contact_data

Room 1.002
Phone: +44 - (0)161 3063094
Manchester Institute of Biotechnology
131 Princess Street
Manchester, UK - M1 7DN

axel{.}soto{at}manchester{.}ac{.}uk

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About me

I am a research associate at the School of Computer Science at the University of Manchester and member of the National Centre for Text Mining (NaCTeM) led by Dr. Sophia Ananiadou.

My former research position was at Dalhousie University for the Visual Text Analytics Group and the MALNIS (Machine Learning and Networked Information Spaces) group. You can browse my old website here.



News



Research

Here are the main research areas I have worked on:


(Visual) Text Analytics

The overall goal in text analytics is to extract actionable insights form large collections of text documents. The approach I have typically taken is by combining text mining and interactive visualizations so that the user is kept in the loop.


Cheminformatics

I am also interested in designing and developing machine learning methods to analyze patterns and quantitatively predict properties on chemical data.



Publications

(preprints are available upon request)

Journals

  1. N. Nguyen, A.J. Soto, G. Kontonatsios, R. Batista-Navarro, S. Ananiadou. "Constructing a Biodiversity Terminological Inventory''. PLOS ONE, 12(4): e0175277, 2017. [paper][bibtex][data][video][demo]
  2. R. Makki, E. Carvalho, A.J. Soto, S. Brooks, M.C. Ferreira de Oliveira, E.E. Milios, R. Minghim. "ATR-Vis: Visual and Interactive Information Retrieval for Parliamentary Discussions in Twitter''. Accepted to ACM Transactions on Knowledge Discovery from Data.[paper][bibtex][data]
  3. A. Cohen, A.J. Soto, Fawcett, J. "Determination of Flow Rates in Capillary Liquid Chromatography Coupled to a Nano Electrospray Source using Droplet Image Analysis Software". Analytical Chemistry. Vol 88, 15, 7476-7480, 2016. [paper][bibtex][code]
  4. A.J. Soto, R. Kiros, V. Keselj, E. Milios. "Exploratory Visual Analysis and Interactive Pattern Extraction from Semi-Structured Data", ACM Transactions on Interactive and Intelligent Systems. Vol 5, 3, Article 16, 2015. [paper][bibtex][code1][code2][video1][video2][video3] 2015 TiiS Best Paper Award
  5. M.J. Martínez, I. Ponzoni, M.F. Díaz, G.E. Vazquez, A.J. Soto. "Visual Analytics in Cheminformatics: User-Supervised Descriptor Selection for QSAR Methods", Journal of Cheminformatics. Vol 7, 39, 2015. [paper][bibtex][code]
  6. L. Kalra, X. Zhao, A.J. Soto, E. Milios. "Detection of Daily Living Activities Using a Two-Stage Markov Model", Journal of Ambient Intelligence and Smart Environments. Vol 5, 273-285, 2013. [paper][bibtex]
  7. D. Palomba, M.J. Martínez, I. Ponzoni, M.F. Díaz, G.E. Vazquez, A.J. Soto. "QSPR Models for Predicting Log Pliver Values for Volatile Organic Compounds Combining Statistical Methods and Domain Knowledge", Molecules. Vol 17, 12, 14937-14953, 2012. [paper][bibtex]
  8. A.J. Soto, G.E. Vazquez, M. Strickert, I. Ponzoni. "Target-Driven Subspace Mapping Methods and Their Applicability Domain Estimation", Molecular Informatics. Vol 30, 9, 779-789, 2011. [paper][bibtex]
  9. A.J. Soto. "On the Use of Machine Learning Methods for Modern Drug Discovery". PhD thesis summary. AI Communications. Vol 24, 99-100. IOS Press, 2011. [paper][bibtex]
  10. A.J. Soto, R.L. Cecchini, G.E. Vazquez, I. Ponzoni. "Multi-Objective Feature Selection in QSAR using a Machine Learning Approach". QSAR & Combinatorial Science. Vol 28, 11-12, 1509-1523, 2009.[paper][bibtex][code]
  11. A.J. Soto, R.L. Cecchini, G.E Vazquez, I. Ponzoni. "An Evolutionary Approach for Feature Selection applied to ADMET Prediction". Ibero American Journal of Artificial Intelligence. Vol 12, 37,55-63, 2008.[paper][bibtex]

