Tooling or Not Tooling? The Impact of Tools on Language Agents for Chemistry Problem Solving

To enhance large language models (LLMs) for chemistry problem solving, several LLM-based agents augmented with tools have been proposed, such as ChemCrow and Coscientist. However, their evaluations are narrow in scope, leaving a large gap in understanding the benefits of tools across diverse chemistry tasks. To bridge this gap, we develop ChemAgent, an enhanced chemistry agent over ChemCrow, and conduct a comprehensive evaluation of its performance on both specialized chemistry tasks and general chemistry questions. Surprisingly, ChemAgent does not consistently outperform its base LLMs without tools. Our error analysis with a chemistry expert suggests that: For specialized chemistry tasks, such as synthesis prediction, we should augment agents with specialized tools; however, for general chemistry questions like those in exams, agents' ability to reason correctly with chemistry knowledge matters more, and tool augmentation does not always help.

Captions Speak Louder than Images (CASLIE): Generalizing Foundation Models for E-commerce from High-quality Multimodal Instruction Data

Leveraging multimodal data to drive breakthroughs in e-commerce applications through Multimodal Foundation Models (MFMs) is gaining increasing attention from the research community. However, there are significant challenges that hinder the optimal use of multimodal e-commerce data by foundation models: (1) the scarcity of large-scale, high-quality multimodal benchmark datasets; and (2) the lack of effective multimodal information integration methods. To address these challenges, in this paper, we introduce MMECInstruct, the first-ever, large-scale, and high-quality multimodal instruction dataset for e-commerce. We also develop CASLIE, a simple, lightweight, yet effective framework for integrating multimodal information for e-commerce. Leveraging MMECInstruct, we fine-tune a series of e-commerce MFMs within CASLIE, denoted as CASLIE models. Our comprehensive evaluation demonstrates that CASLIE models substantially outperform 5 categories of advanced baseline models in the in-domain evaluation. Moreover, CASLIE models show strong generalizability to out-of-domain settings. MMECInstruct and CASLIE models are publicly accessible through https://ninglab.github.io/CASLIE/.

SAPIENT: Mastering Multi-turn Conversational Recommendation with Strategic Planning and Monte Carlo Tree Search

Conversational Recommender Systems (CRS) proactively engage users in interactive dialogues to elicit user preferences and provide personalized recommendations. Existing methods train Reinforcement Learning (RL)-based agent with greedy action selection or sampling strategy, and may suffer from suboptimal conversational planning. To address this, we present a novel Monte Carlo Tree Search (MCTS)-based CRS framework SAPIENT. SAPIENT consists of a conversational agent (S-agent) and a conversational planner (S-planner). S-planner builds a conversational search tree with MCTS based on the initial actions proposed by S-agent to find conversation plans. The best conversation plans from S-planner are used to guide the training of S-agent, creating a self-training loop where S-agent can iteratively improve its capability for conversational planning. Furthermore, we propose an efficient variant SAPIENT-e for trade-off between training efficiency and performance. Extensive experiments on four benchmark datasets validate the effectiveness of our approach, showing that SAPIENT outperforms the state-of-the-art baselines.

ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery

The advancements of language language models (LLMs) have piqued growing interest in developing LLM-based language agents to automate scientific discovery end-to-end, which has sparked both excitement and skepticism about the true capabilities of such agents. In this work, we argue that for an agent to fully automate scientific discovery, it must be able to complete all essential tasks in the workflow. Thus, we call for rigorous assessment of agents on individual tasks in a scientific workflow before making bold claims on end-to-end automation. To this end, we present ScienceAgentBench, a new benchmark for evaluating language agents for data-driven scientific discovery. To ensure the scientific authenticity and real-world relevance of our benchmark, we extract 102 tasks from 44 peer-reviewed publications in four disciplines and engage nine subject matter experts to validate them. We unify the target output for every task to a self-contained Python program file and employ an array of evaluation metrics to examine the generated programs, execution results, and costs. Each task goes through multiple rounds of manual validation by annotators and subject matter experts to ensure its annotation quality and scientific plausibility. We also propose two effective strategies to mitigate data contamination concerns. Using our benchmark, we evaluate five open-weight and proprietary LLMs, each with three frameworks: direct prompting, OpenHands, and self-debug. Given three attempts for each task, the best-performing agent can only solve 32.4% of the tasks independently and 34.3% with expert-provided knowledge. These results underscore the limited capacities of current language agents in generating code for data-driven discovery, let alone end-to-end automation for scientific research.

