Muhammad Bilal

PhD Computer Science |

Assistant Researcher at the Institute of the Environment and Sustainability (IoES), UCLA


Ph.D. in Computer Science with extensive experience in data mining, predictive modeling and simulation of complex systems. Strengths include strong demonstration of analytical thinking and attention to details, and excellent interpersonal, communication and leadership skills.

My research focuses on the development of machine learning/data mining approaches for the environmental impact assessment of engineered nanomaterials (ENMs). I have developed a decision support framework as an online tool that consists of data driven predictive models for the estimation of environmental distribution of ENMs based on experimental data and models for the evaluation of their toxicity/bioactivity. I have participated in the development of various exploration tools for assessing the attributes of high relevance in predicting ENMs impact. In addition, I have extensive experience in designing, implementing, and maintaining high performance computation clusters, server applications, and developing advanced web applications.


C, C++, C#, MATLAB, Java, R, HTML, PHP, Javascript

Web Development

Visualization (d3.js), knockout.js, angularJS, Bootstrap

Software Development Tools

Eclipse, git, NetBeans, Visual Studio

Operating Systems

Linux, Windows

RDMS and Server Applicatinons Deployment

NoSQL (MongoDB), MySQL, PostgreSQL, JDBC, Apache, Tomcat, DHCP, DNS

High Performance Computing

Rocks cluster, Sun Grid Engine, Ganglia


Assistant Researcher
Center for Environmental Implications of Nanotechnology (CEIN)
University of California, Los Angeles

September 2013 - present

  • Lead a team of data specialists and researchers in developing and validating an online decision support system consisting of various machine learning/data mining tools such as Bayesian Networks (BNs), hierarchical clustering, Decision Trees, self organizing maps (SOMs), principle component analysis, and multicriteria decision analysis for assessing the potential environmental impact of ENMs. (Model solvers: MATLAB, R, Java. Interfaces: AngularJS, knockoutJS, PHP, Bootstrap, Javascript
  • Prepare to market and commercialize advanced machine learning tools for government and private sector organizations
  • Maintain a high performance computational cluster using Rocks cluster and Sun Grid Engine, with 22 nodes, 240 CPUs, and 115TB of storage; perform harware diagnostics and troubleshooting
  • Conduct web based first tier screening of the potential environmental impact of ENMs making use of dempster shafer theory on the knowledge transformed in tree structure
  • Conduct case studies using developed models/approaches to demonstrate their performance and applicability domains
  • Design and implement integrated computational tools as client server based web applications, which includes web-based advanced user interface, parameters database, data visualization and model solvers using HTML, PHP, Java, R, Javascript, MySQL, and C++. Develop application programming interface (API) to allow query and access of model and simulation tools by external software components
  • Write for academic journals, conduct and participate in international workshops and presentations for CEIN. Authored and co-authored 15 publications (5 published, 4 ready for submission, 2 under review, 4 in preparation). Delivered more than 10 oral and poster (, , ) presentations in various scientific conferences and meetings.

Research Fellow
School of Computing
University of Leeds, United Kingdom

June 2012 - August 2013

  • Constructed a multi-sensor apparatus for underground data collection in collaboration with a multidisciplinary team
  • Developed data fusion and image processing techniques to build the most likely maps of buried utilities
  • Partnered with peer institutions for data collection and joint research initiatives
  • Hosted and organized symposiums for project partners to present findings

Visiting lecturer
British Broadcasting Corporation (BBC), London, United Kingdom

July 2013

  • Prepared and delivered lectures on internet security and protocols
  • Conducted hands-on exercises on cryptographic techniques for secure network communications

Mobile Application Developer
Metricell, Horsham, United Kingdom

March 2011 - August 2012

  • Developed a mobile application that pinpointed service area problems to drive necessary investment by network operators
  • Worked in a team to improve network service and the customer experience
  • Facilitated detailed analytical recommendations between Metricell and mobile service providers

Associate Lecturer
University of Bradford, Bradford, United Kingdom

February 2010 - May 2012

  • Designed and delivered curriculum for the courses on
    • Computer Communications and Networks
    • Networks and Protocols
    • Internet Security and Protocols
    • Mobile Applications
  • Organized and participated in departmental meetings for student performance calibration
  • Advised graduate students on their theses and supporting projects

