Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages

This study provides the proof of principle that probing the host and the microbe transcriptomes simultaneously is a valuable means to accessing unique information on host pathogen interactions. Our results also underline the extraordinary plasticity of host cell and pathogen responses to infection, and provide a solid framework to further understand the complex mechanisms involved in immunity to M. tuberculosis and in mycobacterial adaptation to different intracellular environments

Continuum-mechanical, Anisotropic Flow model for polar ice masses, based on an anisotropic Flow Enhancement factor

A complete theoretical presentation of the Continuum-mechanical, Anisotropic Flow model, based on an anisotropic Flow Enhancement factor (CAFFE model) is given. The CAFFE model is an application of the theory of mixtures with continuous diversity for the case of large polar ice masses in which induced anisotropy occurs. The anisotropic response of the polycrystalline ice is described by a generalization of Glen's flow law, based on a scalar anisotropic enhancement factor. The enhancement factor depends on the orientation mass density, which is closely related to the orientation distribution function and describes the distribution of grain orientations (fabric). Fabric evolution is governed by the orientation mass balance, which depends on four distinct effects, interpreted as local rigid body rotation, grain rotation, rotation recrystallization (polygonization) and grain boundary migration (migration recrystallization), respectively. It is proven that the flow law of the CAFFE model is truly anisotropic despite the collinearity between the stress deviator and stretching tensors.Comment: 22 pages, 5 figure

Differential Producibility Analysis (DPA) of Transcriptomic Data with Metabolic Networks: Deconstructing the Metabolic Response of M. tuberculosis

A general paucity of knowledge about the metabolic state of Mycobacterium tuberculosis within the host environment is a major factor impeding development of novel drugs against tuberculosis. Current experimental methods do not allow direct determination of the global metabolic state of a bacterial pathogen in vivo, but the transcriptional activity of all encoded genes has been investigated in numerous microarray studies. We describe a novel algorithm, Differential Producibility Analysis (DPA) that uses a metabolic network to extract metabolic signals from transcriptome data. The method utilizes Flux Balance Analysis (FBA) to identify the set of genes that affect the ability to produce each metabolite in the network. Subsequently, Rank Product Analysis is used to identify those metabolites predicted to be most affected by a transcriptional signal. We first apply DPA to investigate the metabolic response of E. coli to both anaerobic growth and inactivation of the FNR global regulator. DPA successfully extracts metabolic signals that correspond to experimental data and provides novel metabolic insights. We next apply DPA to investigate the metabolic response of M. tuberculosis to the macrophage environment, human sputum and a range of in vitro environmental perturbations. The analysis revealed a previously unrecognized feature of the response of M. tuberculosis to the macrophage environment: a down-regulation of genes influencing metabolites in central metabolism and concomitant up-regulation of genes that influence synthesis of cell wall components and virulence factors. DPA suggests that a significant feature of the response of the tubercle bacillus to the intracellular environment is a channeling of resources towards remodeling of its cell envelope, possibly in preparation for attack by host defenses. DPA may be used to unravel the mechanisms of virulence and persistence of M. tuberculosis and other pathogens and may have general application for extracting metabolic signals from other “-omics” data

