OpenRaiser/Intern-Atlas huggingface dataset:
The efficacy of various machine learning models for multi-class classification of RNA-seq expression data
Venue: arXiv cs.LG 2019
Year: 2019

Late diagnosis and high costs are key factors that negatively impact the care of cancer patients worldwide. Although the availability of biological markers for the diagnosis of cancer type is increasing, costs and reliability of tests currently present a barrier to the adoption of their routine use. There is a pressing need for accurate methods that enable early diagnosis and cover a broad range of cancers. The use of machine learning and RNA-seq expression analysis has shown promise in the classification of cancer type. However, research is inconclusive about which type of machine learning models are optimal. The suitability of five algorithms were assessed for the classification of 17 different cancer types. Each algorithm was fine-tuned and trained on the full array of 18,015 genes per sample, for 4,221 samples (75 % of the dataset). They were then tested with 1,408 samples (25 % of the dataset) for which cancer types were withheld to determine the accuracy of prediction. The results show that ensemble algorithms achieve 100% accuracy in the classification of 14 out of 17 types of cancer. The clustering and classification models, while faster than the ensembles, performed poorly due to the high level of noise in the dataset. When the features were reduced to a list of 20 genes, the ensemble algorithms maintained an accuracy above 95% as opposed to the clustering and classification models.
Fine-grained Sentiment Analysis with Faithful Attention
Venue: arXiv cs.CL 2019
Year: 2019

While the general task of textual sentiment classification has been widely studied, much less research looks specifically at sentiment between a specified source and target. To tackle this problem, we experimented with a state-of-the-art relation extraction model. Surprisingly, we found that despite reasonable performance, the model's attention was often systematically misaligned with the words that contribute to sentiment. Thus, we directly trained the model's attention with human rationales and improved our model performance by a robust 4~8 points on all tasks we defined on our data sets. We also present a rigorous analysis of the model's attention, both trained and untrained, using novel and intuitive metrics. Our results show that untrained attention does not provide faithful explanations; however, trained attention with concisely annotated human rationales not only increases performance, but also brings faithful explanations. Encouragingly, a small amount of annotated human rationales suffice to correct the attention in our task.
Towards Linearization Machine Learning Algorithms
Venue: arXiv cs.LG 2019
Year: 2019

This paper is about a machine learning approach based on the multilinear projection of an unknown function (or probability distribution) to be estimated towards a linear (or multilinear) dimensional space E'. The proposal transforms the problem of predicting the target of an observation x into a problem of determining a consensus among the k nearest neighbors of x's image within the dimensional space E'. The algorithms that concretize it allow both regression and binary classification. Implementations carried out using Scala/Spark and assessed on a dozen LIBSVM datasets have demonstrated improvements in prediction accuracies in comparison with other prediction algorithms implemented within Spark MLLib such as multilayer perceptrons, logistic regression classifiers and random forests.
Rebellion on Sugarscape: Case Studies for Greed and Grievance Theory of Civil Conflicts using Agent-Based Models
Venue: arXiv cs.CY 2019
Year: 2019

Public policy making has direct and indirect impacts on social behaviors. However, using system dynamics model alone to assess these impacts fails to consider the interactions among social elements, thus may produce doubtful conclusions. In this study, we examine the political science theory of greed and grievance in modeling civil conflicts. An agent-based model is built based on an existing rebellion model in Netlogo. The modifications and improvements in our model are elaborated. Several case studies are used to demonstrate the use of our model for investigating emergent phenomena and implications of governmental policies.
Relevance Proximity Graphs for Fast Relevance Retrieval
Venue: arXiv cs.IR 2019
Year: 2019

In plenty of machine learning applications, the most relevant items for a particular query should be efficiently extracted, while the relevance function is based on a highly-nonlinear model, e.g., DNNs or GBDTs. Due to the high computational complexity of such models, exhaustive search is infeasible even for medium-scale problems. To address this issue, we introduce Relevance Proximity Graphs (RPG): an efficient non-exhaustive approach that provides a high-quality approximate solution for maximal relevance retrieval. Namely, we extend the recent similarity graphs framework to the setting, when there is no similarity measure defined on item pairs, which is a common practical use-case. By design, our approach directly maximizes off-the-shelf relevance functions and does not require any proxy auxiliary models. Via extensive experiments, we show that the developed method provides excellent retrieval accuracy while requiring only a few model computations, outperforming indirect models. We open-source our implementation as well as two large-scale datasets to support further research on relevance retrieval.
Genetic Algorithms for the Optimization of Diffusion Parameters in Content-Based Image Retrieval
Venue: arXiv cs.CV 2019
Year: 2019

