arXiv subjects

André Freitas

Publications and source records attributed to André Freitas.

At least 73 records · Page 4Linked to original sources

arXiv2024

Multi-Relational Hyperbolic Word Embeddings from Natural Language Definitions

Natural language definitions possess a recursive, self-explanatory semantic structure that can support representation learning methods able to preserve explicit conceptual relations and constraints in the latent space. This paper presents a multi-relational model that explicitly leverages such a structure to derive word embeddings from definitions. By automatically extracting the relations linking defined and defining terms from dictionaries, we demonstrate how the problem of learning word embeddings can be formalised via a translational framework in Hyperbolic space and used as a proxy to capture the global semantic structure of definitions. An extensive empirical analysis demonstrates that the framework can help imposing the desired structural constraints while preserving the semantic mapping required for controllable and interpretable traversal. Moreover, the experiments reveal the superiority of the Hyperbolic word embeddings over the Euclidean counterparts and demonstrate that the multi-relational approach can obtain competitive results when compared to state-of-the-art neural models, with the advantage of being intrinsically more efficient and interpretable.

cs.CL↗

arXiv2024

Enhancing Ethical Explanations of Large Language Models through Iterative Symbolic Refinement

An increasing amount of research in Natural Language Inference (NLI) focuses on the application and evaluation of Large Language Models (LLMs) and their reasoning capabilities. Despite their success, however, LLMs are still prone to factual errors and inconsistencies in their explanations, offering limited control and interpretability for inference in complex domains. In this paper, we focus on ethical NLI, investigating how hybrid neuro-symbolic techniques can enhance the logical validity and alignment of ethical explanations produced by LLMs. Specifically, we present an abductive-deductive framework named Logic-Explainer, which integrates LLMs with an external backward-chaining solver to refine step-wise natural language explanations and jointly verify their correctness, reduce incompleteness and minimise redundancy. An extensive empirical analysis demonstrates that Logic-Explainer can improve explanations generated via in-context learning methods and Chain-of-Thought (CoT) on challenging ethical NLI tasks, while, at the same time, producing formal proofs describing and supporting models' reasoning. As ethical NLI requires commonsense reasoning to identify underlying moral violations, our results suggest the effectiveness of neuro-symbolic methods for multi-step NLI more broadly, opening new opportunities to enhance the logical consistency, reliability, and alignment of LLMs.

cs.CL↗

arXiv2023

LlaMaVAE: Guiding Large Language Model Generation via Continuous Latent Sentence Spaces

Deep generative neural networks, such as Variational AutoEncoders (VAEs), offer an opportunity to better understand and control language models from the perspective of sentence-level latent spaces. To combine the controllability of VAE latent spaces with the state-of-the-art performance of recent large language models (LLMs), we present in this work LlaMaVAE, which combines expressive encoder and decoder models (sentenceT5 and LlaMA) with a VAE architecture, aiming to provide better text generation control to LLMs. In addition, to conditionally guide the VAE generation, we investigate a new approach based on flow-based invertible neural networks (INNs) named Invertible CVAE. Experimental results reveal that LlaMaVAE can outperform the previous state-of-the-art VAE language model, Optimus, across various tasks, including language modelling, semantic textual similarity and definition modelling. Qualitative analysis on interpolation and traversal experiments also indicates an increased degree of semantic clustering and geometric consistency, which enables better generation control.

cs.CL↗

arXiv2023

Graph-Induced Syntactic-Semantic Spaces in Transformer-Based Variational AutoEncoders

The injection of syntactic information in Variational AutoEncoders (VAEs) has been shown to result in an overall improvement of performances and generalisation. An effective strategy to achieve such a goal is to separate the encoding of distributional semantic features and syntactic structures into heterogeneous latent spaces via multi-task learning or dual encoder architectures. However, existing works employing such techniques are limited to LSTM-based VAEs. In this paper, we investigate latent space separation methods for structural syntactic injection in Transformer-based VAE architectures (i.e., Optimus). Specifically, we explore how syntactic structures can be leveraged in the encoding stage through the integration of graph-based and sequential models, and how multiple, specialised latent representations can be injected into the decoder's attention mechanism via low-rank operators. Our empirical evaluation, carried out on natural language sentences and mathematical expressions, reveals that the proposed end-to-end VAE architecture can result in a better overall organisation of the latent space, alleviating the information loss occurring in standard VAE setups, resulting in enhanced performances on language modelling and downstream generation tasks.