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Evaluation in artificial intelligence: From task-oriented to ability-oriented measurement

The final publication is available at Springer via http://dx.doi.org/ 10.1007/s10462-016-9505-7.The evaluation of artificial intelligence systems and components is crucial for the progress of the discipline. In this paper we describe and critically assess the different ways AI systems are evaluated, and the role of components and techniques in these systems. We first focus on the traditional task-oriented evaluation approach. We identify three kinds of evaluation: human discrimination, problem benchmarks and peer confrontation. We describe some of the limitations of the many evaluation schemes and competitions in these three categories, and follow the progression of some of these tests. We then focus on a less customary (and challenging) ability-oriented evaluation approach, where a system is characterised by its (cognitive) abilities, rather than by the tasks it is designed to solve. We discuss several possibilities: the adaptation of cognitive tests used for humans and animals, the development of tests derived from algorithmic information theory or more integrated approaches under the perspective of universal psychometrics. We analyse some evaluation tests from AI that are better positioned for an ability-oriented evaluation and discuss how their problems and limitations can possibly be addressed with some of the tools and ideas that appear within the paper. Finally, we enumerate a series of lessons learnt and generic guidelines to be used when an AI evaluation scheme is under consideration.I thank the organisers of the AEPIA Summer School On Artificial Intelligence, held in September 2014, for giving me the opportunity to give a lecture on 'AI Evaluation'. This paper was born out of and evolved through that lecture. The information about many benchmarks and competitions discussed in this paper have been contrasted with information from and discussions with many people: M. Bedia, A. Cangelosi, C. Dimitrakakis, I. GarcIa-Varea, Katja Hofmann, W. Langdon, E. Messina, S. Mueller, M. Siebers and C. Soares. Figure 4 is courtesy of F. Martinez-Plumed. Finally, I thank the anonymous reviewers, whose comments have helped to significantly improve the balance and coverage of the paper. This work has been partially supported by the EU (FEDER) and the Spanish MINECO under Grants TIN 2013-45732-C4-1-P, TIN 2015-69175-C4-1-R and by Generalitat Valenciana PROMETEOII2015/013.José Hernández-Orallo (2016). Evaluation in artificial intelligence: From task-oriented to ability-oriented measurement. Artificial Intelligence Review. 1-51. https://doi.org/10.1007/s10462-016-9505-7S151Abel D, Agarwal A, Diaz F, Krishnamurthy A, Schapire RE (2016) Exploratory gradient boosting for reinforcement learning in complex domains. arXiv preprint arXiv:1603.04119Adams S, Arel I, Bach J, Coop R, Furlan R, Goertzel B, Hall JS, Samsonovich A, Scheutz M, Schlesinger M, Shapiro SC, Sowa J (2012) Mapping the landscape of human-level artificial general intelligence. AI Mag 33(1):25–42Adams SS, Banavar G, Campbell M (2016) I-athlon: towards a multi-dimensional Turing test. AI Mag 37(1):78–84Alcalá J, Fernández A, Luengo J, Derrac J, García S, Sánchez L, Herrera F (2010) Keel data-mining software tool: data set repository, integration of algorithms and experimental analysis framework. J Mult Valued Logic Soft Comput 17:255–287Alexander JRM, Smales S (1997) Intelligence, learning and long-term memory. Personal Individ Differ 23(5):815–825Alpcan T, Everitt T, Hutter M (2014) Can we measure the difficulty of an optimization problem? In: IEEE information theory workshop (ITW)Alur R, Bodik R, Juniwal G, Martin MMK, Raghothaman M, Seshia SA, Singh R, Solar-Lezama A, Torlak E, Udupa A (2013) Syntax-guided synthesis. In: