United States

Due to the increasing productivity in the scientific community, it is difficult to keep up with the literature without the assistance of AI methods. This paper evaluates various methods for extracting mathematical model variables from epidemiological studies, such as \``infection rate (α),&#39;&#39; \``recovery rate (γ),&#39;&#39; and \``mortality rate (μ).&#39;&#39; Variable extraction appears to be a basic task, but plays a pivotal role in recovering models from scientific literature. Once extracted, we can use these variables for automatic mathematical modeling, simulation, and replication of published results. We also introduce a benchmark dataset comprising manually-annotated variable descriptions and variable values extracted from scientific papers. Our analysis shows that LLM-based solutions perform the best. Despite the incremental benefits of combining rule-based extraction outputs with LLMs, the leap in performance attributed to the transfer-learning and instruction-tuning capabilities of LLMs themselves is far more significant. This investigation demonstrates the potential of LLMs to enhance automatic comprehension of scientific artifacts and for automatic model recovery and simulation.

NAACL 2025

Variable Extraction for Model Recovery in Scientific Literature

variable extraction

information extraction

**Welcome to ACL-IJCNLP 2021!**

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ACL-IJCNLP 2021

The great event is jointly organized by the Association for Computational Linguistics (ACL) and Asian Federation of Natural Language Processing (AFNLP).

Due to the increasing productivity in the scientific community, it is difficult to keep up with the literature without the assistance of AI methods. This paper evaluates various methods for extracting mathematical model variables from epidemiological studies, such as \``infection rate (α),'' \``recovery rate (γ),'' and \``mortality rate (μ).'' Variable extraction appears to be a basic task, but plays a pivotal role in recovering models from scientific literature. Once extracted, we can use these variables for automatic mathematical modeling, simulation, and replication of published results. We also introduce a benchmark dataset comprising manually-annotated variable descriptions and variable values extracted from scientific papers. Our analysis shows that LLM-based solutions perform the best. Despite the incremental benefits of combining rule-based extraction outputs with LLMs, the leap in performance attributed to the transfer-learning and instruction-tuning capabilities of LLMs themselves is far more significant. This investigation demonstrates the potential of LLMs to enhance automatic comprehension of scientific artifacts and for automatic model recovery and simulation.

workshop paper

### Welcome to 2025 Annual Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics

Welcome to the 2025 meeting of the Nations of the Americas Chapter of the Association for Computational Linguistics! I am proud to help organize the first NAACL conference to carry the new name of our organization, one that emphasizes inclusion for all of the Americas. I am also pleased to welcome you to Albuquerque, New Mexico, a state whose unique blend of cultural influences will make for an excellent backdrop for NAACL 2025, especially with this year’s special theme on NLP in a Multicultural World. 
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Welcome to 2025 Annual Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics

Automatic speech recognition (ASR) systems face many sources of extra-linguistic noise that ideally should not affect their transcription of a speech signal. This includes speaker factors, recording quality, or even ``adversarial noise'' designed to disrupt performance. We experimented with the dialect composition of ASR fine-tuning data to study whether balancing the relative proportion of dialects had an impact on models' robustness to two such sources of variation: dialect variation and adversarial perturbations. We fine-tuned XLSR-53 for Catalan ASR using four different dialect compositions. These were defined as 100%, 80%, 50%, and 20% Central Catalan, with the remaining portions split evenly between four other Catalan dialects. While increasing the relative proportion of dialect variants improved models' dialect robustness, this did not have a meaningful impact on adversarial robustness. These findings suggest that while improvements to ASR can be made by diversifying the training data, such changes do not sufficiently counteract adversarial attacks, leaving the technology open to security threats.

The Impact of Dialect Variation on Robust Automatic Speech Recognition for Catalan

Automatic keyword extraction from scientific articles is pivotal for organizing scholarly archives, powering semantic search engines, and mapping interdisciplinary research trends. However, existing methods—including statistical and graph-based approaches—struggle to handle domain-specific challenges such as technical terminology, cross-disciplinary ambiguity, and dynamic scientific jargon. This paper presents an empirical comparison of traditional keyword extraction methods (e.g. TextRank and YAKE) with approaches based on Large Language Model. We introduce a novel evaluation framework that combines fuzzy semantic matching based on Levenshtein Distance with exact-match metrics (F1, precision, recall) to address inconsistencies in keyword normalization across scientific corpora. Through an extensive ablation study across nine different LLMs, we analyze their performance and associated costs. Our findings reveal that LLM-based methods consistently achieve superior precision and relevance compared to traditional approaches. This performance advantage suggests significant potential for improving scientific search systems and information retrieval in academic contexts.

