OpenRaiser/Intern-Atlas huggingface dataset:
Concurrent and Adaptive Extreme Scale Binding Free Energy Calculations
Venue: arXiv cs.DC 2018
Year: 2018

The efficacy of drug treatments depends on how tightly small molecules bind to their target proteins. The rapid and accurate quantification of the strength of these interactions (as measured by binding affinity) is a grand challenge of computational chemistry, surmounting which could revolutionize drug design and provide the platform for patient-specific medicine. Recent evidence suggests that molecular dynamics (MD) can achieve useful predictive accuracy (< 1 kcal/mol). For this predictive accuracy to impact clinical decision making, binding free energy computational campaigns must provide results rapidly and without loss of accuracy. This demands advances in algorithms, scalable software systems, and efficient utilization of supercomputing resources. We introduce a framework called HTBAC, designed to support accurate and scalable drug binding affinity calculations, while marshaling large simulation campaigns. We show that HTBAC supports the specification and execution of free-energy protocols at scale. This paper makes three main contributions: (1) shows the importance of adaptive execution for ensemble-based free energy protocols to improve binding affinity accuracy; (2) presents and characterizes HTBAC -- a software system that enables the scalable and adaptive execution of binding affinity protocols at scale; and (3) for a widely used free-energy protocol (TIES), shows improvements in the accuracy of simulations for a fixed amount of resource, or reduced resource consumption for a fixed accuracy as a consequence of adaptive execution.
Spectre Attacks: Exploiting Speculative Execution
Venue: arXiv cs.CR 2018
Year: 2018

Modern processors use branch prediction and speculative execution to maximize performance. For example, if the destination of a branch depends on a memory value that is in the process of being read, CPUs will try guess the destination and attempt to execute ahead. When the memory value finally arrives, the CPU either discards or commits the speculative computation. Speculative logic is unfaithful in how it executes, can access to the victim's memory and registers, and can perform operations with measurable side effects. Spectre attacks involve inducing a victim to speculatively perform operations that would not occur during correct program execution and which leak the victim's confidential information via a side channel to the adversary. This paper describes practical attacks that combine methodology from side channel attacks, fault attacks, and return-oriented programming that can read arbitrary memory from the victim's process. More broadly, the paper shows that speculative execution implementations violate the security assumptions underpinning numerous software security mechanisms, including operating system process separation, static analysis, containerization, just-in-time (JIT) compilation, and countermeasures to cache timing/side-channel attacks. These attacks represent a serious threat to actual systems, since vulnerable speculative execution capabilities are found in microprocessors from Intel, AMD, and ARM that are used in billions of devices. While makeshift processor-specific countermeasures are possible in some cases, sound solutions will require fixes to processor designs as well as updates to instruction set architectures (ISAs) to give hardware architects and software developers a common understanding as to what computation state CPU implementations are (and are not) permitted to leak.
Predicting Chronic Disease Hospitalizations from Electronic Health Records: An Interpretable Classification Approach
Venue: arXiv cs.LG 2018
Year: 2018

Urban living in modern large cities has significant adverse effects on health, increasing the risk of several chronic diseases. We focus on the two leading clusters of chronic disease, heart disease and diabetes, and develop data-driven methods to predict hospitalizations due to these conditions. We base these predictions on the patients' medical history, recent and more distant, as described in their Electronic Health Records (EHR). We formulate the prediction problem as a binary classification problem and consider a variety of machine learning methods, including kernelized and sparse Support Vector Machines (SVM), sparse logistic regression, and random forests. To strike a balance between accuracy and interpretability of the prediction, which is important in a medical setting, we propose two novel methods: K-LRT, a likelihood ratio test-based method, and a Joint Clustering and Classification (JCC) method which identifies hidden patient clusters and adapts classifiers to each cluster. We develop theoretical out-of-sample guarantees for the latter method. We validate our algorithms on large datasets from the Boston Medical Center, the largest safety-net hospital system in New England.
Depth Not Needed - An Evaluation of RGB-D Feature Encodings for Off-Road Scene Understanding by Convolutional Neural Network
Venue: arXiv cs.CV 2018
Year: 2018