Several computer vision and artificial intelligence projects are nowadays exploiting the manifold data distribution using, e.g., the diffusion process. This approach has produced dramatic improvements on the final performance thanks to the application of such algorithms to the kNN graph. Unfortunately, this recent technique needs a manual configuration of several parameters, thus it is not straightforward to find the best configuration for each dataset. Moreover, the brute-force approach is computationally very demanding when used to optimally set the parameters of the diffusion approach. We propose to use genetic algorithms to find the optimal setting of all the diffusion parameters with respect to retrieval performance for each different dataset. Our approach is faster than others used as references (brute-force, random-search and PSO). A comparison with these methods has been made on three public image datasets: Oxford5k, Paris6k and Oxford105k.
Algorithm Selection for Image Quality Assessment
Venue: arXiv cs.CV 2019
Year: 2019

Subjective perceptual image quality can be assessed in lab studies by human observers. Objective image quality assessment (IQA) refers to algorithms for estimation of the mean subjective quality ratings. Many such methods have been proposed, both for blind IQA in which no original reference image is available as well as for the full-reference case. We compared 8 state-of-the-art algorithms for blind IQA and showed that an oracle, able to predict the best performing method for any given input image, yields a hybrid method that could outperform even the best single existing method by a large margin. In this contribution we address the research question whether established methods to learn such an oracle can improve blind IQA. We applied AutoFolio, a state-of-the-art system that trains an algorithm selector to choose a well-performing algorithm for a given instance. We also trained deep neural networks to predict the best method. Our results did not give a positive answer, algorithm selection did not yield a significant improvement over the single best method. Looking into the results in depth, we observed that the noise in images may have played a role in why our trained classifiers could not predict the oracle. This motivates the consideration of noisiness in IQA methods, a property that has so far not been observed and that opens up several interesting new research questions and applications.
Why So Down? The Role of Negative (and Positive) Pointwise Mutual Information in Distributional Semantics
Venue: arXiv cs.CL 2019
Year: 2019

In distributional semantics, the pointwise mutual information ($\mathit{PMI}$) weighting of the cooccurrence matrix performs far better than raw counts. There is, however, an issue with unobserved pair cooccurrences as $\mathit{PMI}$ goes to negative infinity. This problem is aggravated by unreliable statistics from finite corpora which lead to a large number of such pairs. A common practice is to clip negative $\mathit{PMI}$ ($\mathit{\texttt{-} PMI}$) at $0$, also known as Positive $\mathit{PMI}$ ($\mathit{PPMI}$). In this paper, we investigate alternative ways of dealing with $\mathit{\texttt{-} PMI}$ and, more importantly, study the role that negative information plays in the performance of a low-rank, weighted factorization of different $\mathit{PMI}$ matrices. Using various semantic and syntactic tasks as probes into models which use either negative or positive $\mathit{PMI}$ (or both), we find that most of the encoded semantics and syntax come from positive $\mathit{PMI}$, in contrast to $\mathit{\texttt{-} PMI}$ which contributes almost exclusively syntactic information. Our findings deepen our understanding of distributional semantics, while also introducing novel $PMI$ variants and grounding the popular $PPMI$ measure.
Public release of Atlas under an open source license, which is accelerator enabled and has improved interoperability features
Venue: arXiv cs.DC 2019
Year: 2019

This document is one of the deliverable reports created for the ESCAPE project. ESCAPE stands for Energy-efficient Scalable Algorithms for Weather Prediction at Exascale. The project develops world-class, extreme-scale computing capabilities for European operational numerical weather prediction and future climate models. This is done by identifying Weather & Climate dwarfs which are key patterns in terms of computation and communication (in the spirit of the Berkeley dwarfs). These dwarfs are then optimised for different hardware architectures (single and multi-node) and alternative algorithms are explored. Performance portability is addressed through the use of domain specific languages. Atlas has been presented in deliverable D1.3. With this deliverable D2.3, a first version of the Atlas software libraries is publicly released with a permissive open-source license. The software is freely available for download, and contains a user guide and installation instructions. The Atlas libraries have been carefully designed with the user's perspective in mind. Even though Atlas is mainly coded in C++, an equivalent Fortran interface is presented without additional runtime overhead. The Fortran interfaces are provided to accommodate existing NWP and climate models that typically consist of Fortran subroutines. The mixed Fortran/C++ design enhances interoperability between NWP and climate models and novel data management techniques. Atlas provides interoperability with accelerator hardware, and can serve as foundation to support higher level abstractions as used in domain specific languages.
Domain-Independent turn-level Dialogue Quality Evaluation via User Satisfaction Estimation
Venue: arXiv cs.LG 2019
Year: 2019

