About
I am Professor of Informatics and Computing at Indiana University Luddy School, where I direct RedLab and lead a group researching representing and reasoning for data that is messy, incomplete, and spread across sources. These methods are applied in drug discovery, healthcare, emergency response, economics, cybersecurity and defense.
I trained as a computer scientist and spent the first part of my career in the pharmaceutical industry, leading scientific computing teams in computational chemistry and molecular modeling. I came to Indiana University in 2005 from that industry background, which still shapes how I work: I am equally interested in whether something functions in the field and whether it is elegant in theory.
For over ten years I practised as a volunteer EMT and emergency manager, which gave me a new lens on technology and data in critical decision making. The gap between the data that exists and the decision that has to be made is what most of my work is about.
I love creating and exploring new ideas and possibilities. I still write code, I am a persistent tinkerer with new tools, and I read widely outside my field. I write about AI and its wider consequences at Prior Shift. Originally from the UK; based in Bloomington, Indiana.
Research scope
My research concerns acquiring, building and reasoning over data in domains where data acquisition is difficult, data is incomplete and heterogeneous, and decisions are consequential. Methods include graph, semantic and topological representation, machine learning, embeddings and language models and human-computer interaction design frameworks that put structure in front of the person who has to act.
Application Areas
The mathematical methods apply to any domain where the data is complex, heterogeneous and incomplete. They were developed against the most complex system we know of - the human body - and are now being applied in areas including situational awareness and cybersecurity.
Grounded in
Where the methods were built and where they continue to impact: cheminformatics, bioinformatics, chemogenomics, and link prediction over sparse biological evidence — most recently yielding experimentally confirmed drug candidates for tuberculosis.
Current focus
First responders, disaster responders, and emergency managers have to make decisions in complex, adverse, and data overload contexts. My focus is on filling data gaps, fusing heterogeneous real-time streams, and surfacing the signal in an actionable way in high stress environments.
Extending to
Increasingly decisions have to be made across domains and with overlapping data and expertise structures, for example, in cyber-physical systems. These same methods can be applied at higher or different abstraction levels across domains, maybe even to enable decisions that go beyond human capacity to acquire and fuse data.
Research topics
For full publication list see my Google Scholar profile.
Integrating heterogeneous, often messy sources into a single object that permits inference: semantic frameworks, linked open data, ontological annotation, learned embeddings, and the topography of high-dimensional activity spaces. The representational choices made here determine what can subsequently be computed.
Gao Z, Fu G, Ouyang C, Tsutsui S, Liu X, Yang JJ, Gessner C, Foote B, Wild DJ, Ding Y, Yu Q. edge2vec: representation learning using edge semantics for biomedical knowledge discovery. BMC Bioinformatics 20:306.
Kulkarni VS, Wild DJ. An activity canyon characterization of the pharmacological topography. Journal of Cheminformatics 8:41.
Willighagen EL, Waagmeester A, Spjuth O, Ansell P, Williams AJ, Tkachenko V, Hastings J, Chen B, Wild DJ. The ChEMBL database as linked open data. Journal of Cheminformatics 5:23.
Kong X, Yu PS, Ding Y, Wild DJ. Meta path-based collective classification in heterogeneous information networks. Proceedings of the 21st ACM International Conference on Information and Knowledge Management (CIKM) 1567–1571.
Chen B, Dong X, Jiao D, Wang H, Zhu Q, Ding Y, Wild DJ. Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. BMC Bioinformatics 11:255.
Inference across integrated biological, chemical and clinical evidence: estimating what is absent, treating the pattern of absence as evidence in its own right, and keeping provenance inspectable where ground truth is uncertain. Carried through, in the tuberculosis work, to wet-lab confirmed drug candidates.
Yang JJ, Goff A, Wild DJ, Ding Y, Annis A, Kerber R, Foote B, Passi A, Duerksen JL, London S, Puhl AC, Lane TR, Braunstein M, Waddell SJ, Ekins S. Computational drug repositioning identifies niclosamide and tribromsalan as inhibitors of Mycobacterium tuberculosis and Mycobacterium abscessus. Tuberculosis 146:102500.
Yang JJ, Gessner CR, Duerksen JL, Biber D, Binder JL, Ozturk M, Foote B, McEntire R, Stirling K, Ding Y, Wild DJ. Knowledge graph analytics platform with LINCS and IDG for Parkinson's disease target illumination. BMC Bioinformatics 23:37.