Scene understanding for autonomous vehicles is a challenging computer vision task, with recent advances in convolutional neural networks (CNNs) achieving results that notably surpass prior traditional feature driven approaches. However, limited work investigates the application of such methods either within the highly unstructured off-road environment or to RGBD input data. In this work, we take an existing CNN architecture designed to perform semantic segmentation of RGB images of urban road scenes, then adapt and retrain it to perform the same task with multichannel RGBD images obtained under a range of challenging off-road conditions. We compare two different stereo matching algorithms and five different methods of encoding depth information, including disparity, local normal orientation and HHA (horizontal disparity, height above ground plane, angle with gravity), to create a total of ten experimental variations of our dataset, each of which is used to train and test a CNN so that classification performance can be evaluated against a CNN trained using standard RGB input.
Approximate Ranking from Pairwise Comparisons
Venue: arXiv cs.LG 2018
Year: 2018

A common problem in machine learning is to rank a set of n items based on pairwise comparisons. Here ranking refers to partitioning the items into sets of pre-specified sizes according to their scores, which includes identification of the top-k items as the most prominent special case. The score of a given item is defined as the probability that it beats a randomly chosen other item. Finding an exact ranking typically requires a prohibitively large number of comparisons, but in practice, approximate rankings are often adequate. Accordingly, we study the problem of finding approximate rankings from pairwise comparisons. We analyze an active ranking algorithm that counts the number of comparisons won, and decides whether to stop or which pair of items to compare next, based on confidence intervals computed from the data collected in previous steps. We show that this algorithm succeeds in recovering approximate rankings using a number of comparisons that is close to optimal up to logarithmic factors. We also present numerical results, showing that in practice, approximation can drastically reduce the number of comparisons required to estimate a ranking.
Improved Bounds on Lossless Source Coding and Guessing Moments via Rényi Measures
Venue: arXiv cs.IT 2018
Year: 2018

This paper provides upper and lower bounds on the optimal guessing moments of a random variable taking values on a finite set when side information may be available. These moments quantify the number of guesses required for correctly identifying the unknown object and, similarly to Arikan's bounds, they are expressed in terms of the Arimoto-Rényi conditional entropy. Although Arikan's bounds are asymptotically tight, the improvement of the bounds in this paper is significant in the non-asymptotic regime. Relationships between moments of the optimal guessing function and the MAP error probability are also established, characterizing the exact locus of their attainable values. The bounds on optimal guessing moments serve to improve non-asymptotic bounds on the cumulant generating function of the codeword lengths for fixed-to-variable optimal lossless source coding without prefix constraints. Non-asymptotic bounds on the reliability function of discrete memoryless sources are derived as well. Relying on these techniques, lower bounds on the cumulant generating function of the codeword lengths are derived, by means of the smooth Rényi entropy, for source codes that allow decoding errors.
Text Extraction and Retrieval from Smartphone Screenshots: Building a Repository for Life in Media
Venue: arXiv cs.IR 2018
Year: 2018