An automated metric to evaluate dialogue quality is vital for optimizing data driven dialogue management. The common approach of relying on explicit user feedback during a conversation is intrusive and sparse. Current models to estimate user satisfaction use limited feature sets and rely on annotation schemes with low inter-rater reliability, limiting generalizability to conversations spanning multiple domains. To address these gaps, we created a new Response Quality annotation scheme, based on which we developed turn-level User Satisfaction metric. We introduced five new domain-independent feature sets and experimented with six machine learning models to estimate the new satisfaction metric. Using Response Quality annotation scheme, across randomly sampled single and multi-turn conversations from 26 domains, we achieved high inter-annotator agreement (Spearman's rho 0.94). The Response Quality labels were highly correlated (0.76) with explicit turn-level user ratings. Gradient boosting regression achieved best correlation of ~0.79 between predicted and annotated user satisfaction labels. Multi Layer Perceptron and Gradient Boosting regression models generalized to an unseen domain better (linear correlation 0.67) than other models. Finally, our ablation study verified that our novel features significantly improved model performance.
LogicENN: A Neural Based Knowledge Graphs Embedding Model with Logical Rules
Venue: arXiv cs.AI 2019
Year: 2019

Knowledge graph embedding models have gained significant attention in AI research. Recent works have shown that the inclusion of background knowledge, such as logical rules, can improve the performance of embeddings in downstream machine learning tasks. However, so far, most existing models do not allow the inclusion of rules. We address the challenge of including rules and present a new neural based embedding model (LogicENN). We prove that LogicENN can learn every ground truth of encoded rules in a knowledge graph. To the best of our knowledge, this has not been proved so far for the neural based family of embedding models. Moreover, we derive formulae for the inclusion of various rules, including (anti-)symmetric, inverse, irreflexive and transitive, implication, composition, equivalence and negation. Our formulation allows to avoid grounding for implication and equivalence relations. Our experiments show that LogicENN outperforms the state-of-the-art models in link prediction.
Unfolding Polyhedra
Venue: arXiv cs.CG 2019
Year: 2019

Starting with the unsolved "Dürer's problem" of edge-unfolding a convex polyhedron to a net, we specialize and generalize (a) the types of cuts permitted, and (b) the polyhedra shapes, to highlight both advances established and which problems remain open.
Lemma Generation for Horn Clause Satisfiability: A Preliminary Study
Venue: arXiv cs.LO 2019
Year: 2019

It is known that the verification of imperative, functional, and logic programs can be reduced to the satisfiability of constrained Horn clauses (CHCs), and this satisfiability check can be performed by using CHC solvers, such as Eldarica and Z3. These solvers perform well when they act on simple constraint theories, such as Linear Integer Arithmetic and the theory of Booleans, but their efficacy is very much reduced when the clauses refer to constraints on inductively defined structures, such as lists or trees. Recently, we have presented a transformation technique for eliminating those inductively defined data structures, and hence avoiding the need for incorporating induction principles into CHC solvers. However, this technique may fail when the transformation requires the use of lemmata whose generation needs ingenuity. In this paper we show, through an example, how during the process of transforming CHCs for eliminating inductively defined structures one can introduce suitable predicates, called difference predicates, whose definitions correspond to the lemmata to be introduced. Through a second example, we show that, whenever difference predicates cannot be introduced, we can introduce, instead, auxiliary queries which also correspond to lemmata, and the proof of these lemmata can be done by showing the satisfiability of those queries.
On Integrating Design Thinking for a Human-centered Requirements Engineering
Venue: arXiv cs.SE 2019
Year: 2019

In this position paper, we elaborate on the possibilities and needs to integrate Design Thinking into Requirements Engineering. We draw from our research and project experiences to compare what is understood as Design Thinking and Requirements Engineering considering their involved artifacts. We suggest three approaches for tailoring and integrating Design Thinking and Requirements Engineering with complementary synergies and point at open challenges for research and practice.
Efficiently Improving and Quantifying Robot Accuracy In Situ
Venue: arXiv cs.RO 2019
Year: 2019

The advancement of simulation-assisted robot programming, automation of high-tolerance assembly operations, and improvement of real-world performance engender a need for positionally accurate robots. Despite tight machining tolerances, good mechanical design, and careful assembly, robotic arms typically exhibit average Cartesian positioning errors of several millimeters. Fortunately, the vast majority of this error can be removed in software by proper calibration of the so-called "zero-offsets" of a robot's joints. This research developed an automated, inexpensive, highly portable, in situ calibration method that fine tunes these kinematic parameters, thereby, improving a robot's average positioning accuracy four-fold throughout its workspace. In particular, a prospective low-cost motion capture system and a benchmark laser tracker were used as reference sensors for robot calibration. Bayesian inference produced optimized zero-offset parameters alongside their uncertainty for data from both reference sensors. Relative and absolute accuracy metrics were proposed and applied for quantifying robot positioning accuracy. Uncertainty analysis of a validated, probabilistic robot model quantified the absolute positioning accuracy throughout its entire workspace. Altogether, three measures of accuracy conclusively revealed multi-fold improvement in the positioning accuracy of the robotic arm. Bayesian inference on motion capture data yielded zero-offsets and accuracy calculations comparable to those derived from laser tracker data, ultimately proving this method's viability towards robot calibration.
A Multi-View Discriminant Learning Approach for Indoor Localization Using Bimodal Features of CSI
Venue: arXiv cs.NI 2019
Year: 2019

