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
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2025
| Montague semantics and modifier consistency measurement in neural language models, , , , and , in: 31st International Conference on Computational Linguistics, 2025 |
2024
| A Differentiable Integer Linear Programming Solver for Explanation-Based Natural Language Inference, , and , in: The 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation, 2024 |
| 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 |
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| Aligning Large and Small Language Models via Chain-of-Thought Reasoning, and , in: Proceedings of the 18th Conference of the European Chapter of the Association for Computational Linguistics, 2024 |
| An LLM-based Knowledge Synthesis and Scientific Reasoning Framework for Biomedical Discovery, , , , , , , and , in: Proceedings of the 62nd Annual Meeting of the Association for Computational Linguistics, ACL, Bangkok, Thailand, pages 355-364, 2024 |
[DOI] [URL] |
| Consistent Autoformalization for Constructing Mathematical Libraries, , and , in: The 2024 Conference on Empirical Methods in Natural Language Processing, 2024 |
| Deep Clustering for Data Cleaning and Integration, , and , in: 27th International Conference on Extending Database Technology, 2024 |
| Diffusion Twigs with Loop Guidance for Conditional Graph Generation, , , and , in: Thirty-Eighth Annual Conference on Neural Information Processing Systems, 2024 |
| Empowering Cross-lingual Abilities of Instruction-tuned Large Language Models by Translation-following demonstrations, , and , in: Findings of the ACL, 2024 |
| Enhancing Ethical Explanations of Large Language Models through Iterative Symbolic Refinement, , , and , in: The 18th Conference of the European Chapter of the Association for Computational Linguistics (EACL 2024), 2024 |
| Estimating the Causal Effects of Natural Logic Features in Transformer-Based NLI Models, , and , in: The 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation, 2024 |
| Exploring the Limits of Fine-grained LLM-based Physics Inference via Premise Removal Interventions, , and , in: Findings of EMNLP, 2024 |
| Formal Semantic Controls over Language Models, , and , in: LREC-COLING, 2024 |
| Graph Neural Flows for Unveiling Systemic Interactions Among Irregularly Sampled Time Series, , and , in: Thirty-Eighth Annual Conference on Neural Information Processing Systems, 2024 |
| Graph-Induced Syntactic-Semantic Spaces in Transformer-Based Variational AutoEncoders, , , , and , in: In Findings of the Association for Computational Linguistics: NAACL 2024, 2024 |
| Improving Semantic Control in Discrete Latent Spaces with Transformer Quantized Variational Autoencoders, , , , and , in: Findings of the 18th Conference of the European Chapter of the Association for Computational Linguistics (EACL 2024), 2024 |
| 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 |
| Large Language Models, scientific knowledge and factuality: A framework to streamline human expert evaluation, , , , and , in: Journal of Biomedical Informatics(158), 2024 |
[DOI] [URL] |
| Learning Disentangled Semantic Spaces of Explanations via Invertible Neural Networks, , and , in: The 62nd Annual Meeting of the Association for Computational Linguistics, 2024 |
| Multi-Operational Mathematical Derivations in Latent Space, , , and , in: Proceedings of the 2024 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 1: Long Papers), 2024 |
| Multi-Relational Hyperbolic Word Embeddings from Natural Language Definitions, , and , in: The 18th Conference of the European Chapter of the Association for Computational Linguistics (EACL 2024), 2024 |
| On the Nature of Explanation: An Epistemological-Linguistic Perspective for Explanation-Based Natural Language Inference, and , in: Philosophy & Technology, 2024 |
| Reasoning with Natural Language Explanations, and , in: In Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing: Tutorial Abstracts, 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] |
| 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 |
| 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 |
| Verification and Refinement of Natural Language Explanations through LLM-Symbolic Theorem Proving, , , and , in: Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing, 2024 |
2023
| A Canonical Context-preserving Representation for Open IE: Extracting Semantically Typed Relational Tuples from Complex Sentences, , , and , in: Knowledge-based Systems, 2023 |
| 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] |
| 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 |
| Idiap Scientific Report 2022, , , , , , , , , , , , , , , , , and , Idiap-RR-05-2023 |
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| Introduction to Mathematical Language Processing: Informal Proofs, Word Problems, and Supporting Tasks, and , in: Transactions of the ACL, 2023 |
| Learning Disentangled Representations for Natural Language Definitions, , , and , in: In Findings of the European chapter of Association for Computational Linguistics, 2023 |
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| 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 |
| Meta-analysis informed machine learning: Supporting cytokine storm detection during CAR-T cell Therapy, , , , , , , , , and , in: Journal of Biomedical Informatics, 142, 2023 |
[DOI] |
| 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 |
| On Interventional Probing in High Dimensions: An NLI Case Study, , , and , in: Findings of the 17th European Chapter of the Association for Computational Linguistics, 2023 |
| 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] |
| Transformers, Tables and Frame Semantics, , , and , in: International Conference on Semantic Computing, 2023 |
| What do individuals with visual impairment need and want from a dialogue-based digital assistant?, , , , and , in: Clinical and Experimental Optometry, 2023 |
2022
| 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 |
| 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 |
| Case-Based Abductive Natural Language Inference, , and , in: Proceedings of the 29th International Conference on Computational Linguistics, 2022 |
[URL] |
| Decomposing Natural Logic Inferences for Neural NLI, , , , and , in: BlackBoxNLP: Workshop on analyzing and interpreting neural networks for NLP, 2022 |
| Diff-Explainer: Differentiable Convex Optimization for Explainable Multi-Hop Inference, , , , and , in: Transactions of the Association for Computational Linguistics, 2022 |
[DOI] |
| 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 |
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