Daily engagement in life experiences is increasingly interwoven with mobile device use. Screen capture at the scale of seconds is being used in behavioral studies and to implement "just-in-time" health interventions. The increasing psychological breadth of digital information will continue to make the actual screens that people view a preferred if not required source of data about life experiences. Effective and efficient Information Extraction and Retrieval from digital screenshots is a crucial prerequisite to successful use of screen data. In this paper, we present the experimental workflow we exploited to: (i) pre-process a unique collection of screen captures, (ii) extract unstructured text embedded in the images, (iii) organize image text and metadata based on a structured schema, (iv) index the resulting document collection, and (v) allow for Image Retrieval through a dedicated vertical search engine application. The adopted procedure integrates different open source libraries for traditional image processing, Optical Character Recognition (OCR), and Image Retrieval. Our aim is to assess whether and how state-of-the-art methodologies can be applied to this novel data set. We show how combining OpenCV-based pre-processing modules with a Long short-term memory (LSTM) based release of Tesseract OCR, without ad hoc training, led to a 74% character-level accuracy of the extracted text. Further, we used the processed repository as baseline for a dedicated Image Retrieval system, for the immediate use and application for behavioral and prevention scientists. We discuss issues of Text Information Extraction and Retrieval that are particular to the screenshot image case and suggest important future work.
Deep Cross Polarimetric Thermal-to-visible Face Recognition
Venue: arXiv cs.CV 2018
Year: 2018

In this paper, we present a deep coupled learning frame- work to address the problem of matching polarimetric ther- mal face photos against a gallery of visible faces. Polariza- tion state information of thermal faces provides the miss- ing textural and geometrics details in the thermal face im- agery which exist in visible spectrum. we propose a coupled deep neural network architecture which leverages relatively large visible and thermal datasets to overcome the problem of overfitting and eventually we train it by a polarimetric thermal face dataset which is the first of its kind. The pro- posed architecture is able to make full use of the polari- metric thermal information to train a deep model compared to the conventional shallow thermal-to-visible face recogni- tion methods. Proposed coupled deep neural network also finds global discriminative features in a nonlinear embed- ding space to relate the polarimetric thermal faces to their corresponding visible faces. The results show the superior- ity of our method compared to the state-of-the-art models in cross thermal-to-visible face recognition algorithms.
Slugbot: An Application of a Novel and Scalable Open Domain Socialbot Framework
Venue: arXiv cs.CL 2018
Year: 2018

In this paper we introduce a novel, open domain socialbot for the Amazon Alexa Prize competition, aimed at carrying on friendly conversations with users on a variety of topics. We present our modular system, highlighting our different data sources and how we use the human mind as a model for data management. Additionally we build and employ natural language understanding and information retrieval tools and APIs to expand our knowledge bases. We describe our semistructured, scalable framework for crafting topic-specific dialogue flows, and give details on our dialogue management schemes and scoring mechanisms. Finally we briefly evaluate the performance of our system and observe the challenges that an open domain socialbot faces.
Plan in 2D, execute in 3D: An augmented reality solution for cup placement in total hip arthroplasty
Venue: arXiv cs.CV 2018
Year: 2018

Reproducibly achieving proper implant alignment is a critical step in total hip arthroplasty (THA) procedures that has been shown to substantially affect patient outcome. In current practice, correct alignment of the acetabular cup is verified in C-arm X-ray images that are acquired in an anterior-posterior (AP) view. Favorable surgical outcome is, therefore, heavily dependent on the surgeon's experience in understanding the 3D orientation of a hemispheric implant from 2D AP projection images. This work proposes an easy to use intra-operative component planning system based on two C-arm X-ray images that is combined with 3D augmented reality (AR) visualization that simplifies impactor and cup placement according to the planning by providing a real-time RGBD data overlay. We evaluate the feasibility of our system in a user study comprising four orthopedic surgeons at the Johns Hopkins Hospital, and also report errors in translation, anteversion, and abduction as low as 1.98 mm, 1.10 degrees, and 0.53 degrees, respectively. The promising performance of this AR solution shows that deploying this system could eliminate the need for excessive radiation, simplify the intervention, and enable reproducibly accurate placement of acetabular implants.
Robust PCA for Anomaly Detection in Cyber Networks
Venue: arXiv cs.CR 2018
Year: 2018

