United States

Proteins play critical roles in biological systems, yet 99.7% of over 227 million known protein sequences remain uncharacterized due to the limitations of experimental methods. To assist experimentalists in narrowing down hypotheses and accelerating protein characterization, we present Protein2Text, a multimodal large language model that interprets protein sequences and generates informative text to address open-ended questions about protein functions and attributes. By integrating a resampling mechanism within an adapted LLaVA framework, our model effectively maps protein sequences into a language-compatible space, enhancing its capability to handle diverse and complex queries. Trained on a newly curated dataset derived from PubMed articles and rigorously evaluated using four comprehensive benchmarks—including in-domain and cross-domain evaluations—Protein2Text outperforms several existing models in open-ended question-answering tasks. Our work also highlights the limitations of current evaluation metrics applied to template-based approaches, which may lead to misleading results, emphasizing the need for unbiased assessment methods. By making our datasets and models publicly available, we aim to support ongoing research in computational biology and protein analysis using multimodal language models.

NAACL 2025

Protein2Text: Resampling Mechanism to Translate Protein Sequences into Human-Interpretable Text

protein characterization

open-ended question answering (qa)

resampling mechanism

protein language models (plms)

multimodal learning

### Welcome!
The 62nd Annual Meeting of the Association for Computational Linguistics (ACL 2024) will take place in Bangkok, Thailand from August 11th to 16th, 2024. Our Virtual Poster Sessions will take place online Thursday, August 22, 2024.

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ACL 2024

The 62nd Annual Meeting of the Association for Computational Linguistics (ACL 2024) will take place in Bangkok, Thailand from August 11th to 16th, 2024. More information will be announced soon.

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### 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. 
**[Continue reading...](https://drive.google.com/file/d/1jX-qGhqVSZZCIrAnJaz798pflu5Irrdn/view?usp=sharing)**

*- Colin Cherry, Google, NAACL 2025 General Chair* 

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Welcome to 2025 Annual Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics

Hallucination, a phenomenon where large language models (LLMs) produce output that is factually incorrect or unrelated to the input, is a major challenge for LLM applications that require accuracy and dependability. In this paper, we introduce a reliable and high-speed production system aimed at detecting and rectifying the hallucination issue within LLMs. Our system encompasses named entity recognition (NER), natural language inference (NLI), span-based detection (SBD), and an intricate decision tree-based process to reliably detect a wide range of hallucinations in LLM responses. Furthermore, we have crafted a rewriting mechanism that maintains an optimal mix of precision, response time, and cost-effectiveness. We detail the core elements of our framework and underscore the paramount challenges tied to response time, availability, and performance metrics, which are crucial for real-world deployment of these technologies. Our extensive evaluation, utilizing offline data and live production traffic, confirms the efficacy of our proposed framework and service.

Developing a Reliable, Fast, General-Purpose Hallucination Detection and Mitigation Service

Relevance modeling between queries and items stands as a pivotal component in commercial search engines, directly affecting the user experience. Given the remarkable achievements of large language models (LLMs) in various natural language processing (NLP) tasks, LLM-based relevance modeling is gradually being adopted within industrial search systems. Nevertheless, foundational LLMs lack domain-specific knowledge and do not fully exploit the potential of in-context learning. Furthermore, structured item text remains underutilized, and there is a shortage in the supply of corresponding queries and background knowledge. We thereby propose CPRM (Continual Pre-training for Relevance Modeling), a framework designed for the continual pre-training of LLMs to address these issues. Our CPRM framework includes three modules: 1) employing both queries and multi-field item to jointly pre-train for enhancing domain knowledge, 2) applying in-context pre-training, a novel approach where LLMs are pre-trained on a sequence of related queries or items, and 3) conducting reading comprehension on items to produce associated domain knowledge and background information (e.g., generating summaries and corresponding queries) to further strengthen LLMs. Results on offline experiments and online A/B testing demonstrate that our model achieves convincing performance compared to strong baselines.

