arXiv subjects

André Freitas

Publications and source records attributed to André Freitas.

At least 55 records · Page 3Linked to original sources

arXiv2025

TRACE for Tracking the Emergence of Semantic Representations in Transformers

Modern transformer models exhibit phase transitions during training, distinct shifts from memorisation to abstraction, but the mechanisms underlying these transitions remain poorly understood. Prior work has often focused on endpoint representations or isolated signals like curvature or mutual information, typically in symbolic or arithmetic domains, overlooking the emergence of linguistic structure. We introduce TRACE (Tracking Representation Abstraction and Compositional Emergence), a diagnostic framework combining geometric, informational, and linguistic signals to detect phase transitions in Transformer-based LMs. TRACE leverages a frame-semantic data generation method, ABSynth, that produces annotated synthetic corpora with controllable complexity, lexical distributions, and structural entropy, while being fully annotated with linguistic categories, enabling precise analysis of abstraction emergence. Experiments reveal that (i) phase transitions align with clear intersections between curvature collapse and dimension stabilisation; (ii) these geometric shifts coincide with emerging syntactic and semantic accuracy; (iii) abstraction patterns persist across architectural variants, with components like feedforward networks affecting optimisation stability rather than fundamentally altering trajectories. This work advances our understanding of how linguistic abstractions emerge in LMs, offering insights into model interpretability, training efficiency, and compositional generalisation that could inform more principled approaches to LM development.

cs.CL↗

arXiv2025

CARMA: Enhanced Compositionality in LLMs via Advanced Regularisation and Mutual Information Alignment

Large language models (LLMs) struggle with compositional generalisation, limiting their ability to systematically combine learned components to interpret novel inputs. While architectural modifications, fine-tuning, and data augmentation improve compositionality, they often have limited adaptability, face scalability constraints, or yield diminishing returns on real data. To address this, we propose CARMA, an intervention that enhances the stability and robustness of compositional reasoning in LLMs while preserving fine-tuned performance. CARMA employs mutual information regularisation and layer-wise stability constraints to mitigate feature fragmentation, ensuring structured representations persist across and within layers. We evaluate CARMA on inverse dictionary modelling and sentiment classification, measuring its impact on semantic consistency, performance stability, and robustness to lexical perturbations. Results show that CARMA reduces the variability introduced by fine-tuning, stabilises token representations, and improves compositional reasoning. While its effectiveness varies across architectures, CARMA's key strength lies in reinforcing learned structures rather than introducing new capabilities, making it a scalable auxiliary method. These findings suggest that integrating CARMA with fine-tuning can improve compositional generalisation while maintaining task-specific performance in LLMs.

cs.CL↗

arXiv2025

Interpreting token compositionality in LLMs: A robustness analysis

Understanding the internal mechanisms of large language models (LLMs) is integral to enhancing their reliability, interpretability, and inference processes. We present Constituent-Aware Pooling (CAP), a methodology designed to analyse how LLMs process compositional linguistic structures. Grounded in principles of compositionality, mechanistic interpretability, and information theory, CAP systematically intervenes in model activations through constituent-based pooling at various model levels. Our experiments on inverse definition modelling, hypernym and synonym prediction reveal critical insights into transformers' limitations in handling compositional abstractions. No specific layer integrates tokens into unified semantic representations based on their constituent parts. We observe fragmented information processing, which intensifies with model size, suggesting that larger models struggle more with these interventions and exhibit greater information dispersion. This fragmentation likely stems from transformers' training objectives and architectural design, preventing systematic and cohesive representations. Our findings highlight fundamental limitations in current transformer architectures regarding compositional semantics processing and model interpretability, underscoring the critical need for novel approaches in LLM design to address these challenges.

cs.CL↗

arXiv2025

PEIRCE: Unifying Material and Formal Reasoning via LLM-Driven Neuro-Symbolic Refinement