This paper uses network packet capture data to demonstrate how Robust Principal Component Analysis (RPCA) can be used in a new way to detect anomalies which serve as cyber-network attack indicators. The approach requires only a few parameters to be learned using partitioned training data and shows promise of ameliorating the need for an exhaustive set of examples of different types of network attacks. For Lincoln Lab's DARPA intrusion detection data set, the method achieves low false-positive rates while maintaining reasonable true-positive rates on individual packets. In addition, the method correctly detected packet streams in which an attack which was not previously encountered, or trained on, appears.
Differentially Private Releasing via Deep Generative Model (Technical Report)
Venue: arXiv cs.CR 2018
Year: 2018

Privacy-preserving releasing of complex data (e.g., image, text, audio) represents a long-standing challenge for the data mining research community. Due to rich semantics of the data and lack of a priori knowledge about the analysis task, excessive sanitization is often necessary to ensure privacy, leading to significant loss of the data utility. In this paper, we present dp-GAN, a general private releasing framework for semantic-rich data. Instead of sanitizing and then releasing the data, the data curator publishes a deep generative model which is trained using the original data in a differentially private manner; with the generative model, the analyst is able to produce an unlimited amount of synthetic data for arbitrary analysis tasks. In contrast of alternative solutions, dp-GAN highlights a set of key features: (i) it provides theoretical privacy guarantee via enforcing the differential privacy principle; (ii) it retains desirable utility in the released model, enabling a variety of otherwise impossible analyses; and (iii) most importantly, it achieves practical training scalability and stability by employing multi-fold optimization strategies. Through extensive empirical evaluation on benchmark datasets and analyses, we validate the efficacy of dp-GAN.
Ontology-based Approach for Identifying the Credibility Domain in Social Big Data
Venue: arXiv cs.IR 2018
Year: 2018

A challenge of managing and extracting useful knowledge from social media data sources has attracted much attention from academic and industry. To address this challenge, semantic analysis of textual data is focused in this paper. We propose an ontology-based approach to extract semantics of textual data and define the domain of data. In other words, we semantically analyse the social data at two levels i.e. the entity level and the domain level. We have chosen Twitter as a social channel challenge for a purpose of concept proof. Domain knowledge is captured in ontologies which are then used to enrich the semantics of tweets provided with specific semantic conceptual representation of entities that appear in the tweets. Case studies are used to demonstrate this approach. We experiment and evaluate our proposed approach with a public dataset collected from Twitter and from the politics domain. The ontology-based approach leverages entity extraction and concept mappings in terms of quantity and accuracy of concept identification.
Energy-Efficient User Access Control and Resource Allocation in HCNs with Non-Ideal Circuitry
Venue: arXiv cs.IT 2018
Year: 2018

In this paper, we study the energy-efficient user access control (UAC) based on resource allocation (RA) in heterogeneous cellular networks (HCNs) with the required downlink data rate under non-ideal power amplifiers (PAs) and circuit power. It is proved that the energy consumption minimization is achieved when the typical user accesses only one base station (BS), while the other BSs remain in idle mode on the transmission resource allocated to this user. For this purpose, we reformulate the original non-convex optimization problem into a series of convex optimization problems where, in each case, the transmit power and duration of the accessed BS are determined. Then, the BS with the minimal energy consumption is selected for transmission. Considering the approximate situation, it is showed that the optimal transmit duration of the accessed BS can be estimated in closed form. The benefits of our proposed UAC and RA schemes are validated using numerical simulations, which also characterize the effect that non-ideal PAs have on the total energy consumption of different transmission schemes.
Subquadratic Encodings for Point Configurations
Venue: arXiv cs.CG 2018
Year: 2018