Entity Decomposition with Filtering: A Zero-Shot Clinical Named Entity Recognition Framework

Clinical named entity recognition (NER) aims to retrieve important entities within clinical narratives. Recent works have demonstrated that large language models (LLMs) can achieve strong performance in this task. While previous works focus on proprietary LLMs, we investigate how open NER LLMs, trained specifically for entity recognition, perform in clinical NER. In this paper, we aim to improve them through a novel framework, entity decomposition with filtering, or EDF. Our key idea is to decompose the entity recognition task into several retrievals of sub-entity types. We also introduce a filtering mechanism to remove incorrect entities. Our experimental results demonstrate the efficacy of our framework across all metrics, models, datasets, and entity types. Our analysis reveals that entity decomposition can recognize previously missed entities with substantial improvement. We further provide a comprehensive evaluation of our framework and an in-depth error analysis to pave future works.

LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Dataset

Chemistry plays a crucial role in many domains, such as drug discovery and material science. While large language models (LLMs) such as GPT-4 exhibit remarkable capabilities on natural language processing tasks, existing work shows their performance on chemistry tasks is discouragingly low. In this paper, however, we demonstrate that our developed LLMs can achieve very strong results on a comprehensive set of chemistry tasks, outperforming the most advanced GPT-4 across all the tasks by a substantial margin and approaching the SoTA task-specific models. The key to our success is a large-scale, comprehensive, high-quality dataset for instruction tuning named SMolInstruct. It contains 14 meticulously selected chemistry tasks and over three million high-quality samples, laying a solid foundation for training and evaluating LLMs for chemistry. Based on SMolInstruct, we fine-tune a set of open-source LLMs, among which, we find that Mistral serves as the best base model for chemistry tasks. We further conduct analysis on the impact of trainable parameters, providing insights for future research.

eCeLLM: Generalizing Large Language Models for E-commerce from Large-scale, High-quality Instruction Data

With tremendous efforts on developing effective e-commerce models, conventional e-commerce models show limited success in generalist e-commerce modeling, and suffer from unsatisfactory performance on new users and new products - a typical out-of-domain generalization challenge. Meanwhile, large language models (LLMs) demonstrate outstanding performance in generalist modeling and out-of-domain generalizability in many fields. Toward fully unleashing their power for e-commerce, in this paper, we construct ECInstruct, the first open-sourced, large-scale, and high-quality benchmark instruction dataset for e-commerce. Leveraging ECInstruct, we develop eCeLLM, a series of e-commerce LLMs, by instruction-tuning general-purpose LLMs. Our comprehensive experiments and evaluation demonstrate that eCeLLM models substantially outperform baseline models, including the most advanced GPT-4, and the state-of-the-art task-specific models in in-domain evaluation. Moreover, eCeLLM exhibits excellent generalizability to out-of-domain settings, including unseen products and unseen instructions, highlighting its superiority as a generalist e-commerce model. Both the ECInstruct dataset and the eCeLLM models show great potential in empowering versatile and effective LLMs for e-commerce. ECInstruct and eCeLLM models are publicly accessible through https://ninglab.github.io/eCeLLM.