A persistent challenge in AI is the effective integration of material and formal inference - the former concerning the plausibility and contextual relevance of arguments, while the latter focusing on their logical and structural validity. Large Language Models (LLMs), by virtue of their extensive pre-training on large textual corpora, exhibit strong capabilities in material inference. However, their reasoning often lacks formal rigour and verifiability. At the same time, LLMs' linguistic competence positions them as a promising bridge between natural and formal languages, opening up new opportunities for combining these two modes of reasoning. In this paper, we introduce PEIRCE, a neuro-symbolic framework designed to unify material and formal inference through an iterative conjecture-criticism process. Within this framework, LLMs play the central role of generating candidate solutions in natural and formal languages, which are then evaluated and refined via interaction with external critique models. These critiques include symbolic provers, which assess formal validity, as well as soft evaluators that measure the quality of the generated arguments along linguistic and epistemic dimensions such as plausibility, coherence, and parsimony. While PEIRCE is a general-purpose framework, we demonstrate its capabilities in the domain of natural language explanation generation - a setting that inherently demands both material adequacy and formal correctness.

cs.AI↗

arXiv2025

Solver-in-the-loop approach to closure of shell models of turbulence

This work studies an a posteriori data-driven approach (known as solver-in-the-loop) for sub-grid modeling of a shell model for turbulence. This approach takes advantage of the differentiable physics paradigm of deep learning, allowing a neural network model to interact with the differential equation solver over time during the training process. The closure model is, then, naturally exposed to equations-informed input distributions by accounting for prior corrections over the temporal evolution in training. Such a characteristic makes this approach depart from the conventional a priori instantaneous training paradigm and often leads to a more accurate and stable closure model. Our study demonstrates that the closure learned via this a posteriori approach is able to reproduce high-order statistical moments of interest also in closures of high Reynolds number turbulence. Moreover, we investigate the performance of the learned model by experimenting with the effect of unrolling in time, which has remained for the most part unexplored in the literature. Finally, we discuss potential extensions of this approach to Navier-Stokes equations.

physics.flu-dyn↗

arXiv2025

LangVAE and LangSpace: Building and Probing for Language Model VAEs

We present LangVAE, a novel framework for modular construction of variational autoencoders (VAEs) on top of pre-trained large language models (LLMs). Such language model VAEs can encode the knowledge of their pre-trained components into more compact and semantically disentangled representations. The representations obtained in this way can be analysed with the LangVAE companion framework: LangSpace, which implements a collection of probing methods, such as vector traversal and interpolation, disentanglement measures, and cluster visualisations. LangVAE and LangSpace offer a flexible, efficient and scalable way of building and analysing textual representations, with simple integration for models available on the HuggingFace Hub. Additionally, we conducted a set of experiments with different encoder and decoder combinations, as well as annotated inputs, revealing a wide range of interactions across architectural families and sizes w.r.t. generalisation and disentanglement. Our findings demonstrate a promising framework for systematising the experimentation and understanding of textual representations.

cs.CL↗

arXiv2025

Accelerating Antibiotic Discovery with Large Language Models and Knowledge Graphs

The discovery of novel antibiotics is critical to address the growing antimicrobial resistance (AMR). However, pharmaceutical industries face high costs (over $1 billion), long timelines, and a high failure rate, worsened by the rediscovery of known compounds. We propose an LLM-based pipeline that acts as an alarm system, detecting prior evidence of antibiotic activity to prevent costly rediscoveries. The system integrates organism and chemical literature into a Knowledge Graph (KG), ensuring taxonomic resolution, synonym handling, and multi-level evidence classification. We tested the pipeline on a private list of 73 potential antibiotic-producing organisms, disclosing 12 negative hits for evaluation. The results highlight the effectiveness of the pipeline for evidence reviewing, reducing false negatives, and accelerating decision-making. The KG for negative hits and the user interface for interactive exploration will be made publicly available.