Yang JJ, Grissa D, Lambert CG, Bologa CG, Mathias SL, Waller A, Wild DJ, Jensen LJ, Oprea TI. TIGA: target illumination GWAS analytics. Bioinformatics 37(21):3865–3873.
Seal A, Wild DJ. NetPredictor: R and Shiny package to perform drug–target network analysis and prediction of missing links. BMC Bioinformatics 19:265.
Passi A, Rajput NK, Wild DJ, Bhardwaj A. RepTB: a gene ontology based drug repurposing approach for tuberculosis. Journal of Cheminformatics 10:24.
Seal A, Ahn Y-Y, Wild DJ. Optimizing drug–target interaction prediction based on random walk on heterogeneous networks. Journal of Cheminformatics 7:40.
Seal A, Yogeeswari P, Sriram D, OSDD Consortium, Wild DJ. Enhanced ranking of PknB inhibitors using data fusion methods. Journal of Cheminformatics 5:2.
Chen B, Ding Y, Wild DJ. Assessing drug target association using semantic linked data. PLoS Computational Biology 8(7):e1002574.
Wild DJ, Ding Y, Sheth AP, Harland L, Gifford EM, Lajiness MS. Systems chemical biology and the Semantic Web: what they mean for the future of drug discovery research. Drug Discovery Today 17:469–474.
Getting structure in front of a responder, commander or analyst in a form they can act on — and understanding the people on the other side of it: what information they actually need, how they experience vulnerability, and when such systems are and are not trusted.
Rolfson A, Rosen A, Jennings C, Wild DJ. Using semi-structured interviews to elicit information needs and flows for pre-incident planning and technology implementation in emergency management and response. Journal of Homeland Security and Emergency Management, submitted.
Obi I, Paul LJ, Liao W, Loukil M, Hayashi S, Comer M, Rogers CO, Wild DJ, Shih PC. Project APRED: a web-based data analytics platform for supporting community disaster resilience. Journal of Emergency Management 21(5):399–419.
Hill JJ, Wild DJ, Schmidt PM. Optimizing virtual health technologies through a performance-based readiness model: lessons from the field deployment of the National Emergency Tele-Critical Care Network. Military Medicine 188(Suppl 6):377–384.
Seberger JS, Obi I, Loukil M, Liao W, Wild DJ, Patil S. Speculative vulnerability: uncovering the temporalities of vulnerability in people's experiences of the pandemic. Proceedings of the ACM on Human-Computer Interaction 6(CSCW2):1–27.
Dubois E, Yuan X, Bennett Gayle D, Khurana P, Knight T, Laforce S, Turetsky D, Wild DJ. Socially vulnerable populations adoption of technology to address lifestyle changes amid COVID-19 in the US. Data and Information Management 6(2):100001.
The newest strand: applying the same graph and inference machinery where the adversary is active and the time budget is measured in seconds rather than months.
Vallabhaneni U, Cagwin CL, Wild DJ. SENTINEL-RL: offloading topological reasoning from LLM agents in the security operations center. arXiv:2609.04159 [cs.CR].
How organisations and teams actually adopt these methods: the process, the project management, and the education that has to accompany them.
Bentum S. Digital transformation strategies for applied science domains. Doctoral dissertation, Indiana University; supervised.
Saltz J, Hotz N, Wild DJ, Stirling K. Exploring project management methodologies used within data science teams.
Fox G, Maini S, Rosenbaum H, Wild DJ. Data science and online education. IEEE 7th International Conference on Cloud Computing Technology and Science (CloudCom).
Full list at Google Scholar.
Affiliations
DIRECTOR
Artificial intelligence for command, control and communications, and critical infrastructure technologies for first responders, cybersecurity and defense. Spanning basic research through to operational application. Successor to the Crisis Technologies Innovation Lab.
DIRECTOR
The methodological core: graph and semantic representation, topological structure, and inference under partial observation
Core faculty
Center of foundational and applied research in AI at Indiana University
Faculty fellow
Exploring applications in defense including international disaster response, safety, military medicine and situational awareness.
Faculty Fellow
Alongside faculty appointments in cybersecurity and data science at the Luddy School — the institutional home for the security applications of this work.
Lead Instructor
I am lead instructor or co-instructor for several applied project-based learning classes, including IU's Hacking for Defense program.
Contact