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Jan 7

BioBERT: a pre-trained biomedical language representation model for biomedical text mining

Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), extracting valuable information from biomedical literature has gained popularity among researchers, and deep learning has boosted the development of effective biomedical text mining models. However, directly applying the advancements in NLP to biomedical text mining often yields unsatisfactory results due to a word distribution shift from general domain corpora to biomedical corpora. In this article, we investigate how the recently introduced pre-trained language model BERT can be adapted for biomedical corpora. We introduce BioBERT (Bidirectional Encoder Representations from Transformers for Biomedical Text Mining), which is a domain-specific language representation model pre-trained on large-scale biomedical corpora. With almost the same architecture across tasks, BioBERT largely outperforms BERT and previous state-of-the-art models in a variety of biomedical text mining tasks when pre-trained on biomedical corpora. While BERT obtains performance comparable to that of previous state-of-the-art models, BioBERT significantly outperforms them on the following three representative biomedical text mining tasks: biomedical named entity recognition (0.62% F1 score improvement), biomedical relation extraction (2.80% F1 score improvement) and biomedical question answering (12.24% MRR improvement). Our analysis results show that pre-training BERT on biomedical corpora helps it to understand complex biomedical texts. We make the pre-trained weights of BioBERT freely available at https://github.com/naver/biobert-pretrained, and the source code for fine-tuning BioBERT available at https://github.com/dmis-lab/biobert.

  • 7 authors
·
Jan 25, 2019

CrisisTransformers: Pre-trained language models and sentence encoders for crisis-related social media texts

Social media platforms play an essential role in crisis communication, but analyzing crisis-related social media texts is challenging due to their informal nature. Transformer-based pre-trained models like BERT and RoBERTa have shown success in various NLP tasks, but they are not tailored for crisis-related texts. Furthermore, general-purpose sentence encoders are used to generate sentence embeddings, regardless of the textual complexities in crisis-related texts. Advances in applications like text classification, semantic search, and clustering contribute to effective processing of crisis-related texts, which is essential for emergency responders to gain a comprehensive view of a crisis event, whether historical or real-time. To address these gaps in crisis informatics literature, this study introduces CrisisTransformers, an ensemble of pre-trained language models and sentence encoders trained on an extensive corpus of over 15 billion word tokens from tweets associated with more than 30 crisis events, including disease outbreaks, natural disasters, conflicts, and other critical incidents. We evaluate existing models and CrisisTransformers on 18 crisis-specific public datasets. Our pre-trained models outperform strong baselines across all datasets in classification tasks, and our best-performing sentence encoder improves the state-of-the-art by 17.43% in sentence encoding tasks. Additionally, we investigate the impact of model initialization on convergence and evaluate the significance of domain-specific models in generating semantically meaningful sentence embeddings. All models are publicly released (https://huggingface.co/crisistransformers), with the anticipation that they will serve as a robust baseline for tasks involving the analysis of crisis-related social media texts.

  • 3 authors
·
Sep 11, 2023

Large Language Models Are Strong Audio-Visual Speech Recognition Learners

Multimodal large language models (MLLMs) have recently become a focal point of research due to their formidable multimodal understanding capabilities. For example, in the audio and speech domains, an LLM can be equipped with (automatic) speech recognition (ASR) abilities by just concatenating the audio tokens, computed with an audio encoder, and the text tokens to achieve state-of-the-art results. On the contrary, tasks like visual and audio-visual speech recognition (VSR/AVSR), which also exploit noise-invariant lip movement information, have received little or no attention. To bridge this gap, we propose Llama-AVSR, a new MLLM with strong audio-visual speech recognition capabilities. It leverages pre-trained audio and video encoders to produce modality-specific tokens which, together with the text tokens, are processed by a pre-trained LLM (e.g., Llama3.1-8B) to yield the resulting response in an auto-regressive fashion. Llama-AVSR requires a small number of trainable parameters as only modality-specific projectors and LoRA modules are trained whereas the multi-modal encoders and LLM are kept frozen. We evaluate our proposed approach on LRS3, the largest public AVSR benchmark, and we achieve new state-of-the-art results for the tasks of ASR and AVSR with a WER of 0.81% and 0.77%, respectively. To bolster our results, we investigate the key factors that underpin the effectiveness of Llama-AVSR: the choice of the pre-trained encoders and LLM, the efficient integration of LoRA modules, and the optimal performance-efficiency trade-off obtained via modality-aware compression rates.