Enhancing Molecular Property Prediction with Auxiliary Learning and Task-Specific Adaptation

Pretrained Graph Neural Networks have been widely adopted for various molecular property prediction tasks. Despite their ability to encode structural and relational features of molecules, traditional fine-tuning of such pretrained GNNs on the target task can lead to poor generalization. To address this, we explore the adaptation of pretrained GNNs to the target task by jointly training them with multiple auxiliary tasks. This could enable the GNNs to learn both general and task-specific features, which may benefit the target task. However, a major challenge is to determine the relatedness of auxiliary tasks with the target task. To address this, we investigate multiple strategies to measure the relevance of auxiliary tasks and integrate such tasks by adaptively combining task gradients or by learning task weights via bi-level optimization. Additionally, we propose a novel gradient surgery-based approach, Rotation of Conflicting Gradients ($\mathtt{RCGrad}$), that learns to align conflicting auxiliary task gradients through rotation. Our experiments with state-of-the-art pretrained GNNs demonstrate the efficacy of our proposed methods, with improvements of up to 7.7% over fine-tuning. This suggests that incorporating auxiliary tasks along with target task fine-tuning can be an effective way to improve the generalizability of pretrained GNNs for molecular property prediction.

Modeling Sequences as Star Graphs to Address Over-smoothing in Self-attentive Sequential Recommendation

Self-attention (SA) mechanisms have been widely used in developing sequential recommendation (SR) methods, and demonstrated state-of-the-art performance. However, in this paper, we show that self-attentive SR methods substantially suffer from the over-smoothing issue that item embeddings within a sequence become increasingly similar across attention blocks. As widely demonstrated in the literature, this issue could lead to a loss of information in individual items, and significantly degrade models' scalability and performance. To address the over-smoothing issue, in this paper, we view items within a sequence constituting a star graph and develop a method, denoted as MSSG, for SR. Different from existing self-attentive methods, MSSG introduces an additional internal node to specifically capture the global information within the sequence, and does not require information propagation among items. This design fundamentally addresses the over-smoothing issue and enables MSSG a linear time complexity with respect to the sequence length. We compare MSSG with ten state-of-the-art baseline methods on six public benchmark datasets. Our experimental results demonstrate that MSSG significantly outperforms the baseline methods, with an improvement of as much as 10.10%. Our analysis shows the superior scalability of MSSG over the state-of-the-art self-attentive methods. Our complexity analysis and run-time performance comparison together show that MSSG is both theoretically and practically more efficient than self-attentive methods. Our analysis of the attention weights learned in SA-based methods indicates that on sparse recommendation data, modeling dependencies in all item pairs using the SA mechanism yields limited information gain, and thus, might not benefit the recommendation performance

Modeling Path Importance for Effective Alzheimer's Disease Drug Repurposing

Recently, drug repurposing has emerged as an effective and resource-efficient paradigm for AD drug discovery. Among various methods for drug repurposing, network-based methods have shown promising results as they are capable of leveraging complex networks that integrate multiple interaction types, such as protein-protein interactions, to more effectively identify candidate drugs. However, existing approaches typically assume paths of the same length in the network have equal importance in identifying the therapeutic effect of drugs. Other domains have found that same length paths do not necessarily have the same importance. Thus, relying on this assumption may be deleterious to drug repurposing attempts. In this work, we propose MPI (Modeling Path Importance), a novel network-based method for AD drug repurposing. MPI is unique in that it prioritizes important paths via learned node embeddings, which can effectively capture a network's rich structural information. Thus, leveraging learned embeddings allows MPI to effectively differentiate the importance among paths. We evaluate MPI against a commonly used baseline method that identifies anti-AD drug candidates primarily based on the shortest paths between drugs and AD in the network. We observe that among the top-50 ranked drugs, MPI prioritizes 20.0% more drugs with anti-AD evidence compared to the baseline. Finally, Cox proportional-hazard models produced from insurance claims data aid us in identifying the use of etodolac, nicotine, and BBB-crossing ACE-INHs as having a reduced risk of AD, suggesting such drugs may be viable candidates for repurposing and should be explored further in future studies.