared to previous methods, our method advances in three aspects: (i) pure data-driven model; (ii) the end-to-end system; (iii) superior robustness, accuracy, and applicability. Extensive experiments demonstrate that our DR-Net outperforms the state-of-the-art methods on both synthetic and real images in qualitative and quantitative metrics. Additionally, the utility of DR-Net has been illustrated by its potential usage in several important computer vision tasks.
From knowledge-based to data-driven modeling of fuzzy rule-based systems: A critical reflection
Venue: arXiv cs.AI 2017
Year: 2017

This paper briefly elaborates on a development in (applied) fuzzy logic that has taken place in the last couple of decades, namely, the complementation or even replacement of the traditional knowledge-based approach to fuzzy rule-based systems design by a data-driven one. It is argued that the classical rule-based modeling paradigm is actually more amenable to the knowledge-based approach, for which it has originally been conceived, while being less apt to data-driven model design. An important reason that prevents fuzzy (rule-based) systems from being leveraged in large-scale applications is the flat structure of rule bases, along with the local nature of fuzzy rules and their limited ability to express complex dependencies between variables. This motivates alternative approaches to fuzzy systems modeling, in which functional dependencies can be represented more flexibly and more compactly in terms of hierarchical structures.
Representation and Reinforcement Learning for Personalized Glycemic Control in Septic Patients
Venue: arXiv cs.LG 2017
Year: 2017

Glycemic control is essential for critical care. However, it is a challenging task because there has been no study on personalized optimal strategies for glycemic control. This work aims to learn personalized optimal glycemic trajectories for severely ill septic patients by learning data-driven policies to identify optimal targeted blood glucose levels as a reference for clinicians. We encoded patient states using a sparse autoencoder and adopted a reinforcement learning paradigm using policy iteration to learn the optimal policy from data. We also estimated the expected return following the policy learned from the recorded glycemic trajectories, which yielded a function indicating the relationship between real blood glucose values and 90-day mortality rates. This suggests that the learned optimal policy could reduce the patients' estimated 90-day mortality rate by 6.3%, from 31% to 24.7%. The result demonstrates that reinforcement learning with appropriate patient state encoding can potentially provide optimal glycemic trajectories and allow clinicians to design a personalized strategy for glycemic control in septic patients.
Digraph Polynomials for Counting Cycles and Paths
Venue: arXiv cs.DM 2017
Year: 2017

Many polynomial invariants are defined on graphs for encoding the combinatorial information and researching them algebraically. In this paper, we introduce the cycle polynomial and the path polynomial of directed graphs for counting cycles and paths, respectively. They satisfy recurrence relations with respect to elementary edge or vertex operations. They are related to other polynomials and can also be generalized to the bivariate cycle polynomial, the bivariate path polynomial and the trivariate cycle-path polynomial. And a most general digraph polynomial satisfying such a linear recurrence relation is recursively defined and shown to be co-reducible to the trivariate cycle-path polynomial. We also give an explicit expression of this polynomial.
Spatial PixelCNN: Generating Images from Patches
Venue: arXiv cs.CV 2017
Year: 2017

In this paper we propose Spatial PixelCNN, a conditional autoregressive model that generates images from small patches. By conditioning on a grid of pixel coordinates and global features extracted from a Variational Autoencoder (VAE), we are able to train on patches of images, and reproduce the full-sized image. We show that it not only allows for generating high quality samples at the same resolution as the underlying dataset, but is also capable of upscaling images to arbitrary resolutions (tested at resolutions up to $50\times$) on the MNIST dataset. Compared to a PixelCNN++ baseline, Spatial PixelCNN quantitatively and qualitatively achieves similar performance on the MNIST dataset.