Formal methods in computer-aided design (FMCAD), 2013, IEEE, pp 1–17Alvarado N, Adams SS, Burbeck S, Latta C (2002) Beyond the Turing test: performance metrics for evaluating a computer simulation of the human mind. In: Proceedings of the 2nd international conference on development and learning, IEEE, pp 147–152Amigoni F, Bastianelli E, Berghofer J, Bonarini A, Fontana G, Hochgeschwender N, Iocchi L, Kraetzschmar G, Lima P, Matteucci M, Miraldo P, Nardi D, Schiaffonati V (2015) Competitions for benchmarking: task and functionality scoring complete performance assessment. IEEE Robot Autom Mag 22(3):53–61Anderson J, Lebiere C (2003) The Newell test for a theory of cognition. Behav Brain Sci 26(5):587–601Anderson J, Baltes J, Cheng CT (2011) Robotics competitions as benchmarks for AI research. Knowl Eng Rev 26(01):11–17Arel I, Rose DC, Karnowski TP (2010) Deep machine learning—a new frontier in artificial intelligence research. IEEE Comput Intell Mag 5(4):13–18Asada M, Hosoda K, Kuniyoshi Y, Ishiguro H, Inui T, Yoshikawa Y, Ogino M, Yoshida C (2009) Cognitive developmental robotics: a survey. IEEE Trans Auton Ment Dev 1(1):12–34Aziz H, Brill M, Fischer F, Harrenstein P, Lang J, Seedig HG (2015) Possible and necessary winners of partial tournaments. J Artif Intell Res 54:493–534Bache K, Lichman M (2013) UCI machine learning repository. http://archive.ics.uci.edu/mlBagnall AJ, Zatuchna ZV (2005) On the classification of maze problems. In: Bull L, Kovacs T (eds) Foundations of learning classifier system. Studies in fuzziness and soft computing, vol. 183, Springer, pp 305–316. http://rd.springer.com/chapter/10.1007/11319122_12Baldwin D, Yadav SB (1995) The process of research investigations in artificial intelligence - a unified view. IEEE Trans Syst Man Cybern 25(5):852–861Bellemare MG, Naddaf Y, Veness J, Bowling M (2013) The arcade learning environment: an evaluation platform for general agents. J Artif Intell Res 47:253–279Besold TR (2014) A note on chances and limitations of psychometric ai. In: KI 2014: advances in artificial intelligence. Springer, pp 49–54Biever C (2011) Ultimate IQ: one test to rule them all. New Sci 211(2829, 10 September 2011):42–45Borg M, Johansen SS, Thomsen DL, Kraus M (2012) Practical implementation of a graphics Turing test. In: Advances in visual computing. Springer, pp 305–313Boring EG (1923) Intelligence as the tests test it. New Repub 35–37Bostrom N (2014) Superintelligence: paths, dangers, strategies. Oxford University Press, OxfordBrazdil P, Carrier CG, Soares C, Vilalta R (2008) Metalearning: applications to data mining. Springer, New YorkBringsjord S (2011) Psychometric artificial intelligence. J Exp Theor Artif Intell 23(3):271–277Bringsjord S, Schimanski B (2003) What is artificial intelligence? Psychometric AI as an answer. In: International joint conference on artificial intelligence, pp 887–893Brundage M (2016) Modeling progress in ai. AAAI 2016 Workshop on AI, Ethics, and SocietyBuchanan BG (1988) Artificial intelligence as an experimental science. Springer, New YorkBuhrmester M, Kwang T, Gosling SD (2011) Amazon’s mechanical turk a new source of inexpensive, yet high-quality, data? Perspect Psychol Sci 6(1):3–5Bursztein E, Aigrain J, Moscicki A, Mitchell JC (2014) The end is nigh: generic solving of text-based captchas. In: Proceedings of the 8th USENIX conference on Offensive Technologies, USENIX Association, p 3Campbell M, Hoane AJ, Hsu F (2002) Deep Blue. Artif Intell 134(1–2):57–83Cangelosi A, Schlesinger M, Smith LB (2015) Developmental robotics: from babies to robots. MIT Press, CambridgeCaputo B, Müller H, Martinez-Gomez J, Villegas M, Acar B, Patricia N, Marvasti N, Üsküdarlı S, Paredes R, Cazorla M et al (2014) Imageclef 2014: overview and analysis of the results. In: Information access evaluation. Multilinguality, multimodality, and interaction, Springer, pp 192–211Carlson A, Betteridge J, Kisiel B, Settles