Web Developer
University of Bradford, Bradford, United Kingdom

September 2010 - May 2011

  • Developed an online student coursework repository for interactive feedback to students
  • Created a centralized database for storage and processing of confidential data
  • Organized training sessions for faculty and staff to utilize the repository and database


Nanomaterials Environmental Impact Assessment (CEIN)

A data-driven modeling platform based on Bayesian network (BN) was developed for qualitatively and quantitatively assessing the potential environmental impact of ENMs. BN structure was designed based on domain knowledge of toxicological and transport behaviors of ENMs, relating their physicochemical properties, environmental distribution, exposure concentration, and relevant hazard (or toxicity) information. The conditional probability tables for the BN was populated using data from experimental and computational modeling results of ENM toxicity and exposure levels. The modeling platform was deployed as a web application via custom designed user interface adhering to standard web application principles (i.e., MVC), which enables rapid online expert survey and elicitation.

(Model solver: Java, PHP; Web application: PHP, JavaScript, MySQL)

ToxNano: A Toolkit for Toxicity Data Analysis of Engineered Nanomaterials (CEIN)

An integrated online toolkit (ToxNano) was created for predictive ENMs toxicology via data-driven models to mine toxicity data from published studies and evaluate ENMs toxicity. ToxNano includes a set of advanced models and computational tools based on machine learning/data mining approaches for:

  • Knowledge Discovery and quantitative structure-activity relationships (QSAR) development for high content bioactivity data
  • Tiered approaches to correlate toxicity metrics with qualitative and quantitative information
  • Identification of the parameters that can be used for predictive toxicology
  • Evaluation of the body of evidence w.r.t. ENM bioactivity
  • High Throughput Screening (HTS) data integration with CEIN Data Management System and advanced techniques for HTS data analysis

ToxNano facilitated the development of toxicity QSARs for a wide range of ENMs including, metal, metal-oxides, and QDs, as well as various surface modified ENMs

(Model solvers: Java, MATLAB, R, Netica, PHP; Web application: PHP, JavaScript, MySQL)

NanoDatabank: A Flexible Database Management System for Nanomaterials

NanoDatabank, is a flexible data management system that provides for classification and storage of various ENMs relevant data types. NanoDatabank currently contains data sets on more than about 400 ENM types, and more than 1000 investigations regarding ENM toxicity (including metal oxides, quantum dots, CNTs and more), F&T and ENM characterization. NanoDatabank supports nanoinformatics tools/simulators by providing (a) accessibility to data sets by various simulators and data processing tools, (b) ability to upload raw data and perform various data processing functions, and (c) an intelligent datasets query system. A unique feature of the NanoDatabank is a dynamically built taxonomy/ontology and storage of ENM information/data with various data access/security levels to allow and promote safe data sharing and storage. In addition, reliability (i.e. clarity regarding exactly what is being reported and trustworthiness/reproducibility) and relevance (i.e. usefulness for a particular purpose) of information is stored in NanoDatabank as metadata along with compressed associated information. To address the issues of data sharing and integration, NanoDatabank uses a range of data converters/utilities to integrate the information among computational tools as part of nanoinformatics platform ( for various scenarios such as life cycle assessment of the release of nanomaterials, multimedia exposure analysis of ENMs, QSARs and data driven models for the evaluation of toxicity of ENMs.

(Development environment: PHP, JavaScript, MySQL, KnockoutJS)

Life Cycle Environmental Assessment For The Release Of Nanomaterials (CEIN)

A generalized web-based modeling platform of the life cycle environmental assessment for the release of ENMs (LearNano) was built to estimate the ENMs release rates to the environment by tracking the mass of ENM from production, through the various technical compartments (i.e., waste water treatment, septic systems, waste incineration), to the eventual ENM release to different environmental compartments.

(Model solver: Java, C++, PHP; Web application: PHP, JavaScript, MySQL)

Rapid assessment of Multimedia Environmental Distribution of Nanomaterials (CEIN)

A BN model was developed to enable rapid assessment of the environmental multimedia mass distribution of ENMs utilizing mechanistic models for the estimation of emissions and multimedia environmental distribution of ENMs. The simulation data was generated using design of experiment techniques (CCD and FFD) for BN model development and validation. The BN is capable of providing reasonable real time estimates of ENMs concentrations based on the data for wide ranges of parameters. BN model is suited for “what if” first tier analyses to provide estimations of potential exposure concentrations, impact of ENMs release rates and various other related parameters. BN also provides the causal-effect relationships between the parameters and resulting ENM concentrations in order to visually investigate their variations and their impact on ENMs concentrations. The modeling framework has been implemented as a web-based modeling system, which assists users in rapidly assessing ENMs exposure concentrations by specifying relevant ENMs properties, geographical and meteorological parameters (i.e., regions, temperature, wind speed, rain, etc.), and source emissions, as well as visualizing the results.