cs.CL↗

arXiv2023

Relation Extraction in underexplored biomedical domains: A diversity-optimised sampling and synthetic data generation approach

The sparsity of labelled data is an obstacle to the development of Relation Extraction models and the completion of databases in various biomedical areas. While being of high interest in drug-discovery, the natural-products literature, reporting the identification of potential bioactive compounds from organisms, is a concrete example of such an overlooked topic. To mark the start of this new task, we created the first curated evaluation dataset and extracted literature items from the LOTUS database to build training sets. To this end, we developed a new sampler inspired by diversity metrics in ecology, named Greedy Maximum Entropy sampler, or GME-sampler (https://github.com/idiap/gme-sampler). The strategic optimization of both balance and diversity of the selected items in the evaluation set is important given the resource-intensive nature of manual curation. After quantifying the noise in the training set, in the form of discrepancies between the input abstracts text and the expected output labels, we explored different strategies accordingly. Framing the task as an end-to-end Relation Extraction, we evaluated the performance of standard fine-tuning as a generative task and few-shot learning with open Large Language Models (LLaMA 7B-65B). In addition to their evaluation in few-shot settings, we explore the potential of open Large Language Models (Vicuna-13B) as synthetic data generator and propose a new workflow for this purpose. All evaluated models exhibited substantial improvements when fine-tuned on synthetic abstracts rather than the original noisy data. We provide our best performing (f1-score=59.0) BioGPT-Large model for end-to-end RE of natural-products relationships along with all the generated synthetic data and the evaluation dataset. See more details at https://github.com/idiap/abroad-re.

cs.CL↗

arXiv2023

NLI4CT: Multi-Evidence Natural Language Inference for Clinical Trial Reports

How can we interpret and retrieve medical evidence to support clinical decisions? Clinical trial reports (CTR) amassed over the years contain indispensable information for the development of personalized medicine. However, it is practically infeasible to manually inspect over 400,000+ clinical trial reports in order to find the best evidence for experimental treatments. Natural Language Inference (NLI) offers a potential solution to this problem, by allowing the scalable computation of textual entailment. However, existing NLI models perform poorly on biomedical corpora, and previously published datasets fail to capture the full complexity of inference over CTRs. In this work, we present a novel resource to advance research on NLI for reasoning on CTRs. The resource includes two main tasks. Firstly, to determine the inference relation between a natural language statement, and a CTR. Secondly, to retrieve supporting facts to justify the predicted relation. We provide NLI4CT, a corpus of 2400 statements and CTRs, annotated for these tasks. Baselines on this corpus expose the limitations of existing NLI models, with 6 state-of-the-art NLI models achieving a maximum F1 score of 0.627. To the best of our knowledge, we are the first to design a task that covers the interpretation of full CTRs. To encourage further work on this challenging dataset, we make the corpus, competition leaderboard, website and code to replicate the baseline experiments available at: https://github.com/ai-systems/nli4ct

cs.CL↗

arXiv2023

Discourse-Aware Text Simplification: From Complex Sentences to Linked Propositions

