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 title
A
| A Canonical Context-preserving Representation for Open IE: Extracting Semantically Typed Relational Tuples from Complex Sentences, , , and , in: Knowledge-based Systems, 2023 |
| 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 Mechanistic Interpretation of Syllogistic Reasoning in Auto-Regressive Language Models, , and , in: Findings of the ACL, 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 |
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| 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 |
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| 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 |
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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 evidence-based guidance framework for neural network system diagrams, , and , in: PLOS One, 2025 |
| 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 |
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| 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 |
B
| 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
| 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 |
| Case-Based Abductive Natural Language Inference, , and , in: Proceedings of the 29th International Conference on Computational Linguistics, 2022 |
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| Consistent Autoformalization for Constructing Mathematical Libraries, , and , in: The 2024 Conference on Empirical Methods in Natural Language Processing, 2024 |
| Controlling Equational Reasoning in Large Language Models with Prompt Interventions, , and , in: The 39th Annual AAAI Conference on Artificial Intelligence, 2025 |
| Cost–effective Variational Active Entity Resolution, , , , and , in: 37th IEEE International Conference on Data Engineering (ICDE), 2021 |
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D
| Decomposing Natural Logic Inferences for Neural NLI, , , , and , in: BlackBoxNLP: Workshop on analyzing and interpreting neural networks for NLP, 2022 |
| Deep Clustering for Data Cleaning and Integration, , and , in: 27th International Conference on Extending Database Technology, 2024 |
| 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 |
| Diff-Explainer: Differentiable Convex Optimization for Explainable Multi-Hop Inference, , , , and , in: Transactions of the Association for Computational Linguistics, 2022 |
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| Diffusion Twigs with Loop Guidance for Conditional Graph Generation, , , and , in: Thirty-Eighth Annual Conference on Neural Information Processing Systems, 2024 |
D
| 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 |
D
| Disentangling Generative Factors in Natural Language with Discrete Variational Autoencoders, and , in: The 2021 Conference on Empirical Methods in Natural Language Processing, 2021 |
| Do Natural Language Explanations Represent Valid Logical Arguments? Verifying Entailment in Explainable NLI Gold Standards, , and , in: 14th International Conference on Computational Semantics, 2021 |
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| Does My Representation Capture X? Probe-Ably, , , , and , in: 59th Annual Meeting of the Association for Computational Linguistics (Demonstration track), 2021 |
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E
| Effective Graph and Rank-based Contextual Embeddings for Textual and Multimedia Data, , , , and , in: International Joint Conference on Neural Networks, 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 |
| Empowering Cross-lingual Abilities of Instruction-tuned Large Language Models by Translation-following demonstrations, , and , in: Findings of the ACL, 2024 |
| Encoding Explanatory Knowledge for Zero-shot Science Question Answering, , , and , in: 14th International Conference on Computational Semantics, 2021 |
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| 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 |
| 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 |
| 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 |
| Explainable Inference Over Grounding-Abstract Chains for Science Questions, , and , in: 59th Annual Meeting of the Association for Computational Linguistics (ACL Findings), 2021 |
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| Explainable Natural Language Reasoning via Conceptual Unification, , and , in: 16th conference of the European Chapter of the Association for Computational Linguistics (EACL), 2021 |
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| Exploring the Limits of Fine-grained LLM-based Physics Inference via Premise Removal Interventions, , and , in: Findings of EMNLP, 2024 |
F
| Faithful and Robust LLM-Driven Theorem Proving for NLI Explanations, , , and , in: 63rd Annual Meeting of the Association for Computational Linguistics, 2025 |
| Formal Semantic Controls over Language Models, , and , in: LREC-COLING, 2024 |
| 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 |
G
| Gem: Gaussian Mixture Model Embeddings for Numerical Feature Distributions, , , and , in: 8th International Conference on Extending Database Technology, 2025 |
| 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 |
H
| Hybrid Autoregressive Inference for Scalable Multi-hop Explanation Regeneration, , , and , in: Thirty-Sixth AAAI Conference on Artificial Intelligence, 2022 |
I
| Idiap Scientific Report 2022, , , , , , , , , , , , , , , , , and , Idiap-RR-05-2023 |
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| Improving chain-of-thought reasoning via quasi-symbolic abstractions, , , and , in: 63rd Annual Meeting of the Association for Computational Linguistics, 2025 |
| 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 |
| Inductive Learning of Logical Theories with LLMs: A Complexity-graded Analysis, , and , in: The 39th Annual AAAI Conference on Artificial Intelligence, 2025 |
| 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 |
| Introduction to Mathematical Language Processing: Informal Proofs, Word Problems, and Supporting Tasks, and , in: Transactions of the ACL, 2023 |
L
| 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 |