How Well Do Large Language Models Extract Keywords? A Systematic Evaluation on Scientific Corpora

Recent studies have evaluated creativity, where novelty is an important aspect, of large language models (LLMs) primarily from a semantic perspective, using benchmarks from cognitive science. However, assessing the novelty in scholarly publications, a critical facet of evaluating LLMs as scientific discovery assistants, remains underexplored, despite its potential to accelerate research cycles and prioritize high-impact contributions in scientific workflows. We introduce SchNovel, a benchmark to evaluate LLMs’ ability to assess novelty in scholarly papers, a task central to streamlining discovery pipeline. SchNovel consists of 15000 pairs of papers across six fields sampled from the arXiv dataset with publication dates spanning 2 to 10 years apart. In each pair, the more recently published paper is assumed to be more novel. Additionally, we propose RAG-Novelty, a retrieval-augmented method that mirrors human peer review by grounding novelty assessment in retrieved context. Extensive experiments provide insights into the capabilities of different LLMs to assess novelty and demonstrate that RAG-Novelty outperforms recent baseline models highlight LLMs’ promise as tools for automating novelty detection in scientific workflows.

Evaluating and Enhancing Large Language Models for Novelty Assessment in Scholarly Publications

The study of food pairing has evolved beyond subjective expertise with the advent of machine learning. This paper presents FlavorDiffusion, a novel framework leveraging diffusion models to predict food-chemical interactions and ingredient pairings without relying on chromatography. By integrating graph-based embeddings, diffusion processes, and chemical property encoding, FlavorDiffusion addresses data imbalances and enhances clustering quality. Using a heterogeneous graph derived from datasets like Recipe1M and FlavorDB, our model demonstrates superior performance in reconstructing ingredient-ingredient relationships. The addition of a Chemical Structure Prediction (CSP) layer further refines the embedding space, achieving state-of-the-art NMI scores and enabling meaningful discovery of novel ingredient combinations. The proposed framework represents a significant step forward in computational gastronomy, offering scalable, interpretable, and chemically informed solutions for food science.

FlavorDiffusion: Predicting Food Pairings and Chemical Interactions Using Diffusion Models

Foundation models are increasingly used in scientific research, but evaluating AI-generated scientific work remains challenging. Expert reviews are costly, while large language models (LLMs) as proxy reviewers have proven to be unreliable. To address this, we investigate two automatic evaluation metrics, specifically citation count prediction and review score prediction. We parse all papers of OpenReview and augment each submission with its citation count, reference, and research hypothesis. Our findings reveal that citation count prediction is more viable than review score prediction, and predicting scores is more difficult purely from the research hypothesis than from the full paper. Furthermore, we show that a simple prediction model based solely on title and abstract outperforms LLM-based reviewers, though it still falls short of human-level consistency.

Automatic Evaluation Metrics for Artificially Generated Scientific Research

We introduce Functional Group-Aware Representations for Small Molecules (FARM), a novel foundation model designed to bridge the gap between SMILES, natural language, and molecular graphs. The key innovation of FARM lies in its functional group-aware tokenization, which directly incorporates functional group information into SMILES, enriching SMILES with detailed chemical context. For example, instead of using ``O" to represent all oxygen atoms, we use specific tokens like "O_ketone" and "O_hydroxyl" to differentiate oxygen atoms belonging to distinct functional groups. This tokenization expands the chemical lexicon, effectively bridging the gap between SMILES and natural language in terms of vocabulary size, ultimately enhancing the model’s ability to predict molecular properties. FARM also represents molecules from two perspectives: by (1) using masked language modeling to capture atom-level features and (2) employing graph neural networks to encode the whole molecule topology. FARM leverages contrastive learning to aligns these two views of representations into a unified molecular embedding. We rigorously evaluate FARM on the MoleculeNet dataset, where it achieves state-of-the-art performance on 11 out of 13 tasks. These results highlight FARM’s potential to improve molecular representation learning and demonstrate its strong transfer learning capabilities, paving the way for promising applications in drug discovery and pharmaceutical research.