B, Hruschka ER Jr, Mitchell TM (2010) Toward an architecture for never-ending language learning. In: AAAI, vol 5, p 3Carroll JB (1993) Human cognitive abilities: a survey of factor-analytic studies. Cambridge University Press, CambridgeCaruana R (1997) Multitask learning. Mach Learn 28(1):41–75Chaitin GJ (1982) Gödel’s theorem and information. Int J Theor Phys 21(12):941–954Chandrasekaran B (1990) What kind of information processing is intelligence? In: The foundation of artificial intelligence—a sourcebook. Cambridge University Press, pp 14–46Chater N (1999) The search for simplicity: a fundamental cognitive principle? Q J Exp Psychol Sect A 52(2):273–302Chater N, Vitányi P (2003) Simplicity: a unifying principle in cognitive science? Trends Cogn Sci 7(1):19–22Chu Z, Gianvecchio S, Wang H, Jajodia S (2010) Who is tweeting on twitter: human, bot, or cyborg? In: Proceedings of the 26th annual computer security applications conference, ACM, pp 21–30Cochran WG (2007) Sampling techniques. Wiley, New YorkCohen PR, Howe AE (1988) How evaluation guides AI research: the message still counts more than the medium. AI Mag 9(4):35Cohen Y (2013) Testing and cognitive enhancement. Technical repor, National Institute for Testing and Evaluation, Jerusalem, IsraelConrad JG, Zeleznikow J (2013) The significance of evaluation in AI and law: a case study re-examining ICAIL proceedings. In: Proceedings of the 14th international conference on artificial intelligence and law, ACM, pp 186–191Conrad JG, Zeleznikow J (2015) The role of evaluation in ai and law. In: Proceedings of the 15th international conference on artificial intelligence and law, pp 181–186Deary IJ, Der G, Ford G (2001) Reaction times and intelligence differences: a population-based cohort study. Intelligence 29(5):389–399Decker KS, Durfee EH, Lesser VR (1989) Evaluating research in cooperative distributed problem solving. Distrib Artif Intell 2:487–519Demšar J (2006) Statistical comparisons of classifiers over multiple data sets. J Mach Learn Res 7:1–30Detterman DK (2011) A challenge to Watson. Intelligence 39(2–3):77–78Dimitrakakis C (2016) Personal communicationDimitrakakis C, Li G, Tziortziotis N (2014) The reinforcement learning competition 2014. AI Mag 35(3):61–65Dowe DL (2013) Introduction to Ray Solomonoff 85th memorial conference. In: Dowe DL (ed) Algorithmic probability and friends. Bayesian prediction and artificial intelligence, lecture notes in computer science, vol 7070. Springer, Berlin, pp 1–36Dowe DL, Hajek AR (1997) A computational extension to the Turing Test. In: Proceedings of the 4th conference of the Australasian cognitive science society, University of Newcastle, NSW, AustraliaDowe DL, Hajek AR (1998) A non-behavioural, computational extension to the Turing test. In: International conference on computational intelligence and multimedia applications (ICCIMA’98), Gippsland, Australia, pp 101–106Dowe DL, Hernández-Orallo J (2012) IQ tests are not for machines, yet. Intelligence 40(2):77–81Dowe DL, Hernández-Orallo J (2014) How universal can an intelligence test be? Adapt Behav 22(1):51–69Drummond C (2009) Replicability is not reproducibility: nor is it good science. In: Proceedings of the evaluation methods for machine learning workshop at the 26th ICML, Montreal, CanadaDrummond C, Japkowicz N (2010) Warning: statistical benchmarking is addictive. Kicking the habit in machine learning. J Exp Theor Artif Intell 22(1):67–80Duan Y, Chen X, Houthooft R, Schulman J, Abbeel P (2016) Benchmarking deep reinforcement learning for continuous control. arXiv preprint arXiv:1604.06778Eden AH, Moor JH, Soraker JH, Steinhart E (2013) Singularity hypotheses: a scientific and philosophical assessment. Springer, New YorkEdmondson W (2012) The intelligence in ETI—what can we know? Acta Astronaut 78:37–42Elo AE (1978) The rating of chessplayers, past and present, vol 3. Batsford, LondonEmbretson SE, Reise SP (2000) Item response theory for psychologists. L. Erlbaum, HillsdaleEvans JM, Messina ER (2001) Performance metrics for intelligent systems. NIST Special Publication SP, pp 101–104Everitt T, Lattimore T, Hutter M (2014) Free lunch for optimisation under the universal distribution. In: 2014 IEEE Congress on evolutionary computation (CEC), IEEE, pp 167–174Falkenauer E (1998) On method overfitting. J Heuristics 4(3):281–287Feldman J (2003) Simplicity and complexity in human concept learning. Gen Psychol 38(1):9–15Ferrando PJ (2009) Difficulty, discrimination, and information indices in the linear factor analysis model for continuous item responses. Appl Psychol Meas 33(1):9–24Ferrando PJ (2012) Assessing the discriminating power of item and test scores in the linear factor-analysis model. Psicológica 33:111–139Ferri C, Hernández-Orallo J, Modroiu R (2009) An experimental comparison of performance measures for classification. Pattern Recogn Lett 30(1):27–38Ferrucci D, Brown E, Chu-Carroll J, Fan J, Gondek D, Kalyanpur AA, Lally A, Murdock J, Nyberg E, Prager J et al (2010) Building Watson: an overview of the DeepQA project. AI Mag 31(3):59–79Fogel DB (1991) The evolution of intelligent decision making in gaming. Cybern Syst 22(2):223–236Gaschnig J, Klahr P, Pople H, Shortliffe E, Terry A (1983) Evaluation of expert systems: issues and case studies. Build Exp Syst 1:241–278Geissman JR, Schultz RD (1988) Verification & validation. AI Exp 3(2):26–33Genesereth M, Love N, Pell B (2005) General game playing: overview of the AAAI competition. AI Mag 26(2):62Gerónimo D, López AM (2014) Datasets and benchmarking. In: Vision-based pedestrian protection systems for intelligent vehicles. Springer, pp 87–93Goertzel B, Pennachin C (eds) (2007) Artificial general intelligence. Springer, New YorkGoertzel B, Arel I, Scheutz M (2009) Toward a roadmap for human-level artificial general intelligence: embedding HLAI systems in broad, approachable, physical or virtual contexts. Artif Gen Intell Roadmap InitiatGoldreich O, Vadhan S (2007) Special issue on worst-case versus average-case complexity editors’ foreword. Comput complex 16(4):325–330Gordon BB (2007) Report on panel discussion on (re-)establishing or increasing collaborative links between artificial intelligence and intelligent systems. In: Messina ER, Madhavan R (eds) Proceedings of the 2007 workshop on performance metrics for intelligent systems, pp 302–303Gulwani S, Hernández-Orallo J, Kitzelmann E, Muggleton SH, Schmid U, Zorn B (2015) Inductive programming meets the real world. Commun ACM 58(11):90–99Hand DJ (2004) Measurement theory and practice. A Hodder Arnold Publication, LondonHernández-Orallo J (2000a) Beyond the Turing test. J Logic Lang Inf 9(4):447–466Hernández-Orallo J (2000b) On the computational measurement of intelligence factors. In: Meystel A (ed) Performance metrics for intelligent systems workshop. National Institute of Standards and Technology, Gaithersburg, pp 1–8Hernández-Orallo J (2000c) Thesis: computational measures of information gain and reinforcement in inference processes. AI Commun 13(1):49–50Hernández-Orallo J (2010) A (hopefully) non-biased universal environment class for measuring intelligence of biological and artificial systems. In: Artificial general intelligence, 3rd International Conference. Atlantis Press, Extended report at http://users.dsic.upv.es/proy/anynt/unbiased.pdf , pp 182–183Hernández-Orallo J (2014) On environment difficulty and discriminating power. Auton Agents Multi-Agent Syst. 29(3):402–454. doi: 10.1007/s10458-014-9257-1Hernández-Orallo J, Dowe DL (2010) Measuring universal intelligence: towards an anytime intelligence test. Artif Intell 174(18):1508–1539Hernández-Orallo J, Dowe DL (2013) On potential cognitive abilities in the machine kingdom. Minds Mach 23:179–210Hernández-Orallo J, Minaya-Collado N (1998) A formal definition of intelligence based on an intensional