With the growth of location-based services, indoor localization is attracting great interests as it facilitates further ubiquitous environments. Specifically, device free localization using wireless signals is getting increased attention as human location is estimated using its impact on the surrounding wireless signals without any active device tagged with subject. In this paper, we propose MuDLoc, the first multi-view discriminant learning approach for device free indoor localization using both amplitude and phase features of Channel State Information (CSI) from multiple APs. Multi-view learning is an emerging technique in machine learning which improve performance by utilizing diversity from different view data. In MuDLoc, the localization is modeled as a pattern matching problem, where the target location is predicted based on similarity measure of CSI features of an unknown location with those of the training locations. MuDLoc implements Generalized Inter-view and Intra-view Discriminant Correlation Analysis (GI$^{2}$DCA), a discriminative feature extraction approach using multi-view CSIs. It incorporates inter-view and intra-view class associations while maximizing pairwise correlations across multi-view data sets. A similarity measure is performed to find the best match to localize a subject. Experimental results from two cluttered environments show that MuDLoc can estimate location with high accuracy which outperforms other benchmark approaches.
Assessment of gait normality using a depth camera and mirrors
Venue: arXiv cs.CV 2019
Year: 2019

This paper presents an initial work on assessment of gait normality in which the human body motion is represented by a sequence of enhanced depth maps. The input data is provided by a system consisting of a Time-of-Flight (ToF) depth camera and two mirrors. This approach proposes two feature types to describe characteristics of localized points of interest and the level of posture symmetry. These two features are processed on a sequence of enhanced depth maps with the support of a sliding window to provide two corresponding scores. The gait assessment is finally performed based on a weighted combination of these two scores. The evaluation is performed by experimenting on 6 simulated abnormal gaits.
Human Gait Symmetry Assessment using a Depth Camera and Mirrors
Venue: arXiv cs.CV 2019
Year: 2019

This paper proposes a reliable approach for human gait symmetry assessment using a depth camera and two mirrors. The input of our system is a sequence of 3D point clouds which are formed from a setup including a Time-of-Flight (ToF) depth camera and two mirrors. A cylindrical histogram is estimated for describing the posture in each point cloud. The sequence of such histograms is then separated into two sequences of sub-histograms representing two half-bodies. A cross-correlation technique is finally applied to provide values describing gait symmetry indices. The evaluation was performed on 9 different gait types to demonstrate the ability of our approach in assessing gait symmetry. A comparison between our system and related methods, that employ different input data types, is also provided.
Evaluating Contextualized Embeddings on 54 Languages in POS Tagging, Lemmatization and Dependency Parsing
Venue: arXiv cs.CL 2019
Year: 2019

We present an extensive evaluation of three recently proposed methods for contextualized embeddings on 89 corpora in 54 languages of the Universal Dependencies 2.3 in three tasks: POS tagging, lemmatization, and dependency parsing. Employing the BERT, Flair and ELMo as pretrained embedding inputs in a strong baseline of UDPipe 2.0, one of the best-performing systems of the CoNLL 2018 Shared Task and an overall winner of the EPE 2018, we present a one-to-one comparison of the three contextualized word embedding methods, as well as a comparison with word2vec-like pretrained embeddings and with end-to-end character-level word embeddings. We report state-of-the-art results in all three tasks as compared to results on UD 2.2 in the CoNLL 2018 Shared Task.
Libra: Is it Really about Money?
Venue: arXiv cs.CY 2019
Year: 2019

The announcement by Facebook that Libra will "deliver on the promise of 'the internet of money'" has drawn the attention of the financial world. Regulators, institutions, and users of financial products have all been prompted to react and, so far, no one managed to convince the association behind Libra to apply the brakes or to convince regulators to stop the project altogether. In this article, we propose that Libra might be best seen not as a financial newcomer, but as a critical enabler for Facebook to acquire a new source of personal data. By working with financial regulators seeking to address concerns with money laundering and terrorism, Facebook can position itself for privileged access to high-assurance digital identity information. For this reason, Libra merits the attention of not only financial regulators, but also the state actors that are concerned with reputational risks, the rule of law, public safety, and national defence.