nils-herrmann/clean_scirepeval huggingface dataset:
The neighbor-joining method: a new method for reconstructing phylogenetic trees.

A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
Planning, Learning and Coordination in Multiagent Decision Processes

There has been a growing interest in AI in the design of multiagent systems, especially in multiagent cooperative planning. In this paper, we investigate the extent to which methods from single-agent planning and learning can be applied in multiagent settings. We survey a number of different techniques from decision-theoretic planning and reinforcement learning and describe a number of interesting issues that arise with regard to coordinating the policies of individual agents. To this end, we describe multiagent Markov decision processes as a general model in which to frame this discussion. These are special n-person cooperative games in which agents share the same utility function. We discuss coordination mechanisms based on imposed conventions (or social laws) as well as learning methods for coordination. Our focus is on the decomposition of sequential decision processes so that coordination can be learned (or imposed) locally, at the level of individual states. We also discuss the use of structured problem representations and their role in the generalization of learned conventions and in approximation.
Solving the University Class Scheduling Problem Using Advanced ILP Techniques

The University Class Scheduling Problem (UCSP) is concerned with assigning a number of courses to classrooms taking into consideration constraints like classroom capacities and university regulations. The problem also attempts to optimize the performance criteria and distribute the courses fairly to classrooms depending on the ratio of classroom capacities to course enrollments. The problem is a classical scheduling problem and considered to be NP-complete. It has received some research during the past few years given its wide use in colleges and universities. Several formulations and algorithms have been proposed to solve scheduling problems, most of which are based on local search techniques. In this paper, we propose a complete approach using integer linear programming (ILP) to solve the problem. The ILP model of interest is developed and solved using the three advanced ILP solvers based on generic algorithms and Boolean Satisfiability (SAT) techniques. SAT has been heavily researched in the past few years and has lead to the development of powerful 0-1 ILP solvers that can compete with the best available generic ILP solvers. Experimental results indicate that the proposed model is tractable for reasonable-sized UCSP problems. Index Terms — University Class Scheduling, Optimization, Integer Linear Programming (ILP), Boolean Satisfiability.
Calibration of Confidence Measures in Speech Recognition

Most speech recognition applications in use today rely heavily on confidence measure for making optimal decisions. In this paper, we aim to answer the question: what can be done to improve the quality of confidence measure if we cannot modify the speech recognition engine? The answer provided in this paper is a post-processing step called confidence calibration, which can be viewed as a special adaptation technique applied to confidence measure. Three confidence calibration methods have been developed in this work: the maximum entropy model with distribution constraints, the artificial neural network, and the deep belief network. We compare these approaches and demonstrate the importance of key features exploited: the generic confidence-score, the application-dependent word distribution, and the rule coverage ratio. We demonstrate the effectiveness of confidence calibration on a variety of tasks with significant normalized cross entropy increase and equal error rate reduction.
A Traceability Analysis of Monero's Blockchain

Privacy and anonymity are important desiderata in the use of cryptocurrencies. Monero — a privacy centric cryptocurrency has rapidly gained popularity due to its unlinkability and untraceablity guarantees. It has a market capitalization of USD 290M. In this work, we quantify the efficacy of three attacks on Monero’s untraceability guarantee, which promises to make it hard to trace the origin of a received fund, by analyzing its blockchain data. To this end, we develop three attack routines and evaluate them on the Monero blockchain. Our results show that in 88% of cases, the origin of the funds can be easily determined with certainty. Moreover, we have compelling evidence that two of the attack routines also extend to Monero RingCTs — the second generation Monero that even hides the transaction amount. We further observe that over 98% of the results can in fact be obtained by a simple temporal analysis. In light of our findings, we discuss mitigations to strengthen Monero against these attacks. We shared our findings with the Monero development team and the general community. This has resulted into several discussions and proposals for fixes.
Online Rank Elicitation for Plackett-Luce: A Dueling Bandits Approach

We study the problem of online rank elicitation, assuming that rankings of a set of alternatives obey the Plackett-Luce distribution. Following the setting of the dueling bandits problem, the learner is allowed to query pairwise comparisons between alternatives, i.e., to sample pairwise marginals of the distribution in an online fashion. Using this information, the learner seeks to reliably predict the most probable ranking (or top-alternative). Our approach is based on constructing a surrogate probability distribution over rankings based on a sorting procedure, for which the pairwise marginals provably coincide with the marginals of the PlackettLuce distribution. In addition to a formal performance and complexity analysis, we present first experimental studies.
Efficient RDF Storage and Retrieval in Jena2