CPRM: A LLM-based Continual Pre-training Framework for Relevance Modeling in Commercial Search

GraphQL offers a flexible alternative to REST APIs, allowing precise data retrieval across multiple sources in a single query. However, generating complex GraphQL queries remains a significant challenge. Large Language Models (LLMs), while powerful, often produce suboptimal queries due to limited exposure to GraphQL schemas and their structural intricacies.
Custom prompt engineering with in-context examples is a common approach to guide LLMs, but existing methods, like randomly selecting examples, often yield unsatisfactory results. While semantic similarity-based selection is effective in other domains, it falls short for GraphQL, where understanding schema-specific nuances is crucial for accurate query formulation.


To address this, we propose a Schema and NL-Aware In-context Learning (SNAIL) framework that integrates both structural and semantic information from GraphQL schemas with natural language inputs, enabling schema-aware in-context learning. Unlike existing methods, our approach captures the complexities of GraphQL schemas to improve query generation accuracy.
We validate this framework on a publicly available complex GraphQL test dataset, demonstrating notable performance improvements, with specific query classes showing up to a 20% performance improvement for certain LLMs. As GraphQL adoption grows, with Gartner predicting over 60% of enterprises will use it in production by 2027, this work addresses a critical need, paving the way for more efficient and reliable GraphQL query generation in enterprise applications.

Schema and Natural Language Aware In-Context Learning for Improved GraphQL Query Generation

The Audio Question Answering (AQA) task includes audio event classification, audio captioning, and open-ended reasoning. Recently, AQA has garnered attention due to the advent of Large Audio Language Models (LALMs). Current literature focuses on constructing LALMs by integrating audio encoders with text-only Large Language Models (LLMs) through a projection module. While LALMs excel in general audio understanding, they are limited in temporal reasoning, which may hinder their commercial applications and on-device deployment. This paper addresses these challenges and limitations in audio temporal reasoning. First, we introduce a data augmentation technique for generating reliable audio temporal questions and answers using an LLM. Second, we perform a further fine-tuning of an existing baseline using curriculum learning strategy to specialize in temporal reasoning without compromising performance on fine-tuned tasks. We demonstrate the performance of our model using state-of-the-art LALMs on public audio benchmark datasets. Third, we implement our AQA model on-device locally and investigate its CPU inference for edge applications.

Enhancing Temporal Understanding in Audio Question Answering for Large Audio Language Models

Suggested questions (SQs) provide an effective initial interface for users to engage with their documents in AI-powered reading applications. In practical reading sessions, users have diverse backgrounds and reading goals, yet current SQ features typically ignore such user information, resulting in homogeneous or ineffective questions. We introduce a pipeline that generates personalized SQs by incorporating reader profiles (professions and reading goals) and demonstrate its utility in two ways: 1) as an improved SQ generation pipeline that produces higher quality and more diverse questions compared to current baselines, and 2) as a data generator to fine-tune extremely small models that perform competitively with much larger models on SQ generation. Our approach can not only serve as a drop-in replacement in current SQ systems to immediately improve their performance but also help develop on-device SQ models that can run locally to deliver fast and private SQ experience.

Persona-SQ: A Personalized Suggested Question Generation Framework For Real-world Documents

Firm risk relations are crucial in financial applications, including hedging and portfolio construction. However, the complexity of extracting relevant information from financial reports poses significant challenges in quantifying these relations. To this end, we introduce SURF, a System to Unveil Explainable Risk Relations between Firms. SURF employs a domain-specific encoder and an innovative scoring mechanism to uncover latent risk connections from financial reports. It constructs a network graph to visualize these firm-level risk interactions and incorporates a rationale explainer to elucidate the underlying links. Our evaluation using stock data shows that SURF outperforms baseline methods in effectively capturing firm risk relations. The demo video of the system is publicly available.