FARM: Functional Group-Aware Representations for Small Molecules

Food systems are responsible for a third of human-caused greenhouse gas emissions. We investigate what Large Language Models (LLMs) can contribute to reducing the environmental impacts of food production. We define a typology of design and prediction tasks based on the sustainable food literature and collaboration with domain experts, and evaluate six LLMs on four tasks in our typology. For example, for a sustainable protein design task, food science experts estimated that collaboration with an LLM can reduce time spent by 45% on average, compared to 22% for collaboration with another expert human food scientist. However, for a sustainable menu design task, LLMs produce suboptimal solutions when instructed to consider both human satisfaction and climate impacts. We propose a general framework for integrating LLMs with combinatorial optimization to improve reasoning capabilities. Our approach decreases emissions of food choices by 79% in a hypothetical restaurant while maintaining participants' satisfaction. Our results demonstrate LLMs' potential, supported by optimization techniques, to accelerate sustainable food development and adoption.

What Can Large Language Models Do for Sustainable Food?

Effective generation of novel hypotheses is instrumental to scientific progress. So far, researchers have been the main powerhouse behind hypothesis generation by painstaking data analysis and thinking (also known as the Eureka moment). In this paper, we examine the potential of large language models (LLMs) to generate hypotheses. We focus on hypothesis generation based on data (i.e., labeled examples). To enable LLMs to handle arbitrarily long contexts, we generate initial hypotheses from a small number of examples and then update them iteratively to improve the quality of hypotheses. Inspired by multi-armed bandits, we design a reward function to inform the exploitation-exploration tradeoff in the update process. Our algorithm is able to generate hypotheses that enable much better predictive performance than few-shot prompting in classification tasks, improving accuracy by 31.7% on a synthetic dataset and by 13.9%, 3.3% and, 24.9% on three real-world datasets. We also outperform supervised learning by 12.8% and 11.2% on two challenging real-world datasets. Furthermore, we find that the generated hypotheses not only corroborate human-verified theories but also uncover new insights for the tasks.

Hypothesis Generation with Large Language Models

Citation practices are crucial in shaping the structure of scientific knowledge, yet they are often influenced by contemporary norms and biases. The emergence of Large Language Models (LLMs) introduces a new dynamic to these practices. Interestingly, the characteristics and potential biases of references recommended by LLMs that entirely rely on their parametric knowledge, and not on search or retrieval-augmented generation, remain unexplored. Here, we analyze these characteristics in an experiment using a dataset from AAAI, NeurIPS, ICML, and ICLR, published after GPT-4's knowledge cut-off date. In our experiment, LLMs are tasked with suggesting scholarly references for the anonymized in-text citations within these papers. Our findings reveal a remarkable similarity between human and LLM citation patterns, but with a more pronounced high citation bias, which persists even after controlling for publication year, title length, number of authors, and venue. The results hold for both GPT-4, and the more capable models GPT-4o and Claude 3.5 where the papers are part of the training data. Additionally, we observe a large consistency between the characteristics of LLM's existing and non-existent generated references, indicating the model's internalization of citation patterns. By analyzing citation graphs, we show that the references recommended are embedded in the relevant citation context, suggesting an even deeper conceptual internalization of the citation networks. While LLMs can aid in citation generation, they may also amplify existing biases, such as the Matthew effect, and introduce new ones, potentially skewing scientific knowledge dissemination.

Large Language Models Reflect Human Citation Patterns with a Heightened Citation Bias

Automated scientific discovery promises to accelerate progress across scientific domains. However, developing and evaluating an AI agent's capacity for end-to-end scientific reasoning is challenging as running real-world experiments is often prohibitively expensive or infeasible. In this work we introduce DISCOVERYWORLD, the first virtual environment for developing and benchmarking an agent's ability to perform complete cycles of novel scientific discovery. DISCOVERYWORLD contains a variety of different challenges, covering topics as diverse as radioisotope dating, rocket science, and proteomics, to encourage development of general discovery skills rather than task-specific solutions. DISCOVERYWORLD itself is an inexpensive, simulated, text-based environment (with optional 2D visual overlay). It includes 120 different challenge tasks, spanning eight topics each with three levels of difficulty and several parametric variations. Each task requires an agent to form hypotheses, design and run experiments, analyze results, and act on conclusions. DISCOVERYWORLD further provides three automatic metrics for evaluating performance, based on (a) task completion, (b) task-relevant actions taken, and (c) the discovered explanatory knowledge. We find that strong baseline agents, that perform well in prior published environments, struggle on most DISCOVERYWORLD tasks, suggesting that DISCOVERYWORLD captures some of the novel challenges of discovery, and thus that DISCOVERYWORLD may help accelerate near-term development and assessment of scientific discovery competency in agents. Code available at: http://www.github.com/allenai/discoveryworld

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