(Model Solver: Netica; Web application: PHP, JavaScript)

Conditional dependence assessment and association rule mining of zebrafish phenotypes (CEIN)

A meta-analysis was conducted for the assembly and generalization of ENMs impact on zebrafish and understanding relationships between ENMs properties and Embryonic Zebrafish (EZ) toxicity. Using 7 different types of ENMs (metal, metal oxide, cellulose, dendrimer, carbon, semiconductor, polymeric) as a model system, 1,147 samples from the nanomaterial biological interactions (NBI) knowledgebase were extracted followed by predictive model development to relate EZ metric to the ENM physicochemical and experimental parameters. The EZ metric was integrated using 21 phenotypes including zebrafish 24 and 120 hours post fertilization (HPF) mortality. A range of clustering techniques (i.e., SOM, hierarchical) and association rule mining techniques were developed to assess the relationships and interdependence of zebrafish phenotypes. The association rule mining and other clustering approaches demonstrated that the the olfactory regions (such as eye, snout, jaw) were strongly correlated with each other and heart had stronger correlations with olfactory regions as well as other phenotypes (especially yolk sac edema, curved axis, trunk malfunctioning, touch response, circulation, caudal fin, otic vessicle). Overall, the present work suggests that information derived from literature data mining can provide guidance regarding key ENM attributes (e.g., core properties, surface properties and experimental settings) that should be characterized and reported in EZ toxicity assessment studies. In addition, the present study suggests that the assessment of conditional dependences of zebrafish phenotypes provides useful information on phenotype ranking when integrating them for evaluating ENM toxicity.

(Model Solver: Netica, R, MATLAB)

Inferring the Most Probable Maps of Underground Utilities (University of Leeds, 2013)

An approach for automated creation of revised maps of buried underground utilities was developed by integrating the knowledge extracted from sensors raw data and available statutory records. The combination of statutory records with the hypotheses from sensors was for initial estimation of what might be found underground and roughly where. Data fusion techniques were applied to integrate information from multiple sources followed by Bayesian model development for 2D/3D map (re)construction. The maps were (re)constructed using automated image segmentation techniques for hypotheses extraction and Bayesian classification techniques for segment-manhole connections. The project was funded by Mapping the Underworld (MTU) which is a major initiative in the UK, focused on addressing social, environmental and economic consequences raised from the inability to locate buried underground utilities (such as pipes and cables) by developing multi-sensor mobile device.

(Model Solver: MATLAB)

Cooperative Vehicular Ad hoc Network for safer driving (University of Bradford, 2011)

A game theoretic approach was applied for safer driving using efficient route selection for vehicles especially Emergency Vehicles (EV). A probabilistic route selection mechanism was designed by conditioning on density, number of junctions and number of traffic lights. The vehicle route clearance was incorporated in network simulations by enabling the vehicles connected on the road to share warning message. The level of cooperation by other vehicles in clearing the route was calculated by employing an optimization algorithm called Expectation Maximization (EM) algorithm. An important criterion in safer driving was to assess the level of cooperation by drivers connected on the road depending on their distance from EV, distance from closest junctions, direction, speed and network connectivity strength (signal to noise ratio). Using these features, the cooperation level quantified using EM was used for the distribution of credit among contributing drivers. The credit distribution was implemented using game theoretic concept called the Shapley Value. The technique was proposed to implement a safer and efficient driving system and incorporate cooperative behavior among contributing drivers which could help improve emergency services in terms of improved route selection and vehicle-to-vehicle communication.

(Model Solver: Network Simulator, NCTUns (C++))

Tracesaver: A mobile network service tracker and user centric data analyser (Metricell, 2011)

A mobile appplication (Tracesaver) was developed to pinpoint service area problems for network operators and to use signal coverage facts to drive necessary investment or improvements by network operators. Tracesaver brings Quality of Experience (QoE) from smart phone users and user centric information which when used in conjunction with technical data from network operators helps in better understanding of the customer faced issue/fault and helps in quick and productive/localized rectification efforts. Tracesaver monitors and reports in locations where there is no coverage or data service and this type of data can be used to report serious problematic locations to network operators. Tracesaver is capable of performing intelligent traffic analysis completely transparently to record the "no signal and poor quality" service provided by the operator.

