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Topic models have a rich history with various applications and have recently been reinvigorated by neural topic modeling. However, these numerous topic models adopt totally distinct datasets, implementations, and evaluations. This impedes quick utilization and fair comparisons, and thereby hinders their research progress and applications. To tackle this challenge, we in this paper propose a Topic Modeling System Toolkit (TopMost). Compared to existing toolkits, TopMost stands out by supporting more extensive features. It covers a broader spectrum of topic modeling scenarios with their complete lifecycles, including datasets, preprocessing, models, training, and evaluations. Thanks to its highly cohesive and decoupled modular design, TopMost enables rapid utilization, fair comparisons, and flexible extensions of diverse cutting-edge topic models. Our code, tutorials, and documentation are available at https://github.com/bobxwu/topmost.

ACL 2024

Towards the TopMost: A Topic Modeling System Toolkit

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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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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.

Large Language Models (LLMs) have revolutionized the field of natural language processing, but they fall short in comprehending biological sequences such as proteins. To address this challenge, we propose InstructProtein, an innovative LLM that possesses bidirectional generation capabilities in both human and protein languages: (i) taking a protein sequence as input to predict its textual function description and (ii) using natural language to prompt protein sequence generation. To achieve this, we first pre-train an LLM on both protein and natural language corpora, enabling it to comprehend individual languages. Then supervised instruction tuning is employed to facilitate the alignment of these two distinct languages. Herein, we introduce a knowledge graph-based instruction generation framework to construct a high-quality instruction dataset, addressing the annotation imbalance and the absence of instructional signals in the existing protein-text corpus. In particular, the instructions inherit the structural relations between proteins and function annotations in knowledge graphs, which empowers our model to engage in the causal modeling of protein functions, akin to the chain-of-thought processes in natural languages. Extensive experiments on bidirectional protein-text generation tasks show that InstructProtein outperforms state-of-the-art LLMs by a large margin.

InstructProtein: Aligning Human and Protein Language via Knowledge Instruction

Taxonomy completion, enriching existing taxonomies by inserting new concepts as parents or attaching them as children, has gained significant interest. Previous approaches embed concepts as vectors in Euclidean space, which makes it difficult to model asymmetric relations in taxonomy. In addition, they introduce pseudo-leaves to convert attachment cases into insertion cases, leading to an incorrect bias in network learning dominated by numerous pseudo-leaves. Addressing these, our framework, \textsc{TaxBox}, leverages box containment and center closeness to design two specialized geometric scorers within the box embedding space. These scorers are tailored for insertion and attachment operations and can effectively capture intrinsic relationships between concepts by optimizing on a granular box constraint loss. We employ a dynamic ranking loss mechanism to balance the scores from these scorers, allowing adaptive adjustments of insertion and attachment scores. Experiments on four real-world datasets show that \textsc{TaxBox} significantly outperforms previous methods, yielding substantial improvements over prior methods in real-world datasets, with average performance boosts of 6.7\%, 34.9\%, and 51.4\% in MRR, Hit@1, and Prec@1, respectively.

Insert or Attach: Taxonomy Completion via Box Embedding

Realistic practice and tailored feedback are key processes for training peer counselors with clinical skills. However, existing mechanisms of providing feedback largely rely on human supervision. Peer counselors often lack mechanisms to receive detailed feedback from experienced mentors, making it difficult for them to support the large number of people with mental health issues who use peer counseling. Our work aims to leverage large language models to provide contextualized and multi-level feedback to empower peer counselors, especially novices, at scale. To achieve this, we co-design with a group of senior psychotherapy supervisors to develop a multi-level feedback taxonomy, and then construct a publicly available dataset with comprehensive feedback annotations of 400 emotional support conversations. We further design a self-improvement method on top of large language models to enhance the automatic generation of feedback. Via qualitative and quantitative evaluation with domain experts, we demonstrate that our method minimizes the risk of potentially harmful and low-quality feedback generation which is desirable in such high-stakes scenarios.

Multi-Level Feedback Generation with Large Language Models for Empowering Novice Peer Counselors

Large language models (LLMs) have emerged as a promising alternative to expensive human evaluations. However, the alignment and coverage of LLM-based evaluations are often limited by the scope and potential bias of the evaluation prompts and criteria. To address this challenge, we propose HD-Eval, a novel framework that iteratively aligns LLM-based evaluators with human preference via Hierarchical Criteria Decomposition. HD-Eval inherits the essence from the evaluation mindset of human experts and enhances the alignment of LLM-based evaluators by decomposing a given evaluation task into finer-grained criteria, aggregating them according to estimated human preferences, pruning insignificant criteria with attribution, and further decomposing significant criteria. By integrating these steps within an iterative alignment training process, we obtain a hierarchical decomposition of criteria that comprehensively captures aspects of natural language at multiple levels of granularity. Implemented as a white box, the human preference-guided aggregator is efficient to train and more explainable than relying solely on prompting, and its independence from model parameters makes it applicable to closed-source LLMs. Extensive experiments on three evaluation domains demonstrate the superiority of HD-Eval in further aligning state-of-the-art evaluators and providing deeper insights into the explanation of evaluation results and the task itself.

HD-Eval: Aligning Large Language Model Evaluators Through Hierarchical Criteria Decomposition

Large Language Models (LLMs) have demonstrated impressive capability in different tasks and are bringing transformative changes to many domains. However, keeping the knowledge in LLMs up-to-date remains a challenge once pretraining is complete. It is thus essential to design effective methods to both update obsolete knowledge and induce new knowledge into LLMs. Existing locate-and-edit knowledge editing (KE) method suffers from two limitations. First, the post-edit LLMs by such methods generally have poor capability in answering complex queries that require multi-hop reasoning. Second, the long run-time of such locate-and-edit methods to perform knowledge edits make it infeasible for large scale KE in practice. In this paper, we explore Parameter-Efficient Fine-Tuning (PEFT) techniques as an alternative for KE. We curate a more comprehensive temporal KE dataset with both knowledge update and knowledge injection examples for KE performance benchmarking. We further probe the effect of fine-tuning on a range of layers in an LLM for the multi-hop QA task. We find that PEFT performs better than locate-and-edit techniques for time-sensitive knowledge edits.