variant of Kolmogorov complexity. In: Proceedings of international symposium of engineering of intelligent systems (EIS’98), ICSC Press, pp 146–163Hernández-Orallo J, Dowe DL, España-Cubillo S, Hernández-Lloreda MV, Insa-Cabrera J (2011) On more realistic environment distributions for defining, evaluating and developing intelligence. In: Schmidhuber J, Thórisson K, Looks M (eds) Artificial general intelligence, LNAI, vol 6830. Springer, New York, pp 82–91Hernández-Orallo J, Flach P, Ferri C (2012a) A unified view of performance metrics: translating threshold choice into expected classification loss. J Mach Learn Res 13(1):2813–2869Hernández-Orallo J, Insa-Cabrera J, Dowe DL, Hibbard B (2012b) Turing Tests with Turing machines. In: Voronkov A (ed) Turing-100, EPiC Series, vol 10, pp 140–156Hernández-Orallo J, Dowe DL, Hernández-Lloreda MV (2014) Universal psychometrics: measuring cognitive abilities in the machine kingdom. Cogn Syst Res 27:50–74Hernández-Orallo J, Martínez-Plumed F, Schmid U, Siebers M, Dowe DL (2016) Computer models solving intelligence test problems: progress and implications. Artif Intell 230:74–107Herrmann E, Call J, Hernández-Lloreda MV, Hare B, Tomasello M (2007) Humans have evolved specialized skills of social cognition: the cultural intelligence hypothesis. Science 317(5843):1360–1366Hibbard B (2009) Bias and no free lunch in formal measures of intelligence. J Artif Gen Intell 1(1):54–61Hingston P (2010) A new design for a Turing Test for bots. In: 2010 IEEE symposium on computational intelligence and games (CIG), IEEE, pp 345–350Hingston P (2012) Believable bots: can computers play like people?. Springer, New YorkHo TK, Basu M (2002) Complexity measures of supervised classification problems. IEEE Trans Pattern Anal Mach Intell 24(3):289–300Hutter M (2007) Universal algorithmic intelligence: a mathematical top $$\rightarrow$$ → down approach. In: Goertzel B, Pennachin C (eds) Artificial general intelligence, cognitive technologies. Springer, Berlin, pp 227–290Igel C, Toussaint M (2005) A no-free-lunch theorem for non-uniform distributions of target functions. J Math Model Algorithms 3(4):313–322Insa-Cabrera J (2016) Towards a universal test of social intelligence. Ph.D. thesis, Departament de Sistemes Informátics i Computació, UPVInsa-Cabrera J, Dowe DL, España-Cubillo S, Hernández-Lloreda MV, Hernández-Orallo J (2011a) Comparing humans and ai agents. In: Schmidhuber J, Thórisson K, Looks M (eds) Artificial general intelligence, LNAI, vol 6830. Springer, New York, pp 122–132Insa-Cabrera J, Dowe DL, Hernández-Orallo J (2011) Evaluating a reinforcement learning algorithm with a general intelligence test. In: Lozano JA, Gamez JM (eds) Current topics in artificial intelligence. CAEPIA 2011, LNAI series 7023. Springer, New YorkInsa-Cabrera J, Benacloch-Ayuso JL, Hernández-Orallo J (2012) On measuring social intelligence: experiments on competition and cooperation. In: Bach J, Goertzel B, Iklé M (eds) AGI, lecture notes in computer science, vol 7716. Springer, New York, pp 126–135Jacoff A, Messina E, Weiss BA, Tadokoro S, Nakagawa Y (2003) Test arenas and performance metrics for urban search and rescue robots. In: Proceedings of 2003 IEEE/RSJ international conference on intelligent robots and systems, 2003 (IROS 2003), IEEE, vol 4, pp 3396–3403Japkowicz N, Shah M (2011) Evaluating learning algorithms. Cambridge University Press, CambridgeJiang J (2008) A literature survey on domain adaptation of statistical classifiers. http://sifaka.cs.uiuc.edu/jiang4/domain_adaptation/surveyJohnson M, Hofmann K, Hutton T, Bignell D (2016) The Malmo platform for artificial intelligence experimentation. In: International joint conference on artificial intelligence (IJCAI)Keith TZ, Reynolds MR (2010) Cattell–Horn–Carroll abilities and cognitive tests: what we’ve learned from 20 years of research. Psychol Schools 47(7):635–650Ketter W, Symeonidis A (2012) Competitive