cs.CL↗

arXiv2025

Inference to the Best Explanation in Large Language Models

While Large Language Models (LLMs) have found success in real-world applications, their underlying explanatory process is still poorly understood. This paper proposes IBE-Eval, a framework inspired by philosophical accounts on Inference to the Best Explanation (IBE) to advance the interpretation and evaluation of LLMs' explanations. IBE-Eval estimates the plausibility of natural language explanations through a combination of explicit logical and linguistic features including: consistency, parsimony, coherence, and uncertainty. Extensive experiments are conducted on Causal Question Answering (CQA), where \textit{IBE-Eval} is tasked to select the most plausible causal explanation amongst competing ones generated by LLMs (i.e., GPT 3.5 and Llama 2). The experiments reveal that IBE-Eval can successfully identify the best explanation with up to 77\% accuracy ($\approx 27\%$ above random), improving upon a GPT 3.5-as-a-Judge baseline ($\approx+17\%$) while being intrinsically more efficient and interpretable. Additional analyses suggest that, despite model-specific variances, LLM-generated explanations tend to conform to IBE criteria and that IBE-Eval is significantly correlated with human judgment, opening up opportunities for future development of automated explanation verification tools.

cs.CL↗

arXiv2025

Does Table Source Matter? Benchmarking and Improving Multimodal Scientific Table Understanding and Reasoning

Recent large language models (LLMs) have advanced table understanding capabilities but rely on converting tables into text sequences. While multimodal large language models (MLLMs) enable direct visual processing, they face limitations in handling scientific tables due to fixed input image resolutions and insufficient numerical reasoning capabilities. We present a comprehensive framework for multimodal scientific table understanding and reasoning with dynamic input image resolutions. Our framework consists of three key components: (1) MMSci-Pre, a domain-specific table structure learning dataset of 52K scientific table structure recognition samples, (2) MMSci-Ins, an instruction tuning dataset with 12K samples across three table-based tasks, and (3) MMSci-Eval, a benchmark with 3,114 testing samples specifically designed to evaluate numerical reasoning capabilities. Extensive experiments demonstrate that our domain-specific approach with 52K scientific table images achieves superior performance compared to 150K general-domain tables, highlighting the importance of data quality over quantity. Our proposed table-based MLLMs with dynamic input resolutions show significant improvements in both general table understanding and numerical reasoning capabilities, with strong generalisation to held-out datasets. Our code and data are publicly available at https://github.com/Bernard-Yang/MMSci_Table.

cs.CL↗

arXiv2025

Inductive Learning of Logical Theories with LLMs: An Expressivity-Graded Analysis

This work presents a novel systematic methodology to analyse the capabilities and limitations of Large Language Models (LLMs) with feedback from a formal inference engine, on logic theory induction. The analysis is complexity-graded w.r.t. rule dependency structure, allowing quantification of specific inference challenges on LLM performance. Integrating LLMs with formal methods is a promising frontier in the Natural Language Processing field, as an important avenue for improving model inference control and explainability. In particular, inductive learning over complex sets of facts and rules, poses unique challenges for current autoregressive models, as they lack explicit symbolic grounding. While they can be complemented by formal systems, the properties delivered by LLMs regarding inductive learning, are not well understood and quantified. Empirical results indicate that the largest LLMs can achieve competitive results against a SOTA Inductive Logic Programming (ILP) system baseline, but also that tracking long predicate relationship chains is a more difficult obstacle than theory complexity for LLMs.

cs.CL↗

arXiv2024

Montague semantics and modifier consistency measurement in neural language models

This work proposes a novel methodology for measuring compositional behavior in contemporary language embedding models. Specifically, we focus on adjectival modifier phenomena in adjective-noun phrases. In recent years, distributional language representation models have demonstrated great practical success. At the same time, the need for interpretability has elicited questions on their intrinsic properties and capabilities. Crucially, distributional models are often inconsistent when dealing with compositional phenomena in natural language, which has significant implications for their safety and fairness. Despite this, most current research on compositionality is directed towards improving their performance on similarity tasks only. This work takes a different approach, introducing three novel tests of compositional behavior inspired by Montague semantics. Our experimental results indicate that current neural language models do not behave according to the expected linguistic theories. This indicates that current language models may lack the capability to capture the semantic properties we evaluated on limited context, or that linguistic theories from Montagovian tradition may not match the expected capabilities of distributional models.