Time Sensitive Knowledge Editing through Efficient Finetuning

The scaling of Large Language Models (LLMs) for retrieval-based tasks, particularly in Retrieval Augmented Generation (RAG), faces significant memory constraints, especially when fine-tuning extensive prompt sequences. Current open-source libraries support full-model inference and fine-tuning across multiple GPUs but fall short of accommodating the efficient parameter distribution required for retrieved context. Addressing this gap, we introduce a novel framework for PEFT-compatible fine-tuning of GPT models, leveraging distributed training. Our framework uniquely utilizes JAX's just-in-time (JIT) compilation and tensor-sharding for efficient resource management, thereby enabling accelerated fine-tuning with reduced memory requirements. This advancement significantly improves the scalability and feasibility of fine-tuning LLMs for complex RAG applications, even on systems with limited GPU resources. Our experiments show more than 12x improvement in runtime compared to Hugging Face/DeepSpeed implementation with four GPUs while consuming less than half the VRAM per GPU.

JORA: JAX Tensor-Parallel LoRA Library for Retrieval Augmented Fine-Tuning

Many computational analyses require linking information across noisy text datasets. While large language models (LLMs) offer significant promise, approximate string matching packages in popular statistical softwares such as R and Stata remain predominant in academic applications. These packages have simple interfaces and can be easily extended to a diversity of languages and settings, and for academic applications, ease-of-use and extensibility are essential. In contrast, packages for record linkage with LLMs require significant familiarity with deep learning frameworks and often focus on specialized applications of commercial value in English. The open-source package LinkTransformer aims to bridge this gap by providing an end-to-end software for performing record linkage and other data cleaning tasks with transformer LLMs, treating linkage as a text retrieval problem. At its core is an off-the-shelf toolkit for applying transformer models to record linkage. LinkTransformer contains a rich repository of pre-trained models for multiple languages and supports easy integration of any transformer language model from Hugging Face or OpenAI, providing the extensibility required for many scholarly applications. Its APIs also perform common data processing tasks, e.g., aggregation, noisy de-duplication, and translation-free cross-lingual linkage. LinkTransformer contains comprehensive tools for efficient model tuning, allowing for highly customized applications, and users can easily contribute their custom-trained models to its model hub to ensure reproducibility. Using a novel benchmark dataset geared towards academic applications, we show that LinkTransformer - with both custom models and Hugging Face or OpenAI models off-the-shelf - outperforms string matching by a wide margin. By combining transformer LMs with intuitive APIs, LinkTransformer aims to democratize these performance gains for those who lack familiarity with deep learning frameworks.

LinkTransformer: A Unified Package for Record Linkage with Transformer Language Models

Following the rapid progress in natural language processing (NLP) models, language models are applied to increasingly more complex interactive tasks such as negotiations and conversation moderations. 
Having human evaluators directly interact with these NLP models is essential for adequately evaluating the performance on such interactive tasks. 
We develop BotEval, an easily customizable, open-source, evaluation toolkit that focuses on enabling human-bot interactions as part of the evaluation process, as opposed to human evaluators making judgements for a static input. 
BotEval balances flexibility for customization and user-friendliness by providing templates for common use cases that span various degrees of complexity and built-in compatibility with popular crowdsourcing platforms.
We showcase the numerous useful features of BotEval through a study that evaluates the performance of various chatbots on their effectiveness for conversational moderation and discuss how BotEval differs from other annotation tools.

BotEval: Facilitating Interactive Human Evaluation

We present BioLunar, developed using the Lunar framework, as a tool for supporting biological analyses, with a particular emphasis on molecular-level evidence enrichment for biomarker discovery in oncology. The platform integrates Large Language Models (LLMs) to facilitate complex scientific reasoning across distributed evidence spaces, enhancing the capability for harmonizing and reasoning over heterogeneous data sources. Demonstrating its utility in cancer research, BioLunar leverages modular design, reusable data access and data analysis components, and a low-code user interface, enabling researchers of all programming levels to construct LLM-enabled scientific workflows. By facilitating automatic scientific discovery and inference from heterogeneous evidence, BioLunar exemplifies the potential of the integration between LLMs, specialised databases and biomedical tools to support expert-level knowledge synthesis and discovery.

BioLunar: Knowledge Synthesis and Scientific Reasoning Framework for Biomedical Discovery

Large Language Models (LLMs) have demonstrated impressive zero shot performance on a wide range of NLP tasks, demonstrating the ability to reason and apply commonsense. A relevant application is to use them for creating high quality synthetic datasets for downstream tasks. In this work, we probe whether GPT-4 can be used to augment existing extractive reading comprehension datasets. Automating data annotation processes has the potential to save large amounts of time, money and effort that goes into manually labelling datasets. In this paper, we evaluate the performance of GPT-4 as a replacement for human annotators for low resource reading comprehension tasks, by comparing performance after fine tuning, and the cost associated with annotation. This work serves to be the first analysis of LLMs as synthetic data augmenters for QA systems, highlighting the unique opportunities and challenges. Additionally, we release augmented versions of low resource datasets, that will allow the research community to create further benchmarks for evaluation of generated datasets. Github available at https://anonymous.4open.science/r/qa-gpt4-B10E/

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