Journal Abstracts and Newsletters

  1. A.J. Soto, R. Kiros, V. Keselj, E. Milios. "Machine Learning Meets Visualization for Extracting Insights from Text Data'', ACM-SIGAI AI Matters. Vol 2, 2, 15-17, 2015. [paper][bibtex]
  2. A.J. Soto, M. Strickert, G.E. Vazquez. "Adaptive matrix metrics for molecular descriptor assessment in QSPR classification". Journal of Cheminformatics. Vol 2 (Suppl 1):P47, 2010. [paper][bibtex]

Conferences

  1. A.J. Soto, C. Ryan, F. Peña Silva, T. Das, J. Wołkowicz, E. Milios, S. Brooks. "Data Quality Challenges in Twitter Content Analysis for Informing Policy Making in Health Care". 51st Hawaii International Conference for System Sciences (HICSS-51). January 2-6, 2018; Waikoloa, USA. [paper][bibtex]
  2. W. Wang, A. Mohammad, A. Islam, A.J. Soto, E. Milios. "Non-Uniform Language Detection in Technical Writing". 2016 Conference on Empirical Methods on Natural Language Processing (EMNLP). November 1-5, 2016; Austin, USA. [paper][bibtex][data]
  3. R. Makki, A.J. Soto, S. Brooks, E. Milios. "Twitter Message Recommendation Based on User Interest Profiles". 2016 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM). August 18-21, 2016; San Francisco, USA. [paper][bibtex][data][code]
  4. R. Makki, A.J. Soto, S. Brooks, E. Milios. "Active Information Retrieval for Linking Twitter Posts with Political Debates''. 14th IEEE International Conference on Machine Learning and Applications (ICMLA), 238-245. December 9-11, 2015; Miami, USA. [paper][bibtex][data][code]
  5. A.J. Soto, A. Mohammad, A. Albert, A. Islam, E. Milios, M. Doyle, R. Minghim, M.C.F. de Oliveira. "Similarity-Based Support for Text Reuse in Technical Writing". 15th ACM International Symposium on Document Engineering (DocEng). September 8-11, 2015; Lausanne, Switzerland. [paper][bibtex][code1][code2][data][demo]
  6. A.J. Soto, R. Kiros, V. Keselj, E. Milios. "In-depth Interactive Visual Exploration for Bridging Unstructured and Structured Document Content''. SDM 2014 Workshop on Exploratory Data Analysis, April 26, 2014, Philadelphia, USA. [paper][bibtex]
  7. A. Srivastava, A.J. Soto, E. Milios. "A Graph-based Topic Extraction Method enabling Simple Interactive Customization". 13th ACM International Symposium on Document Engineering (DocEng). September 10-13, 2013; Florence, Italy. [paper][bibtex][code]
  8. A. Srivastava, A.J. Soto, E. Milios. "Text Clustering using One-Mode Projection of Document-Word Bipartite Graphs''. 28th ACM Symposium on Applied Computing, 927-932. March 18-22, 2013; Coimbra, Portugal. [paper][bibtex][code]
  9. R. Kiros, A.J. Soto, E. Milios, V. Keselj. "Representation learning for Sparse, High-Dimensional Multi-Label Classification". In: Jing Tao Yao et al (Eds.). Lecture Notes in Computer Science, Springer-Verlag. 8th International Conference on Rough Sets and Current Trends in Computing 2012. August 17-20, 2012. Chengdu, China. [paper][bibtex]
  10. L. Kalra, X. Zhao, A.J. Soto, E. Milios. "A Two-Stage Corrective Markov Model for Activities of Daily Living Detection''. In: P. Novais et al. (Eds.) Advances in Intelligent and Soft Computing. Vol 153/2012, 171-179, Springer-Verlag. 3rd International Symposium on Ambient Intelligence. March 28-30, 2012; Salamanca, Spain. [paper][bibtex]
  11. A.J. Soto, M. Strickert, G.E. Vazquez, E. Milios. "Subspace Mapping of Noisy Text Documents". In: Cory Butz, Pawan Lingras (Eds.) Lecture Notes in Artificial Intelligence, Vol. 6657, 377-383. Springer-Verlag Berlin Heidelberg. Canadian Conference on Artificial Intelligence 2011. May 25-27, 2011; St. John's, Canada. [paper][bibtex]
  12. A.J. Soto, M. Strickert, G.E. Vazquez, E. Milios. "Adaptive Visualization of Text Documents Incorporating Domain Knowledge". Challenges of Data Visualization. NIPS 2010 Workshop. December 11, 2010; Whistler, Canada. [paper][bibtex]
  13. M. Strickert, A.J. Soto, G.E Vazquez. "Adaptive matrix distances aiming at optimum regression subspaces". European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning - ESANN 2010. April 28-30, 2010; Bruges, Belgium.[paper][bibtex][code]
  14. A.J. Soto, I. Ponzoni, G.E. Vazquez. "Segregating Confident Predictions of Chemicals' Properties for Virtual Screening of Drugs". In: S. Omatu et al. (Eds.) Lecture Notes in Computer Science, Vol. 5518, 1005-1012. Springer-Verlag Berlin Heidelberg. 3rd International Workshop on Practical Applications of Computational Biology and Bioinformatics - IWPACBB 2009. June 10-12, 2009; Salamanca, Spain. [paper][bibtex]
  15. A.J. Soto, R.L. Cecchini, D. Palomba, G.E. Vazquez, I. Ponzoni. "An Evolutionary Approach for Multi-Objective Feature Selection in ADMET Prediction". 34th Latin American Conference on Informatics - CLEI 2008. September 8-12, 2008; Santa Fe, Argentina.[paper][bibtex]
  16. A.J. Soto, R.L. Cecchini, G.E Vazquez, I. Ponzoni. "A Wrapper-based Feature Selection Method for ADMET Prediction using Evolutionary Computing". In: E. Marchiori, J.H. Moore (Eds.) Lecture Notes in Computer Science, Vol. 4973, 188-199. Springer-Verlag Berlin Heidelberg. Sixth European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics - EvoBIO 2008. March 26-28, 2008; Napoli, Italy.[paper][bibtex]
  17. A.J. Soto, I. Ponzoni, G.E. Vazquez. "Predicting Physicochemical Properties for Drug Design Using Clustering and Neural Network Learning". Brazilian Symposium on Bioinformatics 2007. August 29-31, 2007; Angra dos Reis, Brazil.[paper][bibtex]
  18. R.L. Cecchini, A.J. Soto, G.E. Vazquez, I. Ponzoni. "A Genetic Algorithm for Detection of Relevant Descriptors in ADMET Prediction". Brazilian Symposium on Bioinformatics 2007.August 29-31, 2007; Angra dos Reis, Brazil.[paper][bibtex]

