Pre-Doctoral Researcher

Job title:

Pre-Doctoral Researcher

Company:

IBM

Job description

IntroductionThe project will explore the potentially transformative value of Foundation Models (FM), generative AI (GenAI) and Agentic Workflows for accelerating scientific discovery in biological sciences, particularly in the field of glycomics. These emerging in-silico technologies have already given rise to models, such as AlphaFold, which aim to accelerate research in structural biology, drug discovery, and disease understanding. The complexity of glycomics arises from the structural diversity, branching patterns, dynamic modifications, and functional versatility of glycans. These glycans affect cell-cell communication, immune system regulation, protein folding, pathogen recognition, signal recognition and have important implications across biological systems.Current experimental and computational methods continue to generate vast amounts of biological and glycan-related data, yet their integration and analysis remain a bottleneck in translating this information into actionable biological insights and new hypotheses. When combined, these technologies promise to handle large-scale data from multiple sources (e.g., knowledge bases, experiment databases) to learn complex patterns and carry out inferences. Additionally, the development of novel agentic tools and workflows can further bring these technologies together and unlock new research avenues. By iteratively probing multiple models, knowledge, and tools, agents may be used to design and test new hypotheses, perform and validate in-silico experiments, or suggest the most promising experiments to be designed and undertaken. These activities will generate significant novel insight into the fields of Immunology and Neuroscience, progress novel target identification and (bio)therapeutic design as well as advance computational methods and GenAI.The student will focus on building bridges between these technologies and domains to advance the fields of glycobiology and glycoinformatics, bioinformatics and computer science.The student will have access to rich datasets from cutting-edge facilities as well as IBM’s compute infrastructure.We offer a fully funded 4-year PhD position at the intersection between computer systems design and AI as part of a new initiative between IBM Research Europe and Trinity College Dublin (TCD).The PhD project will be jointly supervised by Professor Gavin Davey, School of Biochemistry and Immunology, Trinity College Dublin and Dr Joao Bettencourt-Silva (IBM Research Europe).The selected student will be employed by IBM for the duration of the PhD and be a registered student at TCD with the following benefits:

• Access to resources and expertise both at IBM Research and TCD
• Research experience in both private and public sectors
• A substantial PhD Salary (

40,000 euro per annum) * Full TCD PhD program fees (EU or non-EU level)Your role and responsibilitiesThe following research questions will be tackled by the student:

• How can emerging multimodal foundation models (e.g., for small molecules, proteins, genes), LLMs (e.g., Granite) and other domain-specific models (e.g., AlphaFold) be used together with existing tools and knowledge bases (e.g., Glycologue, UniCarb-DB) to create new, more detailed models, of glycoproteins and advance glycoprotein research?
• How may agentic workflows be developed to integrate heterogeneous experimental datasets, perform iterative hypothesis generation, and guide experimental designs?
• Can models be trained to identify novel glycan targets in human diseases like cancer and optimise antibody design and synthesis?
• How do we use agentic workflows to model glycosyltransferase and glycosidase networks and train them to generate novel glycan structures which have nutritional and therapeutic benefits?
• Investigate how agentic workflows, computational tools and models may be applied and scaled across domains within scientific discovery workflows.

Examples of models, tools and databases and references:

• Glycologue https://glycologue.org
• UniCarb-DB https://unicarb-db.expasy.org
• Alphafold

; * Multi-view Molecular Embedding with Late Fusion (MMELON)
; * Molecular Aligned Multi-Modal Architecture and Language (MAMMAL)

• Otter-Knowledge: benchmarks of multimodal knowledge graph representation learning from different sources for drug discovery
• The Virtual Lab: AI Agents Design New SARS-CoV-2 Nanobodies with Experimental Validation

; * Enhancing foundation models for scientific discovery via multimodal knowledge graph representations
;Required educationBachelor’s DegreePreferred educationMaster’s DegreeRequired technical and professional expertise

• An honours degree in a relevant domain.
• Master’s Degree in one of the relevant fields such as Bioinformatics, Computational Biology, Data Analytics, Computer Science.
• Basic knowledge of Machine Learning and Artificial Intelligence: ML fundamentals and common Deep Learning architectures; experience with AI/ML libraries such as Pytorch.
• Good programming skills: Python, version control, ability to write complex code from scratch and extend existing codes.
• Strong interest in performing basic research work, including: evaluation of existing literature, ideation of possible/alternative solutions, writing research papers.
• Ability to move quickly from idea to software prototype for evaluation and demonstration.
• Excellent spoken and written English.