RDF and related Semantic Web technologies have been the recent focus of much research activity. This work has led to new specifications for RDF and OWL. However, efficient implementations of these standards are needed to realize the vision of a world-wide semantic Web. In particular, implementations that scale to large, enterprise-class data sets are required. Jena2 is the second generation of Jena, a leading semantic web programmers’ toolkit. This paper describes the persistence subsystem of Jena2 which is intended to support large datasets. This paper describes its features, the changes from Jena1, relevant details of the implementation and performance tuning issues. Query optimization for RDF is identified as a promising area for future research.
Item popularity and recommendation accuracy

Recommendations from the long tail of the popularity distribution of items are generally considered to be particularly valuable. On the other hand, recommendation accuracy tends to decrease towards the long tail. In this paper, we quantitatively examine this trade-off between item popularity and recommendation accuracy. To this end, we assume that there is a selection bias towards popular items in the available data. This allows us to define a new accuracy measure that can be gradually tuned towards the long tail. We show that, under this assumption, this measure has the desirable property of providing nearly unbiased estimates concerning recommendation accuracy. In turn, this also motivates a refinement for training collaborative-filtering approaches. In various experiments with real-world data, including a user study, empirical evidence suggests that only a small, if any, bias of the recommendations towards less popular items is appreciated by users.
Exploiting topic modeling to boost metagenomic reads binning

With the rapid development of high-throughput technologies, researchers can sequence the whole metagenome of a microbial community sampled directly from the environment. The assignment of these metagenomic reads into different species or taxonomical classes is a vital step for metagenomic analysis, which is referred to as binning of metagenomic data. In this paper, we propose a new method TM-MCluster for binning metagenomic reads. First, we represent each metagenomic read as a set of "k-mers" with their frequencies occurring in the read. Then, we employ a probabilistic topic model -- the Latent Dirichlet Allocation (LDA) model to the reads, which generates a number of hidden "topics" such that each read can be represented by a distribution vector of the generated topics. Finally, as in the MCluster method, we apply SKWIC -- a variant of the classical K-means algorithm with automatic feature weighting mechanism to cluster these reads represented by topic distributions. Experiments show that the new method TM-MCluster outperforms major existing methods, including AbundanceBin, MetaCluster 3.0/5.0 and MCluster. This result indicates that the exploitation of topic modeling can effectively improve the binning performance of metagenomic reads.
So far away and yet so close: augmenting toponym disambiguation and similarity with text-based networks

Place similarity has a central role in geographic information retrieval and geographic information systems, where spatial proximity is frequently just a poor substitute for semantic relatedness. For applications such as toponym disambiguation, alternative measures are thus required to answer the non-trivial question of place similarity in a given context. In this paper, we discuss a novel approach to the construction of a network of locations from unstructured text data. By deriving similarity scores based on the textual distance of toponyms, we obtain a kind of relatedness that encodes the importance of the co-occurrences of place mentions. Based on the text of the English Wikipedia, we construct and provide such a network of place similarities, including entity linking to Wikidata as an augmentation of the contained information. In an analysis of centrality, we explore the networks capability of capturing the similarity between places. An evaluation of the network for the task of toponym disambiguation on the AIDA CoNLL-YAGO dataset reveals a performance that is in line with state-of-the-art methods.
On the Role of Correlation and Abstraction in Cross-Modal Multimedia Retrieval

The problem of cross-modal retrieval from multimedia repositories is considered. This problem addresses the design of retrieval systems that support queries across content modalities, for example, using an image to search for texts. A mathematical formulation is proposed, equating the design of cross-modal retrieval systems to that of isomorphic feature spaces for different content modalities. Two hypotheses are then investigated regarding the fundamental attributes of these spaces. The first is that low-level cross-modal correlations should be accounted for. The second is that the space should enable semantic abstraction. Three new solutions to the cross-modal retrieval problem are then derived from these hypotheses: correlation matching (CM), an unsupervised method which models cross-modal correlations, semantic matching (SM), a supervised technique that relies on semantic representation, and semantic correlation matching (SCM), which combines both. An extensive evaluation of retrieval performance is conducted to test the validity of the hypotheses. All approaches are shown successful for text retrieval in response to image queries and vice versa. It is concluded that both hypotheses hold, in a complementary form, although evidence in favor of the abstraction hypothesis is stronger than that for correlation.
Bayesian Robust Matrix Factorization for Image and Video Processing