Sentences that present a complex syntax act as a major stumbling block for downstream Natural Language Processing applications whose predictive quality deteriorates with sentence length and complexity. The task of Text Simplification (TS) may remedy this situation. It aims to modify sentences in order to make them easier to process, using a set of rewriting operations, such as reordering, deletion, or splitting. State-of-the-art syntactic TS approaches suffer from two major drawbacks: first, they follow a very conservative approach in that they tend to retain the input rather than transforming it, and second, they ignore the cohesive nature of texts, where context spread across clauses or sentences is needed to infer the true meaning of a statement. To address these problems, we present a discourse-aware TS approach that splits and rephrases complex English sentences within the semantic context in which they occur. Based on a linguistically grounded transformation stage that uses clausal and phrasal disembedding mechanisms, complex sentences are transformed into shorter utterances with a simple canonical structure that can be easily analyzed by downstream applications. With sentence splitting, we thus address a TS task that has hardly been explored so far. Moreover, we introduce the notion of minimality in this context, as we aim to decompose source sentences into a set of self-contained minimal semantic units. To avoid breaking down the input into a disjointed sequence of statements that is difficult to interpret because important contextual information is missing, we incorporate the semantic context between the split propositions in the form of hierarchical structures and semantic relationships. In that way, we generate a semantic hierarchy of minimal propositions that leads to a novel representation of complex assertions that puts a semantic layer on top of the simplified sentences.

cs.CL↗

arXiv2023

SemEval-2023 Task 7: Multi-Evidence Natural Language Inference for Clinical Trial Data

This paper describes the results of SemEval 2023 task 7 -- Multi-Evidence Natural Language Inference for Clinical Trial Data (NLI4CT) -- consisting of 2 tasks, a Natural Language Inference (NLI) task, and an evidence selection task on clinical trial data. The proposed challenges require multi-hop biomedical and numerical reasoning, which are of significant importance to the development of systems capable of large-scale interpretation and retrieval of medical evidence, to provide personalized evidence-based care. Task 1, the entailment task, received 643 submissions from 40 participants, and Task 2, the evidence selection task, received 364 submissions from 23 participants. The tasks are challenging, with the majority of submitted systems failing to significantly outperform the majority class baseline on the entailment task, and we observe significantly better performance on the evidence selection task than on the entailment task. Increasing the number of model parameters leads to a direct increase in performance, far more significant than the effect of biomedical pre-training. Future works could explore the limitations of large models for generalization and numerical inference, and investigate methods to augment clinical datasets to allow for more rigorous testing and to facilitate fine-tuning. We envisage that the dataset, models, and results of this task will be useful to the biomedical NLI and evidence retrieval communities. The dataset, competition leaderboard, and website are publicly available.

cs.CL↗

arXiv2023

A systematic review of biologically-informed deep learning models for cancer: fundamental trends for encoding and interpreting oncology data

There is an increasing interest in the use of Deep Learning (DL) based methods as a supporting analytical framework in oncology. However, most direct applications of DL will deliver models with limited transparency and explainability, which constrain their deployment in biomedical settings. This systematic review discusses DL models used to support inference in cancer biology with a particular emphasis on multi-omics analysis. It focuses on how existing models address the need for better dialogue with prior knowledge, biological plausibility and interpretability, fundamental properties in the biomedical domain. For this, we retrieved and analyzed 42 studies focusing on emerging architectural and methodological advances, the encoding of biological domain knowledge and the integration of explainability methods. We discuss the recent evolutionary arch of DL models in the direction of integrating prior biological relational and network knowledge to support better generalisation (e.g. pathways or Protein-Protein-Interaction networks) and interpretability. This represents a fundamental functional shift towards models which can integrate mechanistic and statistical inference aspects. We introduce a concept of bio-centric interpretability and according to its taxonomy, we discuss representational methodologies for the integration of domain prior knowledge in such models. The paper provides a critical outlook into contemporary methods for explainability and interpretabiltiy used in DL for cancer. The analysis points in the direction of a convergence between encoding prior knowledge and improved interpretability. We introduce bio-centric interpretability which is an important step towards formalisation of biological interpretability of DL models and developing methods that are less problem- or application-specific.