Journals in Spanish

  1. G.G. Vignolo, J.A. Vázquez, A.J. Soto. "Analytical, Numerical and Experimental Study of the Thermal Influence in Strain Measurements on Structural Elements". Ibero American Journal of Mechanical Engineering. Vol 17, 2, 13-30, 2013.[paper]
  2. I. Ponzoni, A.J. Soto, G.E. Vazquez. "Activity Cycle Diagrams and its Application on Discrete Event Simulations". Investigación Operativa. Vol 29, 145-160, 2008.

Conference Abstracts / Papers in Spanish

  1. R. Batista-Navarro, N.T.H. Nguyen, A.J. Soto, W. Ulate, S. Ananiadou. "Argo as a platform for integrating distinct biodiversity analytics tools into workflows for building graph databases". TDWG 2017 Symposium on Semantics for Biodiversity Science, October 1-6, 2017, Ottawa, Canada. [paper][bibtex]
  2. D. Glowacka, E. Milios, A.J. Soto, F. Paulovich. "Exploratory Search and Interactive Data Analytics''. 22nd International Conference on Intelligent User Interfaces. 9--11. March 3, 2017; Limassol, Cyprus. [paper][bibtex]
  3. N.T.H. Nguyen, G. Kontonatsios, R. Batista-Navarro, A.J. Soto, S. Ananiadou. "Enhancing semantic search through the automatic construction of a Biodiversity Terminological Inventory". TDWG 2016 Symposium on Semantics for Biodiversity Science, December 5-7, 2016, Santa Clara, Costa Rica. [paper][bibtex]
  4. R. Batista-Navarro, A.J. Soto, W. Ulate, S. Ananiadou. "Text Mining Workflows for Indexing Archives with Automatically Extracted Semantic Metadata". 20th International Conference on Theory and Practice of Digital Libraries (TPDL 2016); September 5-9, 2016, Hannover, Germany. In: Research and Advanced Technology for Digital Libraries, Lecture Notes in Computer Science, Vol 9819, 471-473, Springer. [paper]
  5. A.J. Soto, C. Zerva, R. Batista-Navarro, S. Ananiadou. "LitPathExplorer: A visual tool for exploring literature-enriched pathway models", Biological Network Visualization Analysis Workshop (BioNetVisA), ECCB 2016, September 4th, 2016, The Hague, Netherlands.
  6. A. Cohen, A.J. Soto. "The Antidote to Nano-LC's Achilles' Heel: Real-Time Post-Column Flowrate Measurements of Nano-LC Eluent by Digital Image Analysis'', 28th Workshop on Tandem Mass Spectrometry, December 3-4, 2015, Lake Louise, Canada.
  7. R. Batista-Navarro, A. Islam, W. Ulate, J. Hammock, A.J. Soto, E. Milios, S. Ananiadou. "Enriching the legacy literature with OCR corrections and text-mined semantic metadata". TDWG 2014 Symposium on Access to Digitisation Tools and Methods, October 27-31, 2014, Jönköping, Sweden. [video][bibtex]
  8. A.J. Soto, V. Keselj, E. Milios. "Interactive Clustering of Semi-Structured Documents''. IBM CASCON 2012 Technology Showcases. November 5-8, 2012. Toronto Canada. Best Technology showcase
  9. D. Palomba, M.J. Martínez, I. Ponzoni, M. Díaz, G.E. Vazquez, A.J. Soto. "Prediction of blood to liver coefficients for volatile organic compounds: a cheminformatics approach''. 3rd Argentine Congress on Bioinformatics and Computational Biology - CABBC 2012. September 26-28, 2012; Oro Verde, Argentina.
  10. A.J. Soto, G.E. Vazquez, M. Strickert, I. Ponzoni. "Confidence Assessment of Candidate Drug Property Predictions by Subspace Mapping Methods''. ISCB Latin America. March 17-21, 2012; Santiago, Chile.
