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
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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 |
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, 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] |
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 |
The 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (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 |
Proceedings of the 2024 Conference of the North American Chapter of the Association for Computational Linguistics (NAACL) (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 |
[URL] |
Proceedings of the 18th Conference of the European Chapter of the Association for Computational Linguistics (2024)
| 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 |
Proceedings of the 62nd Annual Meeting 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] |
The 2024 Conference on Empirical Methods in Natural Language Processing (2024)
| Consistent Autoformalization for Constructing Mathematical Libraries, , and , in: The 2024 Conference on Empirical Methods in Natural Language Processing, 2024 |
27th International Conference on Extending Database Technology (2024)
| Deep Clustering for Data Cleaning and Integration, , and , in: 27th International Conference on Extending Database Technology, 2024 |
Thirty-Eighth Annual Conference on Neural Information Processing Systems (2024)
| Diffusion Twigs with Loop Guidance for Conditional Graph Generation, , , and , in: Thirty-Eighth Annual Conference on Neural Information Processing Systems, 2024 |
Findings of the ACL (2024)
| Empowering Cross-lingual Abilities of Instruction-tuned Large Language Models by Translation-following demonstrations, , and , in: Findings of the ACL, 2024 |
The 18th Conference of the European Chapter of the Association for Computational Linguistics (EACL 2024) (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 |
The 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (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 |
Findings of EMNLP (2024)
| Exploring the Limits of Fine-grained LLM-based Physics Inference via Premise Removal Interventions, , and , in: Findings of EMNLP, 2024 |
LREC-COLING (2024)
| Formal Semantic Controls over Language Models, , and , in: LREC-COLING, 2024 |
Thirty-Eighth Annual Conference on Neural Information Processing Systems (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 |
In Findings of the Association for Computational Linguistics: NAACL 2024 (2024)
| Graph-Induced Syntactic-Semantic Spaces in Transformer-Based Variational AutoEncoders, , , , and , in: In Findings of the Association for Computational Linguistics: NAACL 2024, 2024 |
Findings of the 18th Conference of the European Chapter of the Association for Computational Linguistics (EACL 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 |
In Proceedings of the 62nd Annual Meeting of the Association for Computational Linguistics (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 |
The 62nd Annual Meeting of the Association for Computational Linguistics (2024)
| Learning Disentangled Semantic Spaces of Explanations via Invertible Neural Networks, , and , in: The 62nd Annual Meeting of the Association for Computational Linguistics, 2024 |
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-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 |
The 18th Conference of the European Chapter of the Association for Computational Linguistics (EACL 2024) (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 |
In Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing: Tutorial Abstracts (2024)
| Reasoning with Natural Language Explanations, and , in: In Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing: Tutorial Abstracts, 2024 |
Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing (2024)
| 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 |
In Proceedings of the 18th International Workshop on Semantic Evaluation (SemEval-2024) (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 |
Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing (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 |
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