q-bio.QM↗

arXiv2022

A Framework for Improving Scholarly Neural Network Diagrams

Neural networks are a prevalent and effective machine learning component, and their application is leading to significant scientific progress in many domains. As the field of neural network systems is fast growing, it is important to understand how advances are communicated. Diagrams are key to this, appearing in almost all papers describing novel systems. This paper reports on a study into the use of neural network system diagrams, through interviews, card sorting, and qualitative feedback structured around ecologically-derived examples. We find high diversity of usage, perception and preference in both creation and interpretation of diagrams, examining this in the context of existing design, information visualisation, and user experience guidelines. This interview study is used to derive a framework for improving existing diagrams. This framework is evaluated through a mixed-methods experimental study, and a ``corpus-based'' approach examining properties of published diagrams linking the framework to citations. The studies suggest that the framework captures aspects relating to communicative efficacy of scholarly NN diagrams, and provides simple steps for their implementation.

cs.HC↗

arXiv2022

Assessing the communication gap between AI models and healthcare professionals: explainability, utility and trust in AI-driven clinical decision-making

This paper contributes with a pragmatic evaluation framework for explainable Machine Learning (ML) models for clinical decision support. The study revealed a more nuanced role for ML explanation models, when these are pragmatically embedded in the clinical context. Despite the general positive attitude of healthcare professionals (HCPs) towards explanations as a safety and trust mechanism, for a significant set of participants there were negative effects associated with confirmation bias, accentuating model over-reliance and increased effort to interact with the model. Also, contradicting one of its main intended functions, standard explanatory models showed limited ability to support a critical understanding of the limitations of the model. However, we found new significant positive effects which repositions the role of explanations within a clinical context: these include reduction of automation bias, addressing ambiguous clinical cases (cases where HCPs were not certain about their decision) and support of less experienced HCPs in the acquisition of new domain knowledge.

cs.AI↗

arXiv2022

Microeconomic Foundations of Decentralised Organisations

In this article, we analyse how decentralised digital infrastructures can provide a fundamental change in the structure and dynamics of organisations. The works of R.H.Coase and M. Olson, on the nature of the firm and the logic of collective action, respectively, are revisited under the light of these emerging new digital foundations. We also analyse how these technologies can affect the fundamental assumptions on the role of organisations (either private or public) as mechanisms for the coordination of labour. We propose that these technologies can fundamentally affect: (i) the distribution of rewards within an organisation and (ii) the structure of its transaction costs. These changes bring the potential for addressing some of the trade-offs between the private and public sectors.

cs.CE↗

arXiv2022

Estimating productivity gains in digital automation

This paper proposes a novel productivity estimation model to evaluate the effects of adopting Artificial Intelligence (AI) components in a production chain. Our model provides evidence to address the "AI's" Solow's Paradox. We provide (i) theoretical and empirical evidence to explain Solow's dichotomy; (ii) a data-driven model to estimate and asses productivity variations; (iii) a methodology underpinned on process mining datasets to determine the business process, BP, and productivity; (iv) a set of computer simulation parameters; (v) and empirical analysis on labour-distribution. These provide data on why we consider AI Solow's paradox a consequence of metric mismeasurement.

cs.AI↗

arXiv2022

Case-Based Abductive Natural Language Inference

Most of the contemporary approaches for multi-hop Natural Language Inference (NLI) construct explanations considering each test case in isolation. However, this paradigm is known to suffer from semantic drift, a phenomenon that causes the construction of spurious explanations leading to wrong conclusions. In contrast, this paper proposes an abductive framework for multi-hop NLI exploring the retrieve-reuse-refine paradigm in Case-Based Reasoning (CBR). Specifically, we present Case-Based Abductive Natural Language Inference (CB-ANLI), a model that addresses unseen inference problems by analogical transfer of prior explanations from similar examples. We empirically evaluate the abductive framework on commonsense and scientific question answering tasks, demonstrating that CB-ANLI can be effectively integrated with sparse and dense pre-trained encoders to improve multi-hop inference, or adopted as an evidence retriever for Transformers. Moreover, an empirical analysis of semantic drift reveals that the CBR paradigm boosts the quality of the most challenging explanations, a feature that has a direct impact on robustness and accuracy in downstream inference tasks.