Matrix factorization is a fundamental problem that is often encountered in many computer vision and machine learning tasks. In recent years, enhancing the robustness of matrix factorization methods has attracted much attention in the research community. To benefit from the strengths of full Bayesian treatment over point estimation, we propose here a full Bayesian approach to robust matrix factorization. For the generative process, the model parameters have conjugate priors and the likelihood (or noise model) takes the form of a Laplace mixture. For Bayesian inference, we devise an efficient sampling algorithm by exploiting a hierarchical view of the Laplace distribution. Besides the basic model, we also propose an extension which assumes that the outliers exhibit spatial or temporal proximity as encountered in many computer vision applications. The proposed methods give competitive experimental results when compared with several state-of-the-art methods on some benchmark image and video processing tasks.
OWL 2 Profiles: An Introduction to Lightweight Ontology Languages

This chapter gives an extended introduction to the lightweight profiles OWL EL, OWL QL, and OWL RL of the Web Ontology Language OWL. The three ontology language standards are sublanguages of OWL DL that are restricted in ways that significantly simplify ontological reasoning. Compared to OWL DL as a whole, reasoning algorithms for the OWL profiles show higher performance, are easier to implement, and can scale to larger amounts of data. Since ontological reasoning is of great importance for designing and deploying OWL ontologies, the profiles are highly attractive for many applications. These advantages come at a price: various modelling features of OWL are not available in all or some of the OWL profiles. Moreover, the profiles are mutually incomparable in the sense that each of them offers a combination of features that is available in none of the others. This chapter provides an overview of these differences and explains why some of them are essential to retain the desired properties. To this end, we recall the relationship between OWL and description logics (DLs), and show how each of the profiles is typically treated in reasoning algorithms.
An Almost-Linear-Time Algorithm for Approximate Max Flow in Undirected Graphs, and its Multicommodity Generalizations

In this paper, we introduce a new framework for approximately solving flow problems in capacitated, undirected graphs and apply it to provide asymptotically faster algorithms for the maximum s-t flow and maximum concurrent multicommodity flow problems. For graphs with n vertices and m edges, it allows us to find an ε-approximate maximum s-t flow in time O(m1+o(1)ε−2), improving on the previous best bound of Õ(mn1/3poly(ε−1)). Applying the same framework in the multicommodity setting solves a maximum concurrent multicommodity flow problem with k commodities in O(m1+o(1)ε−2k2) time, improving on the existing bound of Õ(mpoly(k, ε−1)). Our algorithms utilize several new technical tools that we believe may be of independent interest: • We give a non-Euclidean generalization of gradient descent and provide bounds on its performance. Using this, we show how to reduce approximate maximum flow and maximum concurrent flow to oblivious routing. • We define and provide an efficient construction of a new type of flow sparsifier. Previous sparsifier constructions approximately preserved the size of cuts and, by duality, the value of the maximum flows as well. However, they did not provide any direct way to route flows in the sparsifier G′ back in the original graph G, leading to a longstanding gap between the efficacy of sparsification on flow and cut problems. We ameliorate this by constructing a sparsifier G′ that can be embedded (very efficiently) into G with low congestion, allowing one to transfer flows from G′ back to G. • We give the first almost-linear-time construction of an O(m)-competitive oblivious routing scheme. No previous such algorithm ran in time better than Ω̃(mn). By reducing the running time to almost-linear, our work provides a powerful new primitive for constructing very fast graph algorithms. The interested reader is referred to the full version of the paper  for a more complete treatment of these results. ∗This work was partially supported by NSF awards 0843915 and 1111109, NSF award 1319460, a Sloan Fellowship, NSF Graduate Research Fellowship (grant no. 1122374) and Hong Kong RGC grant 2150701. †Massachusetts Institute of Technology. ‡Massachusetts Institute of Technology §Massachusetts Institute of Technology. ¶Massachusetts Institute of Technology.
Part-Based Pedestrian Detection and Feature-Based Tracking for Driver Assistance: Real-Time, Robust Algorithms, and Evaluation

Detecting pedestrians is still a challenging task for automotive vision systems due to the extreme variability of targets, lighting conditions, occlusion, and high-speed vehicle motion. Much research has been focused on this problem in the last ten years and detectors based on classifiers have gained a special place among the different approaches presented. This paper presents a state-of-the-art pedestrian detection system based on a two-stage classifier. Candidates are extracted with a Haar cascade classifier trained with the Daimler Detection Benchmark data set and then validated through a part-based histogram-of-oriented-gradient (HOG) classifier with the aim of lowering the number of false positives. The surviving candidates are then filtered with feature-based tracking to enhance the recognition robustness and improve the results' stability. The system has been implemented on a prototype vehicle and offers high performance in terms of several metrics, such as detection rate, false positives per hour, and frame rate. The novelty of this system relies on the combination of a HOG part-based approach, tracking based on a specific optimized feature, and porting on a real prototype.
Efficiently Implementing Episodic Memory

