Keywords:
- Antibiotic discovery
- Cancer Genomics
- Cytokine stormExplainable AIHealthcare predictive analysisMachine learning for diagnosis
- deep learning
- Domain Knowledge Integration
- evaluation
- Explainable AI
- Factual knowledge
- Graph Neural Networks
- Large Language Models
- Multi-omics Data
- Prompting
- Relation Extraction
- Retrieval-augmented generation
- Sparse Neural Networks
- Synthetic Dataset
Publications of Andre Freitas sorted by first author
A
| CARMA: Enhanced Compositionality in LLMs via Advanced Regularisation and Mutual Information Alignment, , and , in: The 2025 Conference on Empirical Methods in Natural Language Processing, 2025 |
| TRACE: Training and Inference-Time Interpretability Analysis for Language Models, , and , in: Demonstration at the 2025 Conference on Empirical Methods in Natural Language Processing, 2025 |
| Effective Graph and Rank-based Contextual Embeddings for Textual and Multimedia Data, , , , and , in: International Joint Conference on Neural Networks, 2025 |
B
| Cost–effective Variational Active Entity Resolution, , , , and , in: 37th IEEE International Conference on Data Engineering (ICDE), 2021 |
[URL] |
| Voyager: Data Discovery for Onboarding in Data Science, , , and , in: 37th IEEE International Conference on Data Engineering (ICDE), 2022 |
| Meta-analysis informed machine learning: Supporting cytokine storm detection during CAR-T cell Therapy, , , , , , , , , and , in: Journal of Biomedical Informatics, 142, 2023 |
[DOI] |
| Idiap Scientific Report 2022, , , , , , , , , , , , , , , , , and , Idiap-RR-05-2023 |
|
| Biomarker identification using dynamic time warping analysis: a longitudinal cohort study of COVID-19 patients in a UK tertiary hospital, , , , , and , in: BMJ Open, 2022 |
C
| Montague semantics and modifier consistency measurement in neural language models, , , , and , in: 31st International Conference on Computational Linguistics, 2025 |
| Montague semantics and modifier consistency measurement in neural language models, , , , and , in: 31st International Conference on Computational Linguistics, 2025 |
| Learning Disentangled Representations for Natural Language Definitions, , , and , in: In Findings of the European chapter of Association for Computational Linguistics, 2023 |
|
| Formal Semantic Controls over Language Models, , and , in: LREC-COLING, 2024 |
| LangVAE and LangSpace: Building and Probing for Language Model VAEs, , , and , in: Demonstration at the 2025 Conference on Empirical Methods in Natural Language Processing (EMNLP), 2025 |
| Learning Lessons from the COVID-19 pandemic for Real World Evidence research in Oncology–shared perspectives from an international consortia, , and , in: ESMO Open, 2023 |
D
| Inference to the Best Explanation in Large Language Models, , , and , in: In Proceedings of the 62nd Annual Meeting of the Association for Computational Linguistics, 2024 |
| Relation Extraction in Underexplored Biomedical Domains: A Diversity-optimized Sampling and Synthetic Data Generation Approach, , and , in: Computational Linguistics, Volume 50(Issue 3):953–1000, 2024 |
[DOI] [URL] |
| Accelerating Antibiotic Discovery with Large Language Models and Knowledge Graphs, , , and , in: 63rd Annual Meeting of the Association for Computational Linguistics, Vienna, pages 693–705, Association for Computational Linguistics, 2025 |
[DOI] [URL] |
F
| Wave comparisons of clinical characteristics and outcomes of COVID-19 admissions - Exploring the impact of treatment and strain dynamics, , , , , , and , in: Journal of Clinical Virology, 2022 |
| Self-Refine Instruction-Tuning for Aligning Reasoning in Language Models, and , in: Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing, 2024 |
| Patient Attrition in Molecular Tumour Boards: A Systematic Review, , , , , and , in: British Journal of Cancer, 2022 |
G
| Inductive Learning of Logical Theories with LLMs: A Complexity-graded Analysis, , and , in: The 39th Annual AAAI Conference on Artificial Intelligence, 2025 |
J