cs.AI↗

arXiv2022

Transformers and the representation of biomedical background knowledge

Specialised transformers-based models (such as BioBERT and BioMegatron) are adapted for the biomedical domain based on publicly available biomedical corpora. As such, they have the potential to encode large-scale biological knowledge. We investigate the encoding and representation of biological knowledge in these models, and its potential utility to support inference in cancer precision medicine - namely, the interpretation of the clinical significance of genomic alterations. We compare the performance of different transformer baselines; we use probing to determine the consistency of encodings for distinct entities; and we use clustering methods to compare and contrast the internal properties of the embeddings for genes, variants, drugs and diseases. We show that these models do indeed encode biological knowledge, although some of this is lost in fine-tuning for specific tasks. Finally, we analyse how the models behave with regard to biases and imbalances in the dataset.

cs.CL↗

arXiv2022

Going Beyond Approximation: Encoding Constraints for Explainable Multi-hop Inference via Differentiable Combinatorial Solvers

Integer Linear Programming (ILP) provides a viable mechanism to encode explicit and controllable assumptions about explainable multi-hop inference with natural language. However, an ILP formulation is non-differentiable and cannot be integrated into broader deep learning architectures. Recently, Thayaparan et al. (2021a) proposed a novel methodology to integrate ILP with Transformers to achieve end-to-end differentiability for complex multi-hop inference. While this hybrid framework has been demonstrated to deliver better answer and explanation selection than transformer-based and existing ILP solvers, the neuro-symbolic integration still relies on a convex relaxation of the ILP formulation, which can produce sub-optimal solutions. To improve these limitations, we propose Diff-Comb Explainer, a novel neuro-symbolic architecture based on Differentiable BlackBox Combinatorial solvers (DBCS) (Pogančić et al., 2019). Unlike existing differentiable solvers, the presented model does not require the transformation and relaxation of the explicit semantic constraints, allowing for direct and more efficient integration of ILP formulations. Diff-Comb Explainer demonstrates improved accuracy and explainability over non-differentiable solvers, Transformers and existing differentiable constraint-based multi-hop inference frameworks.

cs.AI↗

arXiv2022

Active entailment encoding for explanation tree construction using parsimonious generation of hard negatives

Entailment trees have been proposed to simulate the human reasoning process of explanation generation in the context of open--domain textual question answering. However, in practice, manually constructing these explanation trees proves a laborious process that requires active human involvement. Given the complexity of capturing the line of reasoning from question to the answer or from claim to premises, the issue arises of how to assist the user in efficiently constructing multi--level entailment trees given a large set of available facts. In this paper, we frame the construction of entailment trees as a sequence of active premise selection steps, i.e., for each intermediate node in an explanation tree, the expert needs to annotate positive and negative examples of premise facts from a large candidate list. We then iteratively fine--tune pre--trained Transformer models with the resulting positive and tightly controlled negative samples and aim to balance the encoding of semantic relationships and explanatory entailment relationships. Experimental evaluation confirms the measurable efficiency gains of the proposed active fine--tuning method in facilitating entailment trees construction: up to 20\% improvement in explanatory premise selection when compared against several alternatives.

cs.CL↗

arXiv2022

Diff-Explainer: Differentiable Convex Optimization for Explainable Multi-hop Inference

This paper presents Diff-Explainer, the first hybrid framework for explainable multi-hop inference that integrates explicit constraints with neural architectures through differentiable convex optimization. Specifically, Diff-Explainer allows for the fine-tuning of neural representations within a constrained optimization framework to answer and explain multi-hop questions in natural language. To demonstrate the efficacy of the hybrid framework, we combine existing ILP-based solvers for multi-hop Question Answering (QA) with Transformer-based representations. An extensive empirical evaluation on scientific and commonsense QA tasks demonstrates that the integration of explicit constraints in an end-to-end differentiable framework can significantly improve the performance of non-differentiable ILP solvers (8.91% - 13.3%). Moreover, additional analysis reveals that Diff-Explainer is able to achieve strong performance when compared to standalone Transformers and previous multi-hop approaches while still providing structured explanations in support of its predictions.

cs.CL↗