Thailand

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.

ACL 2024

BioLunar: Knowledge Synthesis and Scientific Reasoning Framework for Biomedical Discovery

evidence reasoning

biomarker discovery

knowledge synthesis

large language models (llms)

automated scientific discovery

poster

### 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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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

With the launch of ChatGPT, large language models (LLMs) have attracted global attention. In the realm of article writing, LLMs have witnessed extensive utilization, giving rise to concerns related to intellectual property protection, personal privacy, and academic integrity. In response, AI-text detection has emerged to distinguish between human and machine-generated content. However, recent research indicates that these detection systems often lack robustness and struggle to effectively differentiate perturbed texts. Currently, there is a lack of systematic evaluations regarding detection performance in real-world applications, and a comprehensive examination of perturbation techniques and detector robustness is also absent. To bridge this gap, our work simulates real-world scenarios in both informal and professional writing, exploring the out-of-the-box performance of current detectors. Additionally, we have constructed 12 black-box text perturbation methods to assess the robustness of current detection models across various perturbation granularities. Furthermore, through adversarial learning experiments, we investigate the impact of perturbation data augmentation on the robustness of AI-text detectors. We have released our code and data at https://github.com/zhouying20/ai-text-detector-evaluation.

Navigating the Shadows: Unveiling Effective Disturbances for Modern AI Content Detectors

Large language models (LLMs) often require task-relevant knowledge to augment their internal knowledge through prompts. However, simply injecting external knowledge into prompts does not guarantee that LLMs can identify and use relevant information in the prompts to conduct chain-of-thought reasoning, especially when the LLM's internal knowledge is derived from biased information on the pretraining data. In this paper, we propose a novel causal view to formally explain the internal knowledge bias of LLMs via a Structural Causal Model (SCM). We review the chain-of-thought (CoT) prompting from a causal perspective and discover that the biased information from pretrained models can impair LLMs' reasoning abilities. When the CoT reasoning paths are misled by irrelevant information from prompts and are logically incorrect, simply editing factual information is insufficient to reach the correct answer. To estimate the confounding effect on CoT reasoning in LLMs, we use external knowledge as an instrumental variable. We further introduce CoT as a mediator to conduct front-door adjustment and generate logically correct CoTs where the spurious correlation between LLMs' pretrained knowledge and task queries is reduced. With extensive experiments, we validate that our approach enables more accurate CoT reasoning and enhances LLM generation on knowledge-intensive tasks.

DeCoT: Debiasing Chain-of-Thought for Knowledge-Intensive Tasks in Large Language Models via Causal Intervention

Literature review requires researchers to synthesize a large amount of information and is increasingly challenging as the scientific literature expands. In this work, we investigate the potential of LLMs for producing hierarchical organizations of scientific studies to assist researchers with literature review. We define hierarchical organizations as tree structures where nodes refer to topical categories and every node is linked to the studies assigned to that category. Our naive LLM-based pipeline for hierarchy generation from a set of studies produces promising yet imperfect hierarchies, motivating us to collect CHIME, an expert-curated dataset for this task focused on biomedicine. Given the challenging and time-consuming nature of building hierarchies from scratch, we use a human-in-the-loop process in which experts correct errors (both links between categories and study assignment) in LLM-generated hierarchies. CHIME contains 2,174 LLM-generated hierarchies covering 472 topics, and expert-corrected hierarchies for a subset of 100 topics. Expert corrections allow us to quantify LLM performance, and we find that while they are quite good at generating and organizing categories, their assignment of studies to categories could be improved. 
We attempt to train a corrector model with human feedback which improves study assignment by 12.6 F1 points. We release our dataset and models to encourage research on developing better assistive tools for literature review.

CHIME: LLM-Assisted Hierarchical Organization of Scientific Studies for Literature Review Support

Despite the significant advancements in keyphrase extraction and keyphrase generation methods, the predominant approach for evaluation mainly relies on exact matching with human references. This scheme fails to recognize systems that generate keyphrases semantically equivalent to the references or diverse keyphrases that carry practical utility. To better assess the capability of keyphrase systems, we propose KPEval, a comprehensive evaluation framework consisting of four critical aspects: reference agreement, faithfulness, diversity, and utility. For each aspect, we design semantic-based metrics to reflect the evaluation objectives. Meta-evaluation studies demonstrate that our evaluation strategy correlates better with human preferences compared to a range of previously proposed metrics. Using KPEval, we re-evaluate 23 keyphrase systems and discover that (1) established model comparison results have blind-spots especially when considering reference-free evaluation; (2) large language models are underestimated by prior evaluation works; and (3) there is no single best model that can excel in all the aspects.

KPEval: Towards Fine-Grained Semantic-Based Keyphrase Evaluation

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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BioLunar: Knowledge Synthesis and Scientific Reasoning Framework for Biomedical Discovery

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InstructProtein: Aligning Human and Protein Language via Knowledge Instruction

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