benchmarking: lessons learned from the trading agent competition. AI Mag 33(2):103Khreich W, Granger E, Miri A, Sabourin R (2012) A survey of techniques for incremental learning of HMM parameters. Inf Sci 197:105–130Kim JH (2004) Soccer robotics, vol 11. Springer, New YorkKitano H, Asada M, Kuniyoshi Y, Noda I, Osawa E (1997) Robocup: the robot world cup initiative. In: Proceedings of the first international conference on autonomous agents, ACM, pp 340–347Kleiner K (2011) Who are you calling bird-brained? An attempt is being made to devise a universal intelligence test. Economist 398(8723, 5 March 2011):82Knuth DE (1973) Sorting and searching, volume 3 of the art of computer programming. Addison-Wesley, ReadingKoza JR (2010) Human-competitive results produced by genetic programming. Genet Program Evolvable Mach 11(3–4):251–284Krueger J, Osherson D (1980) On the psychology of structural simplicity. In: Jusczyk PW, Klein RM (eds) The nature of thought: essays in honor of D. O. Hebb. Psychology Press, London, pp 187–205Langford J (2005) Clever methods of overfitting. Machine Learning (Theory). http://hunch.netLangley P (1987) Research papers in machine learning. Mach Learn 2(3):195–198Langley P (2011) The changing science of machine learning. Mach Learn 82(3):275–279Langley P (2012) The cognitive systems paradigm. Adv Cogn Syst 1:3–13Lattimore T, Hutter M (2013) No free lunch versus Occam’s razor in supervised learning. Algorithmic Probability and Friends. Springer, Bayesian Prediction and Artificial Intelligence, pp 223–235Leeuwenberg ELJ, Van Der Helm PA (2012) Structural information theory: the simplicity of visual form. Cambridge University Press, CambridgeLegg S, Hutter M (2007a) Tests of machine intelligence. In: Lungarella M, Iida F, Bongard J, Pfeifer R (eds) 50 Years of Artificial Intelligence, Lecture Notes in Computer Science, vol 4850, Springer Berlin Heidelberg, pp 232–242. doi: 10.1007/978-3-540-77296-5_22Legg S, Hutter M (2007b) Universal intelligence: a definition of machine intelligence. Minds Mach 17(4):391–444Legg S, Veness J (2013) An approximation of the universal intelligence measure. Algorithmic Probability and Friends. Springer, Bayesian Prediction and Artificial Intelligence, pp 236–249Levesque HJ (2014) On our best behaviour. Artif Intell 212:27–35Levesque HJ, Davis E, Morgenstern L (2012) The winog

Population genomics of sub-Saharan Drosophila melanogaster: African diversity and non-African admixture

(ABRIDGED) We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were sequenced above 25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection method. Admixture proportions varied among populations, with greater admixture in urban locations. Admixture levels also varied across the genome, with localized peaks and valleys suggestive of a non-neutral introgression process. Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. After removing putatively admixed genomic segments, the greatest genetic diversity was observed in southern Africa (e.g. Zambia), while diversity in other populations was largely consistent with a geographic expansion from this potentially ancestral region. The European population showed different levels of diversity reduction on each chromosome arm, and some African populations displayed chromosome arm-specific diversity reductions. Inversions in the European sample were associated with strong elevations in diversity across chromosome arms. Genomic scans were conducted to identify loci that may represent targets of positive selection. A disproportionate number of candidate selective sweep regions were located near genes with varied roles in gene regulation. Outliers for Europe-Africa FST were found to be enriched in genomic regions of locally elevated cosmopolitan admixture, possibly reflecting a role for some of these loci in driving the introgression of non-African alleles into African populations