ReactXT: Understanding Molecular "Reaction-ship" via Reaction-Contextualized Molecule-Text Pretraining

Molecule-text modeling, which aims to facilitate molecule-relevant tasks with a textual interface and textual knowledge, is an emerging research direction. Beyond single molecules, studying reaction-text modeling holds promise for helping the synthesis of new materials and drugs. However, previous works mostly neglect reaction-text modeling: they primarily focus on modeling individual molecule-text pairs or learning chemical reactions without texts in context. Additionally, one key task of reaction-text modeling -- experimental procedure prediction -- is less explored due to the absence of an open-source dataset. The task is to predict step-by-step actions of conducting chemical experiments and is crucial to automating chemical synthesis. To resolve the challenges above, we propose a new pretraining method, ReactXT, for reaction-text modeling, and a new dataset, OpenExp, for experimental procedure prediction. Specifically, ReactXT features three types of input contexts to incrementally pretrain LMs. Each of the three input contexts corresponds to a pretraining task to improve the text-based understanding of either reactions or single molecules. ReactXT demonstrates consistent improvements in experimental procedure prediction and molecule captioning and offers competitive results in retrosynthesis. Our code is available at https://github.com/syr-cn/ReactXT.

Uni-SMART: Universal Science Multimodal Analysis and Research Transformer

In scientific research and its application, scientific literature analysis is crucial as it allows researchers to build on the work of others. However, the fast growth of scientific knowledge has led to a massive increase in scholarly articles, making in-depth literature analysis increasingly challenging and time-consuming. The emergence of Large Language Models (LLMs) has offered a new way to address this challenge. Known for their strong abilities in summarizing texts, LLMs are seen as a potential tool to improve the analysis of scientific literature. However, existing LLMs have their own limits. Scientific literature often includes a wide range of multimodal elements, such as molecular structure, tables, and charts, which are hard for text-focused LLMs to understand and analyze. This issue points to the urgent need for new solutions that can fully understand and analyze multimodal content in scientific literature. To answer this demand, we present Uni-SMART (Universal Science Multimodal Analysis and Research Transformer), an innovative model designed for in-depth understanding of multimodal scientific literature. Through rigorous quantitative evaluation across several domains, Uni-SMART demonstrates superior performance over leading text-focused LLMs. Furthermore, our exploration extends to practical applications, including patent infringement detection and nuanced analysis of charts. These applications not only highlight Uni-SMART's adaptability but also its potential to revolutionize how we interact with scientific literature.

SciAssess: Benchmarking LLM Proficiency in Scientific Literature Analysis

Recent breakthroughs in Large Language Models (LLMs) have revolutionized natural language understanding and generation, igniting a surge of interest in leveraging these technologies in the field of scientific literature analysis. Existing benchmarks, however, inadequately evaluate the proficiency of LLMs in scientific literature analysis, especially in scenarios involving complex comprehension and multimodal data. In response, we introduced SciAssess, a benchmark tailored for the in-depth analysis of scientific literature, crafted to provide a thorough assessment of LLMs' efficacy. SciAssess focuses on evaluating LLMs' abilities in memorization, comprehension, and analysis within the context of scientific literature analysis. It includes representative tasks from diverse scientific fields, such as general chemistry, organic materials, and alloy materials. And rigorous quality control measures ensure its reliability in terms of correctness, anonymization, and copyright compliance. SciAssess evaluates leading LLMs, including GPT-4, GPT-3.5, and Gemini, identifying their strengths and aspects for improvement and supporting the ongoing development of LLM applications in scientific literature analysis. SciAssess and its resources are made available at https://sci-assess.github.io, offering a valuable tool for advancing LLM capabilities in scientific literature analysis.

