Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language and symbolic notations, with emerging extensions to incorporate multi-modal inputs. To advance this emerging field, this survey provides an up-to-date and forward-looking review of the emerging use of LLMs for two central tasks: molecule generation and molecule optimization. We organize our survey around four fundamental challenges that have emerged as critical evaluation dimensions in recent studies: ensuring validity, enhancing synthesizability, achieving precise property control, and maximizing diversity. Based on this, we systematically analyze how current LLM learning paradigms are applied to tackle each challenge, revealing the distinct capabilities and inherent limitations of each approach. In addition, we include the commonly used datasets and evaluation protocols aligned with these challenges. We conclude by discussing future directions, positioning this survey as a resource for researchers working at the intersection of LLMs and molecular science. A continuously updated reading list is available at https://github.com/REAL-Lab-NU/Awesome-LLM-Centric-Molecular-Discovery.

Multi-agent simulation based on LLMs has increasingly emerged as a new paradigm for exploring complex social phenomena and validating theoretical hypotheses. However, traditional experimental design in the social sciences relies heavily on interdisciplinary expert knowledge, involving cumbersome procedures and high technical barriers. While LLM-driven agents demonstrate broad prospects for designing experiments, their limitations regarding reliability and scientific rigor continue to significantly hinder their in-depth application in social science research. To address these challenges, this paper proposes FSTS, an automated framework for multi-agent experiment design based on script generation. Drawing on the concept of the "Decision Theater," the framework deconstructs experimental design into three core phases: Script Composition, Script Finalization, and Actor Generation. Tests across multiple scenarios indicate that the agents generated by this framework can enact the script within the "experimental theater," reproducing results consistent with real-world situations. The proposal of FSTS not only effectively lowers the barrier for social science experimental design but also provides scientifically grounded decision support for policy-making.

Continual learning (CL) is crucial for language models to dynamically adapt to the evolving real-world demands. To mitigate the catastrophic forgetting problem in CL, data replay has been proven a simple and effective strategy, and the subsequent data-replay-based distillation can further enhance the performance. However, existing methods fail to fully exploit the knowledge embedded in models from previous tasks, resulting in the need for a relatively large number of replay samples to achieve good results. In this work, we first explore and emphasize the importance of attention weights in knowledge retention, and then propose a SElective attEntion-guided Knowledge Retention method (SEEKR) for data-efficient replay-based continual learning of large language models (LLMs). Specifically, SEEKR performs attention distillation on the selected attention heads for finer-grained knowledge retention, where the proposed forgettability-based and task-sensitivity-based measures are used to identify the most valuable attention heads. Experimental results on two continual learning benchmarks for LLMs demonstrate the superiority of SEEKR over the existing methods on both performance and efficiency. Explicitly, SEEKR achieves comparable or even better performance with only 1/10 of the replayed data used by other methods, and reduces the proportion of replayed data to 1%. The code is available at https://github.com/jinghan1he/SEEKR.

Heart sound auscultation holds significant importance in the diagnosis of congenital heart disease. However, existing methods for Heart Sound Diagnosis (HSD) tasks are predominantly limited to a few fixed categories, framing the HSD task as a rigid classification problem that does not fully align with medical practice and offers only limited information to physicians. Besides, such methods do not utilize echocardiography reports, the gold standard in the diagnosis of related diseases. To tackle this challenge, we introduce HSDreport, a new benchmark for HSD, which mandates the direct utilization of heart sounds obtained from auscultation to predict echocardiography reports. This benchmark aims to merge the convenience of auscultation with the comprehensive nature of echocardiography reports. First, we collect a new dataset for this benchmark, comprising 2,275 heart sound samples along with their corresponding reports. Subsequently, we develop a knowledge-aware query-based transformer to handle this task. The intent is to leverage the capabilities of medically pre-trained models and the internal knowledge of large language models (LLMs) to address the task’s inherent complexity and variability, thereby enhancing the robustness and scientific validity of the method. Furthermore, our experimental results indicate that our method significantly outperforms traditional HSD approaches and existing multimodal LLMs in detecting key abnormalities in heart sounds.

Recently, the structural reading comprehension (SRC) task on web pages has attracted increasing research interests. Although previous SRC work has leveraged extra information such as HTML tags or XPaths, the informative topology of web pages is not effectively exploited. In this work, we propose a Topological Information Enhanced model (TIE), which transforms the token-level task into a tag-level task by introducing a two-stage process (i.e. node locating and answer refining). Based on that, TIE integrates Graph Attention Network (GAT) and Pre-trained Language Model (PLM) to leverage the topological information of both logical structures and spatial structures. Experimental results demonstrate that our model outperforms strong baselines and achieves state-of-the-art performances on the web-based SRC benchmark WebSRC at the time of writing. The code of TIE will be publicly available at https://github.com/X-LANCE/TIE.

Web search is an essential way for humans to obtain information, but it’s still a great challenge for machines to understand the contents of web pages. In this paper, we introduce the task of web-based structural reading comprehension. Given a web page and a question about it, the task is to find an answer from the web page. This task requires a system not only to understand the semantics of texts but also the structure of the web page. Moreover, we proposed WebSRC, a novel Web-based Structural Reading Comprehension dataset. WebSRC consists of 400K question-answer pairs, which are collected from 6.4K web pages with corresponding HTML source code, screenshots, and metadata. Each question in WebSRC requires a certain structural understanding of a web page to answer, and the answer is either a text span on the web page or yes/no. We evaluate various strong baselines on our dataset to show the difficulty of our task. We also investigate the usefulness of structural information and visual features. Our dataset and baselines have been publicly available.