cs.CL↗

arXiv2024

Verification and Refinement of Natural Language Explanations through LLM-Symbolic Theorem Proving

Natural language explanations represent a proxy for evaluating explanation-based and multi-step Natural Language Inference (NLI) models. However, assessing the validity of explanations for NLI is challenging as it typically involves the crowd-sourcing of apposite datasets, a process that is time-consuming and prone to logical errors. To address existing limitations, this paper investigates the verification and refinement of natural language explanations through the integration of Large Language Models (LLMs) and Theorem Provers (TPs). Specifically, we present a neuro-symbolic framework, named Explanation-Refiner, that integrates TPs with LLMs to generate and formalise explanatory sentences and suggest potential inference strategies for NLI. In turn, the TP is employed to provide formal guarantees on the logical validity of the explanations and to generate feedback for subsequent improvements. We demonstrate how Explanation-Refiner can be jointly used to evaluate explanatory reasoning, autoformalisation, and error correction mechanisms of state-of-the-art LLMs as well as to automatically enhance the quality of explanations of variable complexity in different domains.

cs.CL↗

arXiv2024

Reasoning with Natural Language Explanations

Explanation constitutes an archetypal feature of human rationality, underpinning learning and generalisation, and representing one of the media supporting scientific discovery and communication. Due to the importance of explanations in human reasoning, an increasing amount of research in Natural Language Inference (NLI) has started reconsidering the role that explanations play in learning and inference, attempting to build explanation-based NLI models that can effectively encode and use natural language explanations on downstream tasks. Research in explanation-based NLI, however, presents specific challenges and opportunities, as explanatory reasoning reflects aspects of both material and formal inference, making it a particularly rich setting to model and deliver complex reasoning. In this tutorial, we provide a comprehensive introduction to the field of explanation-based NLI, grounding this discussion on the epistemological-linguistic foundations of explanations, systematically describing the main architectural trends and evaluation methodologies that can be used to build systems capable of explanatory reasoning.

cs.CL↗

arXiv2024

Learning Disentangled Semantic Spaces of Explanations via Invertible Neural Networks

Disentangled latent spaces usually have better semantic separability and geometrical properties, which leads to better interpretability and more controllable data generation. While this has been well investigated in Computer Vision, in tasks such as image disentanglement, in the NLP domain sentence disentanglement is still comparatively under-investigated. Most previous work have concentrated on disentangling task-specific generative factors, such as sentiment, within the context of style transfer. In this work, we focus on a more general form of sentence disentanglement, targeting the localised modification and control of more general sentence semantic features. To achieve this, we contribute to a novel notion of sentence semantic disentanglement and introduce a flow-based invertible neural network (INN) mechanism integrated with a transformer-based language Autoencoder (AE) in order to deliver latent spaces with better separability properties. Experimental results demonstrate that the model can conform the distributed latent space into a better semantically disentangled sentence space, leading to improved language interpretability and controlled generation when compared to the recent state-of-the-art language VAE models.

cs.CL↗

arXiv2024

SemEval-2024 Task 2: Safe Biomedical Natural Language Inference for Clinical Trials

Large Language Models (LLMs) are at the forefront of NLP achievements but fall short in dealing with shortcut learning, factual inconsistency, and vulnerability to adversarial inputs.These shortcomings are especially critical in medical contexts, where they can misrepresent actual model capabilities. Addressing this, we present SemEval-2024 Task 2: Safe Biomedical Natural Language Inference for ClinicalTrials. Our contributions include the refined NLI4CT-P dataset (i.e., Natural Language Inference for Clinical Trials - Perturbed), designed to challenge LLMs with interventional and causal reasoning tasks, along with a comprehensive evaluation of methods and results for participant submissions. A total of 106 participants registered for the task contributing to over 1200 individual submissions and 25 system overview papers. This initiative aims to advance the robustness and applicability of NLI models in healthcare, ensuring safer and more dependable AI assistance in clinical decision-making. We anticipate that the dataset, models, and outcomes of this task can support future research in the field of biomedical NLI. The dataset, competition leaderboard, and website are publicly available.