Preferred technical and professional experience

• An honours degree in biological sciences, biochemistry, bioinformatics or similar.
• A background in computational and/or data-driven methods.
• Experience applying computational methods to scientific or biological data.
• Knowledge of foundation model architectures with a specific focus on models using biological data and multi-modality.
• Knowledge of Agentic Workflows, common architectures and frameworks.
• Knowledge of GenAI approaches: model architectures, fine-tuning, transfer learning.
• Advanced programming skills: Python and data preprocessing (Pandas, Xarray).
• Understanding or an interest in the fields of Glycobiology, Glycomics.
• Mass Spectrometry & Experimental techniques (optional).
• Track record of published academic papers.

ABOUT BUSINESS UNITIBM Research is the organic growth engine of IBM and an innovation engine for our customers and partners. As part of this mission, IBM Research anticipates and examines ‘What’s Next in Computing’ to ultimately create and integrate the technologies the world relies upon to solve big challenges and unlock new opportunities. We create and pioneer new markets for IBM, our partners and customers as exemplified in our ongoing quest to reach practical and large-scale quantum computing. Across IBM Research, we realize the power and potential to accelerate discovery with our partners and clients by combining the power of high performance computing, AI, and Quantum, all integrated through the hybrid cloud.YOUR LIFE @ IBMIn a world where technology never stands still, we understand that, dedication to our clients success, innovation that matters, and trust and personal responsibility in all our relationships, lives in what we do as IBMers as we strive to be the catalyst that makes the world work better.Being an IBMer means you’ll be able to learn and develop yourself and your career, you’ll be encouraged to be courageous and experiment everyday, all whilst having continuous trust and support in an environment where everyone can thrive whatever their personal or professional background.Our IBMers are growth minded, always staying curious, open to feedback and learning new information and skills to constantly transform themselves and our company. They are trusted to provide on-going feedback to help other IBMers grow, as well as collaborate with colleagues keeping in mind a team focused approach to include different perspectives to drive exceptional outcomes for our customers. The courage our IBMers have to make critical decisions everyday is essential to IBM becoming the catalyst for progress, always embracing challenges with resources they have to hand, a can-do attitude and always striving for an outcome focused approach within everything that they do.Are you ready to be an IBMer?ABOUT IBMIBM’s greatest invention is the IBMer. We believe that through the application of intelligence, reason and science, we can improve business, society and the human condition, bringing the power of an open hybrid cloud and AI strategy to life for our clients and partners around the world.Restlessly reinventing since 1911, we are not only one of the largest corporate organizations in the world, we’re also one of the biggest technology and consulting employers, with many of the Fortune 50 companies relying on the IBM Cloud to run their business.At IBM, we pride ourselves on being an early adopter of artificial intelligence, quantum computing and blockchain. Now it’s time for you to join us on our journey to being a responsible technology innovator and a force for good in the world.IBM is proud to be an equal-opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, gender, gender identity or expression, sexual orientation, national origin, caste, genetics, pregnancy, disability, neurodivergence, age, veteran status, or other characteristics. IBM is also committed to compliance with all fair employment practices regarding citizenship and immigration status.OTHER RELEVANT JOB DETAILSFor additional information about location requirements, please discuss with the recruiter following submission of your application.Job TitlePre-Doctoral ResearcherJob ID20194City / Township / VillageDublinState / ProvinceDublinCountryIrelandWork arrangementHybridArea of workResearchEmployment typeIntern (Fixed Term)Position typeInternshipTravel requiredNo TravelCompany(0066) IBM Ireland LimitedShiftGeneral (daytime)Is this role a commissionable/sales incentive based position?No

Expected salary

Location

Dublin

Job date

Fri, 25 Apr 2025 22:41:29 GMT

To help us track our recruitment effort, please indicate in your email/cover letter where (vacanciesin.eu) you saw this job posting.