  11. A.J. Soto, I. Ponzoni, G.E. Vazquez. "Identifying the Applicability Domain of QSPR Models using Machine Learning Methods". 1st International Conference on Bioinformatics (SoIBio), pp 48. September 26-28, 2010; Chillá n, Chile.
  12. A.J. Soto, M. Strickert, G.E. Vazquez. "A mapping method for linking chemical compounds to biological and physicochemical properties in drug discovery". ISCB Latin America. March 13-16, 2010; Montevideo, Uruguay.
  13. A.J. Soto, R.L Cecchini, G.E. Vazquez, I. Ponzoni. "A new method for multi-objective selection of molecular descriptors for QSAR/QSPR". ISCB Latin America. March 13-16, 2010; Montevideo, Uruguay.
  14. A.J. Soto, J. Martinez, R.L. Cecchini, G.E. Vazquez, Ignacio Ponzoni. "A Prototype Software Tool for Selection of Relevant Descriptors in QSAR Models". 1st Argentine Congress on Bioinformatics and Computational Biology - CABBC 2010. May 12-14, 2010; Quilmes, Argentina.
  15. A.J. Soto, I. Ponzoni, G.E. Vazquez. "On defining applicability domains for prediction models in chemoinformatics". 1st Argentine Congress on Bioinformatics and Computational Biology - CABBC 2010. May 12-14, 2010; Quilmes, Argentina.
  16. A.J. Soto, M. Strickert, G.E. Vazquez. "Adaptive matrix metrics for molecular descriptor assessment in QSPR classification". 5th German Conference on Chemoinformatics. November 8-10, 2009; Goslar, Germany.1
  17. M. Strickert, A.J. Soto, J. Keilwagen, G.E. Vazquez. "Towards matrix-based selection of feature pairs for efficient ADMET prediction". 10th Argentine Symposium on Artificial Intelligence - ASAI 2009, August 24-25, 2009; Mar del Plata, Argentina.
  18. A.J. Soto, D. Palomba, M. Diaz, G.E. Vazquez, I. Ponzoni. "Computational Intelligence Methods on Chemical Compound Clusters". XVII Congress on Numerical Methods and their Applications - ENIEF 2008. November 10-13, 2008; San Luis, Argentina.
  19. A.J. Soto, R.L. Cecchini, I. Ponzoni, G.E. Vazquez. "Computational Intelligence Methods for Physicochemical Property Prediction". 9th Latin American Conference on Physical Organic Chemistry. September 30 - October 5, 2007; Los Cocos, Argentina.
  20. A.J. Soto, R.L. Cecchini, G.E. Vazquez, I. Ponzoni. "Feature Selection for ADMET Prediction using Genetic Algorithms". 9th Argentine Symposium on Artificial Intelligence - ASAI 2007. August 27-28, 2007; Mar del Plata, Argentina.2
  21. A.J Soto, I. Ponzoni, G.E. Vazquez. "Numerical Analysis of Different Similarity Criteria on Clustering Algorithms". XV Congress on Numerical Methods and their Applications - ENIEF 2006. November 7-10, 2006; Santa Fe, Argentina.
  22. A.J Soto, I. Ponzoni, G.E Vazquez. "Parallel Distributed Solving of Linear Equations using a Graph Decomposition Technique". VIII Congress on Computational Mechanics - MECOM 2005. November 16-18, 2005; Buenos Aires, Argentina.
  23. A.J. Soto, I. Ponzoni, G.E. Vazquez. "A Novel Parallel Distributed Algorithm for System of Linear Equations Solving". XIV Congress on Numerical Methods and their Applications - ENIEF 2004. November 8-11, 2004; Bariloche, Argentina

