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.

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.

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.

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 gain 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.

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.

Natural language explanations have become a proxy for evaluating explainable 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 augments a TP 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 human-annotated explanations of variable complexity in different domains.

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.

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.

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.

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.