  • 8 authors
·
Sep 18, 2024

Open-Universe Indoor Scene Generation using LLM Program Synthesis and Uncurated Object Databases

We present a system for generating indoor scenes in response to text prompts. The prompts are not limited to a fixed vocabulary of scene descriptions, and the objects in generated scenes are not restricted to a fixed set of object categories -- we call this setting indoor scene generation. Unlike most prior work on indoor scene generation, our system does not require a large training dataset of existing 3D scenes. Instead, it leverages the world knowledge encoded in pre-trained large language models (LLMs) to synthesize programs in a domain-specific layout language that describe objects and spatial relations between them. Executing such a program produces a specification of a constraint satisfaction problem, which the system solves using a gradient-based optimization scheme to produce object positions and orientations. To produce object geometry, the system retrieves 3D meshes from a database. Unlike prior work which uses databases of category-annotated, mutually-aligned meshes, we develop a pipeline using vision-language models (VLMs) to retrieve meshes from massive databases of un-annotated, inconsistently-aligned meshes. Experimental evaluations show that our system outperforms generative models trained on 3D data for traditional, closed-universe scene generation tasks; it also outperforms a recent LLM-based layout generation method on open-universe scene generation.

  • 10 authors
·
Feb 4, 2024

Cross-Task Generalization via Natural Language Crowdsourcing Instructions

Humans (e.g., crowdworkers) have a remarkable ability in solving different tasks, by simply reading textual instructions that define them and looking at a few examples. Despite the success of the conventional supervised learning on individual datasets, such models often struggle with generalization across tasks (e.g., a question-answering system cannot solve classification tasks). A long-standing challenge in AI is to build a model that learns a new task by understanding the human-readable instructions that define it. To study this, we introduce NATURAL INSTRUCTIONS, a dataset of 61 distinct tasks, their human-authored instructions, and 193k task instances (input-output pairs). The instructions are obtained from crowdsourcing instructions used to create existing NLP datasets and mapped to a unified schema. Using this meta-dataset, we measure cross-task generalization by training models on seen tasks and measuring generalization to the remaining unseen ones. We adopt generative pre-trained language models to encode task-specific instructions along with input and generate task output. Our results indicate that models benefit from instructions when evaluated in terms of generalization to unseen tasks (19% better for models utilizing instructions). These models, however, are far behind an estimated performance upperbound indicating significant room for more progress in this direction.

  • 4 authors
·
Apr 18, 2021

FedNano: Toward Lightweight Federated Tuning for Pretrained Multimodal Large Language Models

Multimodal Large Language Models (MLLMs) excel in tasks like multimodal reasoning and cross-modal retrieval but face deployment challenges in real-world scenarios due to distributed multimodal data and strict privacy requirements. Federated Learning (FL) offers a solution by enabling collaborative model training without centralizing data. However, realizing FL for MLLMs presents significant challenges, including high computational demands, limited client capacity, substantial communication costs, and heterogeneous client data. Existing FL methods assume client-side deployment of full models, an assumption that breaks down for large-scale MLLMs due to their massive size and communication demands. To address these limitations, we propose FedNano, the first FL framework that centralizes the LLM on the server while introducing NanoEdge, a lightweight module for client-specific adaptation. NanoEdge employs modality-specific encoders, connectors, and trainable NanoAdapters with low-rank adaptation. This design eliminates the need to deploy LLM on clients, reducing client-side storage by 95%, and limiting communication overhead to only 0.01% of the model parameters. By transmitting only compact NanoAdapter updates, FedNano handles heterogeneous client data and resource constraints while preserving privacy. Experiments demonstrate that FedNano outperforms prior FL baselines, bridging the gap between MLLM scale and FL feasibility, and enabling scalable, decentralized multimodal AI systems.

  • 6 authors
·
Jun 12, 2025 2

Encoder-Decoder Framework for Interactive Free Verses with Generation with Controllable High-Quality Rhyming

Composing poetry or lyrics involves several creative factors, but a challenging aspect of generation is the adherence to a more or less strict metric and rhyming pattern. To address this challenge specifically, previous work on the task has mainly focused on reverse language modeling, which brings the critical selection of each rhyming word to the forefront of each verse. On the other hand, reversing the word order requires that models be trained from scratch with this task-specific goal and cannot take advantage of transfer learning from a Pretrained Language Model (PLM). We propose a novel fine-tuning approach that prepends the rhyming word at the start of each lyric, which allows the critical rhyming decision to be made before the model commits to the content of the lyric (as during reverse language modeling), but maintains compatibility with the word order of regular PLMs as the lyric itself is still generated in left-to-right order. We conducted extensive experiments to compare this fine-tuning against the current state-of-the-art strategies for rhyming, finding that our approach generates more readable text and better rhyming capabilities. Furthermore, we furnish a high-quality dataset in English and 12 other languages, analyse the approach's feasibility in a multilingual context, provide extensive experimental results shedding light on good and bad practices for lyrics generation, and propose metrics to compare methods in the future.

  • 8 authors
·
May 8, 2024