(Model Solver: NetBeans (Java))


Ph.D. in Computer Science
University of Bradford, United Kingdom

October 2011

School of Electrical Engineering and Computer Science (Networks and Performance Engineering)
Dissertation: Game Theoretic Coalitional Routing in Cooperative Vehicular Ad hoc Networks
Advisor: Dr Pauline ML Chan

Entrepreneurship for Science, Medicine and Technology (ESMT)
University of California, Los Angeles
ESMT course helped our team build a business plan to commercialize the platform.

July 2015

Post Graduate Certificate (PGCert) in High Education Practice
Center for Educational Development, University of Bradford, United Kingdom
I attended PGCHEP course to become accredited member of high education commission in the United Kingdom during my role as lecturer at the University of Bradford.

September 2012

MSc in Computer Science (Pervasive Computing)
Birmingham City University, Birmingham, United Kingdom

November 2007

BSc (Mathematics, Physics, Geography)
University of Punjab, Pakistan

February 2003


E. Oh, R. Liu, A. Nel, K. Gemill, Bilal, M. Y. Cohen & I. Medintz, Meta-analysis of cellular toxicity for cadmium-containing quantum dots Nature Nanotechnology 2016.

Liu R., Rallo R., Bilal, M., Cohen Y. Quantitative structure-activity relationships for cellular uptake of surface-modified nanoparticles. Combinatorial Chemistry & High Throughput Screening 2015, 18(4): 365-375.

Bilal, M. , Liu, H., Liu, R., & Cohen, Y. Bayesian Network as Support Tool for Rapid Query of the Environmental Multimedia Distribution of Nanomaterials, Nanoscale, 2017, doi: 10.1039/C6NR08583K.

John Thompson, Anditya Rahardianto, Soomin Kim, Muhammad Bilal, Richard Breckenridge, Yoram Cohen. Real-time direct detection of silica scaling on RO membranes., Journal of Membrane Science, Volume 528, 15 April 2017, Pages 346-358, ISSN 0376-7388,

Romero, M., Godwin, H., Bilal, M., Cohen, Y. Needs and Challenges for Assessing the Environmental Impacts of Engineered Nanomaterials (ENMs), Beilstein J. Nanotechnol. 2017, 8, 989–1014.

Bilal, M. , Liu, H., Liu, R., & Cohen, Y. A Bayesian Network decision support tool for the evaluation of cellular toxicity of cadmium-containing quantum dots based on meta-analysis. (ready for submission).

Bilal, M., Church, P., Liu R., Liu H., & Cohen, Y. NanoDatabank: A Flexible Database Management System for Nanomaterials (Ready for submission).

Bilal, M. , Harper, S., Harper, B., Liu, H., Liu, R., & Cohen, Y. Association rule mining for assessing the relationships among biological responses of embryonic zebrafish. (ready for submission).

Bilal, M. , Liu, H., Liu, R., & Cohen, Y. Assessment of embryonic zebrafish (EZ) toxicity of diverse nanomaterials based on meta-analysis. (ready for submission).

Liu, H. H., Bilal, M., Lazareva, A., Keller, A., & Cohen, Y., Simulation Tool for Assessing the Releases and Environmental Distribution of Nanomaterials. Beilstein Journal of Nanotechnology. 2015, 6, 938–951.

Khan, W., Darren, A., Kuru, K. & Bilal, M. The Flight Guardian: Autonomous Flight Safety Improvement by Monitoring Aircraft Cockpit Instruments. (accepted), (2017) Journal of Aerospace Information Systems.

Bilal, M., Dou, Q., & Cohn, A. G. Inferring the most probable maps of buried underground utilities using Bayesian mapping model. (accepted), (2017) Journal of Applied Geophysics.

Bilal, M., Khan, W., & Pauline, C. Cooperative Network for Emergency Communications: Fair Distribution of Reward among Players based on their Marginal Contribution., Cyberjournals, (2016).

Khan, W., Bilal, M., Chan, P. & Jiang, P. A creative application of wavelet transform and kalman filter for children proof-reading and continuous speech tracking in online stories and TV programs., Creative computing, (2015).