cs.CL↗

arXiv2024

Multi-Operational Mathematical Derivations in Latent Space

This paper investigates the possibility of approximating multiple mathematical operations in latent space for expression derivation. To this end, we introduce different multi-operational representation paradigms, modelling mathematical operations as explicit geometric transformations. By leveraging a symbolic engine, we construct a large-scale dataset comprising 1.7M derivation steps stemming from 61K premises and 6 operators, analysing the properties of each paradigm when instantiated with state-of-the-art neural encoders. Specifically, we investigate how different encoding mechanisms can approximate expression manipulation in latent space, exploring the trade-off between learning different operators and specialising within single operations, as well as the ability to support multi-step derivations and out-of-distribution generalisation. Our empirical analysis reveals that the multi-operational paradigm is crucial for disentangling different operators, while discriminating the conclusions for a single operation is achievable in the original expression encoder. Moreover, we show that architectural choices can heavily affect the training dynamics, structural organisation, and generalisation of the latent space, resulting in significant variations across paradigms and classes of encoders.

cs.LG↗

arXiv2024

Estimating the Causal Effects of Natural Logic Features in Transformer-Based NLI Models

Rigorous evaluation of the causal effects of semantic features on language model predictions can be hard to achieve for natural language reasoning problems. However, this is such a desirable form of analysis from both an interpretability and model evaluation perspective, that it is valuable to investigate specific patterns of reasoning with enough structure and regularity to identify and quantify systematic reasoning failures in widely-used models. In this vein, we pick a portion of the NLI task for which an explicit causal diagram can be systematically constructed: the case where across two sentences (the premise and hypothesis), two related words/terms occur in a shared context. In this work, we apply causal effect estimation strategies to measure the effect of context interventions (whose effect on the entailment label is mediated by the semantic monotonicity characteristic) and interventions on the inserted word-pair (whose effect on the entailment label is mediated by the relation between these words). Extending related work on causal analysis of NLP models in different settings, we perform an extensive interventional study on the NLI task to investigate robustness to irrelevant changes and sensitivity to impactful changes of Transformers. The results strongly bolster the fact that similar benchmark accuracy scores may be observed for models that exhibit very different behaviour. Moreover, our methodology reinforces previously suspected biases from a causal perspective, including biases in favour of upward-monotone contexts and ignoring the effects of negation markers.

cs.CL↗

arXiv2024

A Differentiable Integer Linear Programming Solver for Explanation-Based Natural Language Inference

Integer Linear Programming (ILP) has been proposed as a formalism for encoding precise structural and semantic constraints for Natural Language Inference (NLI). However, traditional ILP frameworks are non-differentiable, posing critical challenges for the integration of continuous language representations based on deep learning. In this paper, we introduce a novel approach, named Diff-Comb Explainer, a neuro-symbolic architecture for explanation-based NLI based on Differentiable BlackBox Combinatorial Solvers (DBCS). Differently from existing neuro-symbolic solvers, Diff-Comb Explainer does not necessitate a continuous relaxation of the semantic constraints, enabling a direct, more precise, and efficient incorporation of neural representations into the ILP formulation. Our experiments demonstrate that Diff-Comb Explainer achieves superior performance when compared to conventional ILP solvers, neuro-symbolic black-box solvers, and Transformer-based encoders. Moreover, a deeper analysis reveals that Diff-Comb Explainer can significantly improve the precision, consistency, and faithfulness of the constructed explanations, opening new opportunities for research on neuro-symbolic architectures for explainable and transparent NLI in complex domains.

cs.CL↗