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 journal and type
Publications of type Idiap-RR
2023
| Idiap Scientific Report 2022, , , , , , , , , , , , , , , , , and , Idiap-RR-05-2023 |
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Artificial Intelligence
| Assessing the communication gap between AI models and healthcare professionals: explainability, utility and trust in AI-driven clinical decision-making, , , , , , and , in: Artificial Intelligence, 2022 |
BMC Bioinformatics
| A systematic review of biologically-informed deep learning models for cancer: fundamental trends for encoding and interpreting oncology data, , , , and , in: BMC Bioinformatics, 24(198), 2023 |
[DOI] |
BMJ Open
| 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 |
British Journal of Cancer
| Patient Attrition in Molecular Tumour Boards: A Systematic Review, , , , , and , in: British Journal of Cancer, 2022 |
Clinical and Experimental Optometry
| What do individuals with visual impairment need and want from a dialogue-based digital assistant?, , , , and , in: Clinical and Experimental Optometry, 2023 |
Clinical Cancer Informatics
| 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 |
Computational Linguistics
| 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] |
| Transformers and the representation of biomedical background knowledge, , , , , and , in: Computational Linguistics, 2022 |
Diagrams
| Number and quality of diagrams in scholarly publications is associated with number of citations, , and , in: Diagrams, 2021 |
ESMO Open
| 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 |
| 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 |
European Journal of Cancer
| Defining the role of real-world data in cancer clinical research: the position of the European Organisation for Research and Treatment of Cancer, , and , in: European Journal of Cancer, 2023 |
Frontiers in Digital Health
| UpSMART: five years of digital innovation in cancer clinical research---achievements, challenges, and recommendations, , , , , , , , , , , , , , , , , , , , , and , in: Frontiers in Digital Health, 7, 2025 |
[DOI] |
JCO Clinical Cancer Informatics
| digital ECMT cancer trial matching tool, an open source research application to support oncologists in the identification of precision medicine clinical trials,, , and , in: JCO Clinical Cancer Informatics, 2022 |
Journal of Biomedical Informatics
| Large Language Models, scientific knowledge and factuality: A framework to streamline human expert evaluation, , , , and , in: Journal of Biomedical Informatics(158), 2024 |
[DOI] [URL] |
| Meta-analysis informed machine learning: Supporting cytokine storm detection during CAR-T cell Therapy, , , , , , , , , and , in: Journal of Biomedical Informatics, 142, 2023 |
[DOI] |
Journal of Clinical Virology
| 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 |
Knowledge-based Systems
| A Canonical Context-preserving Representation for Open IE: Extracting Semantically Typed Relational Tuples from Complex Sentences, , , and , in: Knowledge-based Systems, 2023 |
Philosophy & Technology
| On the Nature of Explanation: An Epistemological-Linguistic Perspective for Explanation-Based Natural Language Inference, and , in: Philosophy & Technology, 2025 |
| On the Nature of Explanation: An Epistemological-Linguistic Perspective for Explanation-Based Natural Language Inference, and , in: Philosophy & Technology, 2024 |
Physics Review Research
| Similarity-Based Equational Inference in Physics, and , in: Physics Review Research, 2021 |
Transactions of the ACL
| Introduction to Mathematical Language Processing: Informal Proofs, Word Problems, and Supporting Tasks, and , in: Transactions of the ACL, 2023 |
Transactions of the Association for Computational Linguistics
| Diff-Explainer: Differentiable Convex Optimization for Explainable Multi-Hop Inference, , , , and , in: Transactions of the Association for Computational Linguistics, 2022 |
[DOI] |
The 40th Annual AAAI Conference on Artificial Intelligence (2026)
| Learning to Disentangle Latent Reasoning Rules with Language VAEs: A Systematic Study, , , and , in: The 40th Annual AAAI Conference on Artificial Intelligence, 2026 |