Endowing an intelligent agent with an episodic memory affords it a multitude of cognitive capabilities. However, providing efficient storage and retrieval in a task-independent episodic memory presents considerable theoretical and practical challenges. We characterize the computational issues bounding an episodic memory. We explore whether even with intractable asymptotic growth, it is possible to develop efficient algorithms and data structures for episodic memory systems that are practical for real-world tasks. We present and evaluate formal and empirical results using Soar-EpMem: a task-independent integration of episodic memory with Soar 9, providing a baseline for graph-based, taskindependent episodic memory systems.
Efficient Maximum Power Point Tracking for a Distributed PV System under Rapidly Changing Environmental Conditions

When conventional maximum power point tracking (MPPT) techniques are required to operate fast under rapidly changing environmental conditions, a large power loss can be caused by slow tracking speed, output power fluctuation, or additionally required ad hoc parameters. This paper proposes a fast and efficient MPPT technique that minimizes the power loss with the adaptively binary-weighted step (ABWS) followed by the monotonically decreased step (MDS) without causing output power fluctuation or requiring additional ad hoc parameter. The proposed MPPT system for a photovoltaic (PV) module is implemented by a boost converter with a microcontroller unit. The theoretical analysis and the simulation results show that the proposed MPPT provides fast and accurate tracking under rapidly changing environmental conditions. The experimental results based on a distributed PV system demonstrate that the proposed MPPT technique is superior to the conventional perturb and observe (P&O) technique, which reduces the tracking time and the overall power loss by up to 82.95%, 91.51% and 82.46%, 97.71% for two PV modules, respectively.
Smaller and Faster: Parallel Processing of Compressed Graphs with Ligra+

We study compression techniques for parallel in-memory graph algorithms, and show that we can achieve reduced space usage while obtaining competitive or improved performance compared to running the algorithms on uncompressed graphs. We integrate the compression techniques into Ligra, a recent shared-memory graph processing system. This system, which we call Ligra+, is able to represent graphs using about half of the space for the uncompressed graphs on average. Furthermore, Ligra+ is slightly faster than Ligra on average on a 40-core machine with hyper-threading. Our experimental study shows that Ligra+ is able to process graphs using less memory, while performing as well as or faster than Ligra.
Depth from a Single Image by Harmonizing Overcomplete Local Network Predictions

A single color image can contain many cues informative towards different aspects of local geometric structure. We approach the problem of monocular depth estimation by using a neural network to produce a mid-level representation that summarizes these cues. This network is trained to characterize local scene geometry by predicting, at every image location, depth derivatives of different orders, orientations and scales. However, instead of a single estimate for each derivative, the network outputs probability distributions that allow it to express confidence about some coefficients, and ambiguity about others. Scene depth is then estimated by harmonizing this overcomplete set of network predictions, using a globalization procedure that finds a single consistent depth map that best matches all the local derivative distributions. We demonstrate the efficacy of this approach through evaluation on the NYU v2 depth data set.
Recursive Context Propagation Network for Semantic Scene Labeling

We propose a deep feed-forward neural network architecture for pixel-wise semantic scene labeling. It uses a novel recursive neural network architecture for context propagation, referred to as rCPN. It first maps the local visual features into a semantic space followed by a bottom-up aggregation of local information into a global representation of the entire image. Then a top-down propagation of the aggregated information takes place that enhances the contextual information of each local feature. Therefore, the information from every location in the image is propagated to every other location. Experimental results on Stanford background and SIFT Flow datasets show that the proposed method outperforms previous approaches. It is also orders of magnitude faster than previous methods and takes only 0.07 seconds on a GPU for pixel-wise labeling of a 256 x 256 image starting from raw RGB pixel values, given the super-pixel mask that takes an additional 0.3 seconds using an off-the-shelf implementation.
Fractal video compression in OpenCL: An evaluation of CPUs, GPUs, and FPGAs as acceleration platforms

Fractal compression is an efficient technique for image and video encoding that uses the concept of self-referential codes. Although offering compression quality that matches or exceeds traditional techniques with a simpler and faster decoding process, fractal techniques have not gained widespread acceptance due to the computationally intensive nature of its encoding algorithm. In this paper, we present a real-time implementation of a fractal compression algorithm in OpenCL . We show how the algorithm can be efficiently implemented in OpenCL and optimized for multi-CPUs, GPUs, and FPGAs. We demonstrate that the core computation implemented on the FPGA through OpenCL is 3× faster than a high-end GPU and 114× faster than a multi-core CPU, with significant power advantages. We also compare to a hand coded FPGA implementation to showcase the effectiveness of an OpenCL-to-FPGA compilation tool.