SURF: A System to Unveil Explainable Risk Relations between Firms

Classification tasks in NLP are typically addressed by selecting a pre-trained language model (PLM) from a model hub, and fine-tuning it for the task at hand. However, given the very large number of PLMs that are currently available, a practical challenge is to determine which of them will perform best for a specific downstream task. With this paper, we introduce TransformerRanker, a lightweight library that efficiently ranks PLMs for classification tasks without the need for computationally costly fine-tuning. Our library implements current approaches for transferability estimation (LogME, H-Score, kNN), in combination with layer aggregation options, which we empirically showed to yield state-of-the-art rankings of PLMs (Garbas et al., 2024). We designed the interface to be lightweight and easy to use, allowing users to directly connect to the HuggingFace Transformers and Dataset libraries. Users need only select a downstream classification task and a list of PLMs to create a ranking of likely best-suited PLMs for their task. We make TransformerRanker available as a pip-installable open-source library.

TransformerRanker: A Tool for Efficiently Finding the Best-Suited Language Models for Downstream Classification Tasks

Adapting Large Language Models (LLMs) to novel tasks and enhancing their overall capabilities often requires large, high-quality training datasets. Synthetic data, generated at scale, serves a valuable alternative when real-world data is scarce or difficult to obtain. However, ensuring the quality of synthetic datasets is challenging, as developers must manually inspect and refine numerous samples to identify errors and areas for improvement. This process is time-consuming and requires specialized tools. We introduce NeMo-Inspector, an open-source tool designed to simplify the analysis of synthetic datasets with integrated inference capabilities. We demonstrate its effectiveness through two real-world cases. Analysis and cleaning of the synthetically generated GSM-Plus dataset with NeMo-Inspector led to a significant decrease in low-quality samples from 46.99% to 19.51%. The tool also helped identify and correct generation errors in OpenMath models, improving accuracy by 1.92% on the MATH dataset and by 4.17% on the GSM8K dataset for a Meta-Llama-3-8B model fine-tuned on synthetic data generated from Nemotron-4-340B.

NeMo-Inspector: A Visualization Tool for LLM Generation Analysis

Fine-tuning large language models (LLMs) for code generation is challenging due to computational costs and the underrepresentation of some programming languages (PLs) in pre-training. We propose PLEX, a lottery-ticket based parameter-efficient fine-tuning (PEFT) method that adapts LLMs to either well-supported and underrepresented PLs.
During lottery ticket selection, PLEX employs a dual strategy: for well-represented PLs, it leverages the LLM's full parametric knowledge by selecting from full layers, while for underrepresented PLs, it narrows the selection scope to dense layers, prioritizing the most influential parameters.
Additionally, PLEX-E, a low-rank extension of PLEX, further reduces computational costs by limiting the scope of fine-tuning. 
On MultiPL-E benchmarks, PLEX achieves state-of-the-art performance among PEFT methods, while PLEX-E maintains competitive results with reduced computational overhead. Both variants demonstrate effective adaptation across diverse programming languages, particularly for those underrepresented in pre-training.

PLEX: Adaptive Parameter-Efficient Fine-Tuning for Code LLMs using Lottery-Tickets

Large Language Models (LLMs) have demonstrated exceptional versatility across diverse domains, yet their application in e-commerce remains underexplored due to a lack of domain-specific datasets. To address this gap, we introduce eC-Tab2Text, a novel dataset designed to capture the intricacies of e-commerce, including detailed product attributes and user-specific queries. Leveraging eC-Tab2Text, we focus on text generation from product tables, enabling LLMs to produce high-quality, attribute-specific product reviews from structured tabular data. Fine-tuned models were rigorously evaluated using standard Table2Text metrics, alongside correctness, faithfulness, and fluency assessments. Our results demonstrate substantial improvements in generating contextually accurate reviews, highlighting the transformative potential of tailored datasets and fine-tuning methodologies in optimizing e-commerce workflows. This work highlights the potential of LLMs in e-commerce workflows and the essential role of domain-specific datasets in tailoring them to industry-specific challenges.

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Developing a Reliable, Fast, General-Purpose Hallucination Detection and Mitigation Service

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