For most algorithms dealing with sets of points in the plane, the only relevant information carried by the input is the combinatorial configuration of the points: the orientation of each triple of points in the set (clockwise, counterclockwise, or collinear). This information is called the order type of the point set. In the dual, realizable order types and abstract order types are combinatorial analogues of line arrangements and pseudoline arrangements. Too often in the literature we analyze algorithms in the real-RAM model for simplicity, putting aside the fact that computers as we know them cannot handle arbitrary real numbers without some sort of encoding. Encoding an order type by the integer coordinates of some realizing point set is known to yield doubly exponential coordinates in some cases. Other known encodings can achieve quadratic space or fast orientation queries, but not both. In this contribution, we give a compact encoding for abstract order types that allows efficient query of the orientation of any triple: the encoding uses O(n^2) bits and an orientation query takes O(log n) time in the word-RAM model. This encoding is space-optimal for abstract order types. We show how to shorten the encoding to O(n^2 (loglog n)^2 / log n) bits for realizable order types, giving the first subquadratic encoding for those order types with fast orientation queries. We further refine our encoding to attain O(log n/loglog n) query time without blowing up the space requirement. In the realizable case, we show that all those encodings can be computed efficiently. Finally, we generalize our results to the encoding of point configurations in higher dimension.
A Reliability Theory of Truth
Venue: arXiv cs.AI 2018
Year: 2018

Our approach is basically a coherence approach, but we avoid the well-known pitfalls of coherence theories of truth. Consistency is replaced by reliability, which expresses support and attack, and, in principle, every theory (or agent, message) counts. At the same time, we do not require a priviledged access to "reality". A centerpiece of our approach is that we attribute reliability also to agents, messages, etc., so an unreliable source of information will be less important in future. Our ideas can also be extended to value systems, and even actions, e.g., of animals.
Spatially Coupled Sparse Regression Codes: Design and State Evolution Analysis
Venue: arXiv cs.IT 2018
Year: 2018

We consider the design and analysis of spatially coupled sparse regression codes (SC-SPARCs), which were recently introduced by Barbier et al. for efficient communication over the additive white Gaussian noise channel. SC-SPARCs can be efficiently decoded using an Approximate Message Passing (AMP) decoder, whose performance in each iteration can be predicted via a set of equations called state evolution. In this paper, we give an asymptotic characterization of the state evolution equations for SC-SPARCs. For any given base matrix (that defines the coupling structure of the SC-SPARC) and rate, this characterization can be used to predict whether or not AMP decoding will succeed in the large system limit. We then consider a simple base matrix defined by two parameters $(ω, Λ)$, and show that AMP decoding succeeds in the large system limit for all rates $R < \mathcal{C}$. The asymptotic result also indicates how the parameters of the base matrix affect the decoding progression. Simulation results are presented to evaluate the performance of SC-SPARCs defined with the proposed base matrix.
Scheduling Policies for Minimizing Age of Information in Broadcast Wireless Networks
Venue: arXiv cs.NI 2018
Year: 2018

We consider a wireless broadcast network with a base station sending time-sensitive information to a number of clients through unreliable channels. The Age of Information (AoI), namely the amount of time that elapsed since the most recently delivered packet was generated, captures the freshness of the information. We formulate a discrete-time decision problem to find a transmission scheduling policy that minimizes the expected weighted sum AoI of the clients in the network. We first show that in symmetric networks a Greedy policy, which transmits the packet with highest current age, is optimal. For general networks, we develop three low-complexity scheduling policies: a randomized policy, a Max-Weight policy and a Whittle's Index policy, and derive performance guarantees as a function of the network configuration. To the best of our knowledge, this is the first work to derive performance guarantees for scheduling policies that attempt to minimize AoI in wireless networks with unreliable channels. Numerical results show that both Max-Weight and Whittle's Index policies outperform the other scheduling policies in every configuration simulated, and achieve near optimal performance.
Bringing Information Centric Networking to Challenged Environments: An overview of the Second Workshop on Future Internet Architecture for Developing Regions
Venue: arXiv cs.NI 2018
Year: 2018

The 2nd workshop on Future Internet Architecture for Developing Regions (FI4D) took place on January 8th, 2017. The workshop was hosted by the 14th Annual IEEE Consumer Communications $\&$ Networking Conference in Las Vegas, USA. This report summarizes the motivation, discussions and perspectives held during the half-day event.