1 Article selected for a Journal Abstract
2 Article selected for a Journal Article.



Teaching

Graduate and undergraduate courses

University of Manchester:

Dalhousie University (Canada):

Universidad Nacional del Sur (Argentina):

  • 2010, Fall - Introduction to Computers (7710)
  • 2009, Spring - Head TA in Discrete Event Simulations (5946)
  • 2009, Fall - Head TA in Scientific Computing (7595)

 

Tutorials at conferences

Text mining workflows for indexing archives with automatically extracted semantic metadata - Conference link: http://www.tpdl2016.org/tutorials

  • 20th International Conference on Theory and Practice of Digital Libraries -- Hannover, September 5--9, 2016.

Visual Text Analytics (jointly with Dr. Evangelos Milios) - Last updated link: http://bit.ly/1LEQk8P

  • 6th Argentinean Conference on Bioinformatics and Computational Biology (CAB2C), Bahía Blanca, Argentina, October 2015
  • 15th International Joint Conference in Artificial Intelligence (IJCAI), Buenos Aires, Argentina, July 2015
  • 28th Canadian Artificial Intelligence Conference (CaAI), Halifax, Canada, June 2015.
  • 2015 SIAM Data Mining Conference (SIAM DM), Vancouver, Canada, May 2015.

 

Invited courses

Visual Text Analytics (prepared jointly with Dr. Evangelos Milios)

  • Universidad Nacional del Sur, Argentina (November 2014 - 25 hours)
  • Warsaw University of Technology, Poland (December 2014 - 20 hours)