| Mitigating Content Effects on Reasoning in Language Models through Fine-Grained Activation Steering, , , , and , in: The 40th Annual AAAI Conference on Artificial Intelligence, 2026 |
Findings of the ACL (2025)
| A Mechanistic Interpretation of Syllogistic Reasoning in Auto-Regressive Language Models, , and , in: Findings of the ACL, 2025 |
PLOS One (2025)
| An evidence-based guidance framework for neural network system diagrams, , and , in: PLOS One, 2025 |
The 2025 Conference on Empirical Methods in Natural Language Processing (2025)
| 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 |
The 39th Annual AAAI Conference on Artificial Intelligence (2025)
| Controlling Equational Reasoning in Large Language Models with Prompt Interventions, , and , in: The 39th Annual AAAI Conference on Artificial Intelligence, 2025 |
International Joint Conference on Neural Networks (2025)
| Effective Graph and Rank-based Contextual Embeddings for Textual and Multimedia Data, , , , and , in: International Joint Conference on Neural Networks, 2025 |
Annual Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics (2025)
| Eliciting Critical Reasoning in Retrieval-Augmented Language Models via Contrastive Explanations, , and , in: Annual Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics, 2025 |
63rd Annual Meeting of the Association for Computational Linguistics (2025)
| Faithful and Robust LLM-Driven Theorem Proving for NLI Explanations, , , and , in: 63rd Annual Meeting of the Association for Computational Linguistics, 2025 |
The 2025 Conference on Empirical Methods in Natural Language Processing (best resource paper award) (2025)
| Formalizing Complex Mathematical Statements with LLMs: A Study on Mathematical Definitions, , and , in: The 2025 Conference on Empirical Methods in Natural Language Processing (best resource paper award), 2025 |
8th International Conference on Extending Database Technology (2025)
| Gem: Gaussian Mixture Model Embeddings for Numerical Feature Distributions, , , and , in: 8th International Conference on Extending Database Technology, 2025 |
63rd Annual Meeting of the Association for Computational Linguistics (2025)
| Improving chain-of-thought reasoning via quasi-symbolic abstractions, , , and , in: 63rd Annual Meeting of the Association for Computational Linguistics, 2025 |
The 39th Annual AAAI Conference on Artificial Intelligence (2025)
| Inductive Learning of Logical Theories with LLMs: A Complexity-graded Analysis, , and , in: The 39th Annual AAAI Conference on Artificial Intelligence, 2025 |
Demonstration at the 2025 Conference on Empirical Methods in Natural Language Processing (EMNLP) (2025)
| 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 |
Demonstration at the 2025 Conference on Empirical Methods in Natural Language Processing (2025)
| MASA: A Modular Framework for LLM-Driven Multi-Agent Systems for Autoformalization, , and , in: Demonstration at the 2025 Conference on Empirical Methods in Natural Language Processing, 2025 |
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 |
| Montague semantics and modifier consistency measurement in neural language models, , , , and , in: 31st International Conference on Computational Linguistics, 2025 |
ACM Multimedia (2025)
| Nexus: An Omni-Perceptive And-Interactive Model for Language, Audio, And Vision, , , , , , , , , , , , , , , , , , and , in: ACM Multimedia, 2025 |
Demonstration at 63rd Annual Meeting of the Association for Computational Linguistics (2025)
| PEIRCE: Unifying Material and Formal Reasoning via LLM-Driven Neuro-Symbolic Refinement, , , , and , in: Demonstration at 63rd Annual Meeting of the Association for Computational Linguistics, 2025 |
29th Conference on Computational Natural Language Learning (nominated for a best paper award) (2025)
| Quasi-symbolic Semantic Geometry over Transformer-based Variational AutoEncoders, , and , in: 29th Conference on Computational Natural Language Learning (nominated for a best paper award), 2025 |
Annual Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics (2025)
| SylloBio-NLI: Evaluating Large Language Models on Biomedical Syllogistic Reasoning, , , , and , in: Annual Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics, 2025 |