| SemEval-2024 Task 2: Safe Biomedical Natural Language Inference for Clinical Trials, , and , in: In Proceedings of the 18th International Workshop on Semantic Evaluation (SemEval-2024), 2024 |
| SemEval-2023 Task 7: Multi-Evidence Natural Language Inference for Clinical Trial Data, , , , , and , in: Proceedings of the 17th International Workshop on Semantic Evaluation (SemEval-2023), Association for Computational Linguistics, 2023 |
[DOI] [URL] |
| NLI4CT: Multi-Evidence Natural Language Inference for Clinical Trial Reports, , , , , and , in: Proceedings of The 2023 Conference on Empirical Methods in Natural Language Processing (EMNLP 2023), 2023 |
K
| A Mechanistic Interpretation of Syllogistic Reasoning in Auto-Regressive Language Models, , and , in: Findings of the ACL, 2025 |
L
| Establishment of CORONET, COVID-19 Risk in Oncology Evaluation Tool, to Identify Cancer Patients at Low Versus High Risk of Severe Complications of COVID-19 Infection Upon Presentation to Hospital, , , and , in: Clinical Cancer Informatics, 2022 |
| Longitudinal characterisation of haematological and biochemical parameters in cancer patients prior to and during COVID-19 reveals features associated with outcome, , , and , in: ESMO Open, 2021 |
| Nexus: An Omni-Perceptive And-Interactive Model for Language, Audio, And Vision, , , , , , , , , , , , , , , , , , and , in: ACM Multimedia, 2025 |
M
| Systematicity, Compositionality and Transitivity of Deep NLP Models: a Metamorphic Testing Perspective, , , , and , in: Findings of the ACL, 2022 |
| An evidence-based guidance framework for neural network system diagrams, , and , in: PLOS One, 2025 |
| Why Scholars Are Diagramming Neural Network Models, , and , in: 13th International Conference on the Theory and Application of Diagrams, 2022 |
| Scholarly AI system diagrams as an access point to mental models, , and , in: Diagrams, 2021 |
| Structuralist analysis for neural network system diagrams, , and , in: Diagrams, 2021 |
| Number and quality of diagrams in scholarly publications is associated with number of citations, , and , in: Diagrams, 2021 |
| Switching Contexts: Transportability Measures for NLP, , , and , in: 14th International Conference on Computational Semantics, 2021 |
[URL] |
| Introduction to Mathematical Language Processing: Informal Proofs, Word Problems, and Supporting Tasks, and , in: Transactions of the ACL, 2023 |
| Similarity-Based Equational Inference in Physics, and , in: Physics Review Research, 2021 |
| Exploring the Limits of Fine-grained LLM-based Physics Inference via Premise Removal Interventions, , and , in: Findings of EMNLP, 2024 |
| Controlling Equational Reasoning in Large Language Models with Prompt Interventions, , and , in: The 39th Annual AAAI Conference on Artificial Intelligence, 2025 |
| A Symbolic Framework for Systematic Evaluation of Mathematical Reasoning with Transformers, , , and , in: Proceedings of the 2024 Conference of the North American Chapter of the Association for Computational Linguistics (NAACL), 2024 |
[URL] |
| STAR: Cross-modal Statement Representation for Selecting Relevant Mathematical Premises, and , in: 16th conference of the European Chapter of the Association for Computational Linguistics (EACL), 2021 |
| Does My Representation Capture X? Probe-Ably, , , , and , in: 59th Annual Meeting of the Association for Computational Linguistics (Demonstration track), 2021 |
[URL] |
| To be or not to be an Integer? Encoding Variables for Mathematical Text, , , , and , in: Findings of the ACL, 2022 |
| Disentangling Generative Factors in Natural Language with Discrete Variational Autoencoders, and , in: The 2021 Conference on Empirical Methods in Natural Language Processing, 2021 |
| Graph Neural Flows for Unveiling Systemic Interactions Among Irregularly Sampled Time Series, , and , in: Thirty-Eighth Annual Conference on Neural Information Processing Systems, 2024 |
| Symmetry-induced Disentanglement on Graphs, , and , in: Advances in Neural Information Processing Systems 35, 2022 |
| Diffusion Twigs with Loop Guidance for Conditional Graph Generation, , , and , in: Thirty-Eighth Annual Conference on Neural Information Processing Systems, 2024 |