Liu, H. H., Bilal, M., Lazareva, A., Keller, A., Cohen, Y., Regional multimedia distribution of nanomaterials and associated exposures: A software platform. 2014 IEEE International Conference on Bioinformatics and Biomedicine. 2014, 10.

Bilal, M., Awan, I. & Mockford, S. A Unique Global Mobile Network Service Tracker and User Centric Data Analyzer. BWCCA. 2012, 7, 534-539.

Bilal, M., Yar, A., Mockford, S., Khan, W. & Awan, I. Tracesaver: A Tool for Network Service Improvement and Personalized Analysis of User Centric Statistics. AIP Conf. Proc. 1499, 215, 2012.

Bilal, M., Hussain, M. O., & Chan, P. A Reception Based Node Selection Protocol for Multi-hop Routing in Vehicular Ad-hoc Networks. 11th International Conference on Trust, Security and Privacy in Computing and Communications. 2012, 1593-1600.

Bilal, M., Chan, P., Meddings, F., & Konstadopoulo, A. Learner Centred E-Assessment with a Universal Marking Scheme. 3rd International Conference of Teaching and Learning (ICTL), 2011.

Bilal, M., & Chan, P. Student Coursework Repository (SCORE): The hub for online assessment and learner support repository. Bradford LTA Conference, 2011.

Bilal, M., & Chan, P. A Coalitional Incentive Scheme based on Game Theory for Multi-hop Routing in Vehicular Ad hoc Networks. IEEE 6th international Conference on frontier computer science and technology (FCST) 2011.

Bilal, M., Chan, P. & Pillai, P. A fastest multi-hop routing scheme for information dissemination in Vehicular Communication systems. International conference on Software, Telecommunications and Computer Networks (SoftCOM), 2010, 35-41.

Bilal, M., Chan, P. & Pillai, P. Fastest-Vehicle Multi-hop Routing in Vehicular Ad hoc Networks. 10th International conference on Computer and Information Technology (CIT), 2010, 773-778.

Evans, C., & Bilal, M..Developing a WAP application for Mobile Retail Customers. 2nd International Conference on Pervasive Computing and Applications (ICPCA), 2007, 328-332.


ToxNano: A Toolkit for Toxicity Data Analysis of Engineered Nanomaterials. Gordon Research Conference, June 21-26, 2015, WestDover, VT.

Development of a Framework for Environmental Impact Assessment of Engineered Nanomaterials (ENMs). Gordon Research Conference, June 21-26, 2015, WestDover, VT.

Probabilistic Assessment of the Potential Environmental Impact of Engineered Nanomaterials. Nanoinformatics Workshop, Jan 26-28, 2015, Arlington, VA. An integrated Nanoinformatics Web Portal Nanoinformatics Workshop, Jan. 28, 2015, Arlington, VA

Probabilistic nanoinformatics modeling platform for assessing the potential environmental impact of engineered nanomaterials. American Chemical Society National Meeting, Aug. 11, 2014, San Francisco, CA

Nanoinformatics platform for assessing the potential environmental distribution and exposure levels of engineered nanomaterials (ENMs) American Chemical Society National Meeting, Aug. 11, 2014, San Francisco, CA

Nanoinformatics Platform for Environmental Impact Assessment of Nanomaterials UCLA Tech Forum, 2014, Los Angeles, CA.

Regional multimedia distribution of nanomaterials and associated exposures: A software platform IEEE International Conference on Bioinformatics and Biomedicine, Nov. 2, 2014, Belfast, UK

A Reception Based Node Selection Protocol for Multi-hop Routing in Vehicular Ad-hoc Networks. International conferrence. IEEE IUCC, Liverpool, UK, 25-27 June 2012.

Leaner Centered E-Assessment with a Universal Marking Scheme. IEEE International Conferenceon Teaching & Learning. ICTL. Penang, Malaysia, Nov, 2011.

Leaner Centered E-Assessment with a Universal Marking Scheme. 10th Annual Learning, Teaching & Assessment (LTA) conference, University of Bradford, 2011.

A Fastest-Vehicle Multi-Hop Routing in Vehicular Ad hoc Networks. IEEE International Conference on Computer & information Technology (CIT) – 2010, Bradford, UK 2010.



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© 2016 Muhammad Bilal