MolTC: Towards Molecular Relational Modeling In Language Models

Molecular Relational Learning (MRL), aiming to understand interactions between molecular pairs, plays a pivotal role in advancing biochemical research. Recently, the adoption of large language models (LLMs), known for their vast knowledge repositories and advanced logical inference capabilities, has emerged as a promising way for efficient and effective MRL. Despite their potential, these methods predominantly rely on the textual data, thus not fully harnessing the wealth of structural information inherent in molecular graphs. Moreover, the absence of a unified framework exacerbates the issue of information underutilization, as it hinders the sharing of interaction mechanism learned across diverse datasets. To address these challenges, this work proposes a novel LLM-based multi-modal framework for Molecular inTeraction prediction following Chain-of-Thought (CoT) theory, termed MolTC, which effectively integrate graphical information of two molecules in pair. For achieving a unified MRL, MolTC innovatively develops a dynamic parameter-sharing strategy for cross-dataset information sharing. Moreover, to train MolTC efficiently, we introduce a Multi-hierarchical CoT concept to refine its training paradigm, and conduct a comprehensive Molecular Interactive Instructions dataset for the development of biochemical LLMs involving MRL. Our experiments, conducted across various datasets involving over 4,000,000 molecular pairs, exhibit the superiority of our method over current GNN and LLM-based baselines. Code is available at https://github.com/MangoKiller/MolTC.

Towards 3D Molecule-Text Interpretation in Language Models

Language Models (LMs) have greatly influenced diverse domains. However, their inherent limitation in comprehending 3D molecular structures has considerably constrained their potential in the biomolecular domain. To bridge this gap, we focus on 3D molecule-text interpretation, and propose 3D-MoLM: 3D-Molecular Language Modeling. Specifically, 3D-MoLM enables an LM to interpret and analyze 3D molecules by equipping the LM with a 3D molecular encoder. This integration is achieved by a 3D molecule-text projector, bridging the 3D molecular encoder's representation space and the LM's input space. Moreover, to enhance 3D-MoLM's ability of cross-modal molecular understanding and instruction following, we meticulously curated a 3D molecule-centric instruction tuning dataset -- 3D-MoIT. Through 3D molecule-text alignment and 3D molecule-centric instruction tuning, 3D-MoLM establishes an integration of 3D molecular encoder and LM. It significantly surpasses existing baselines on downstream tasks, including molecule-text retrieval, molecule captioning, and more challenging open-text molecular QA tasks, especially focusing on 3D-dependent properties.

LLaRA: Aligning Large Language Models with Sequential Recommenders

Sequential recommendation aims to predict the subsequent items matching user preference based on her/his historical interactions. With the development of Large Language Models (LLMs), there is growing interest in exploring the potential of LLMs for sequential recommendation by framing it as a language modeling task. Prior works represent items in the textual prompts using either ID indexing or text indexing and feed the prompts into LLMs, but falling short of either encapsulating comprehensive world knowledge or exhibiting sufficient sequential understanding. To harness the complementary strengths of traditional recommenders (which encode user behavioral knowledge) and LLMs (which possess world knowledge about items), we propose LLaRA -- a Large Language and Recommendation Assistant framework. Specifically, LLaRA represents items in LLM's input prompts using a novel hybrid approach that integrates ID-based item embeddings from traditional recommenders with textual item features. Viewing the ``sequential behavior of the user'' as a new modality in recommendation, we employ an adapter to bridge the modality gap between ID embeddings of the traditional recommenders and the input space of LLMs. Furthermore, instead of directly exposing the hybrid prompt to LLMs, we apply a curriculum learning approach to gradually ramp up training complexity. We first warm up the LLM with text-only prompting, which aligns more naturally with the LLM's language modeling capabilities. Thereafter, we progressively transition to hybrid prompting, training the adapter to incorporate behavioral knowledge from the traditional sequential recommender into the LLM. Extensive experiments demonstrate the efficacy of LLaRA framework. Our code and data are available at https://github.com/ljy0ustc/LLaRA .

BianQue: Balancing the Questioning and Suggestion Ability of Health LLMs with Multi-turn Health Conversations Polished by ChatGPT

Large language models (LLMs) have performed well in providing general and extensive health suggestions in single-turn conversations, exemplified by systems such as ChatGPT, ChatGLM, ChatDoctor, DoctorGLM, and etc. However, the limited information provided by users during single turn results in inadequate personalization and targeting of the generated suggestions, which requires users to independently select the useful part. It is mainly caused by the missing ability to engage in multi-turn questioning. In real-world medical consultations, doctors usually employ a series of iterative inquiries to comprehend the patient's condition thoroughly, enabling them to provide effective and personalized suggestions subsequently, which can be defined as chain of questioning (CoQ) for LLMs. To improve the CoQ of LLMs, we propose BianQue, a ChatGLM-based LLM finetuned with the self-constructed health conversation dataset BianQueCorpus that is consist of multiple turns of questioning and health suggestions polished by ChatGPT. Experimental results demonstrate that the proposed BianQue can simultaneously balance the capabilities of both questioning and health suggestions, which will help promote the research and application of LLMs in the field of proactive health.

MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter

Language Models (LMs) have demonstrated impressive molecule understanding ability on various 1D text-related tasks. However, they inherently lack 2D graph perception - a critical ability of human professionals in comprehending molecules' topological structures. To bridge this gap, we propose MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter. MolCA enables an LM (e.g., Galactica) to understand both text- and graph-based molecular contents via the cross-modal projector. Specifically, the cross-modal projector is implemented as a Q-Former to connect a graph encoder's representation space and an LM's text space. Further, MolCA employs a uni-modal adapter (i.e., LoRA) for the LM's efficient adaptation to downstream tasks. Unlike previous studies that couple an LM with a graph encoder via cross-modal contrastive learning, MolCA retains the LM's ability of open-ended text generation and augments it with 2D graph information. To showcase its effectiveness, we extensively benchmark MolCA on tasks of molecule captioning, IUPAC name prediction, and molecule-text retrieval, on which MolCA significantly outperforms the baselines. Our codes and checkpoints can be found at https://github.com/acharkq/MolCA.

Towards Dynamic and Small Objects Refinement for Unsupervised Domain Adaptative Nighttime Semantic Segmentation

Nighttime semantic segmentation is essential for various applications, e.g., autonomous driving, which often faces challenges due to poor illumination and the lack of well-annotated datasets. Unsupervised domain adaptation (UDA) has shown potential for addressing the challenges and achieved remarkable results for nighttime semantic segmentation. However, existing methods still face limitations in 1) their reliance on style transfer or relighting models, which struggle to generalize to complex nighttime environments, and 2) their ignorance of dynamic and small objects like vehicles and traffic signs, which are difficult to be directly learned from other domains. This paper proposes a novel UDA method that refines both label and feature levels for dynamic and small objects for nighttime semantic segmentation. First, we propose a dynamic and small object refinement module to complement the knowledge of dynamic and small objects from the source domain to target nighttime domain. These dynamic and small objects are normally context-inconsistent in under-exposed conditions. Then, we design a feature prototype alignment module to reduce the domain gap by deploying contrastive learning between features and prototypes of the same class from different domains, while re-weighting the categories of dynamic and small objects. Extensive experiments on four benchmark datasets demonstrate that our method outperforms prior arts by a large margin for nighttime segmentation. Project page: https://rorisis.github.io/DSRNSS/.

National Origin Discrimination in Deep-learning-powered Automated Resume Screening

Many companies and organizations have started to use some form of AIenabled auto mated tools to assist in their hiring process, e.g. screening resumes, interviewing candi dates, performance evaluation. While those AI tools have greatly improved human re source operations efficiency and provided conveniences to job seekers as well, there are increasing concerns on unfair treatment to candidates, caused by underlying bias in AI systems. Laws around equal opportunity and fairness, like GDPR, CCPA, are introduced or under development, in attempt to regulate AI. However, it is difficult to implement AI regulations in practice, as technologies are constantly advancing and the risk perti nent to their applications can fail to be recognized. This study examined deep learning methods, a recent technology breakthrough, with focus on their application to automated resume screening. One impressive performance of deep learning methods is the represen tation of individual words as lowdimensional numerical vectors, called word embedding, which are learned from aggregated global wordword cooccurrence statistics from a cor pus, like Wikipedia or Google news. The resulting word representations possess interest ing linear substructures of the word vector space and have been widely used in down stream tasks, like resume screening. However, word embedding inherits and reinforces the stereotyping from the training corpus, as deep learning models essentially learn a probability distribution of words and their relations from history data. Our study finds out that if we rely on such deeplearningpowered automated resume screening tools, it may lead to decisions favoring or disfavoring certain demographic groups and raise eth ical, even legal, concerns. To address the issue, we developed bias mitigation method. Extensive experiments on real candidate resumes are conducted to validate our study