MolParser: End-to-end Visual Recognition of Molecule Structures in the Wild

In recent decades, chemistry publications and patents have increased rapidly. A significant portion of key information is embedded in molecular structure figures, complicating large-scale literature searches and limiting the application of large language models in fields such as biology, chemistry, and pharmaceuticals. The automatic extraction of precise chemical structures is of critical importance. However, the presence of numerous Markush structures in real-world documents, along with variations in molecular image quality, drawing styles, and noise, significantly limits the performance of existing optical chemical structure recognition (OCSR) methods. We present MolParser, a novel end-to-end OCSR method that efficiently and accurately recognizes chemical structures from real-world documents, including difficult Markush structure. We use a extended SMILES encoding rule to annotate our training dataset. Under this rule, we build MolParser-7M, the largest annotated molecular image dataset to our knowledge. While utilizing a large amount of synthetic data, we employed active learning methods to incorporate substantial in-the-wild data, specifically samples cropped from real patents and scientific literature, into the training process. We trained an end-to-end molecular image captioning model, MolParser, using a curriculum learning approach. MolParser significantly outperforms classical and learning-based methods across most scenarios, with potential for broader downstream applications. The dataset is publicly available.

Copiloting Diagnosis of Autism in Real Clinical Scenarios via LLMs

Autism spectrum disorder(ASD) is a pervasive developmental disorder that significantly impacts the daily functioning and social participation of individuals. Despite the abundance of research focused on supporting the clinical diagnosis of ASD, there is still a lack of systematic and comprehensive exploration in the field of methods based on Large Language Models (LLMs), particularly regarding the real-world clinical diagnostic scenarios based on Autism Diagnostic Observation Schedule, Second Edition (ADOS-2). Therefore, we have proposed a framework called ADOS-Copilot, which strikes a balance between scoring and explanation and explored the factors that influence the performance of LLMs in this task. The experimental results indicate that our proposed framework is competitive with the diagnostic results of clinicians, with a minimum MAE of 0.4643, binary classification F1-score of 81.79\%, and ternary classification F1-score of 78.37\%. Furthermore, we have systematically elucidated the strengths and limitations of current LLMs in this task from the perspectives of ADOS-2, LLMs' capabilities, language, and model scale aiming to inspire and guide the future application of LLMs in a broader fields of mental health disorders. We hope for more research to be transferred into real clinical practice, opening a window of kindness to the world for eccentric children.

A high-accuracy multi-model mixing retrosynthetic method

The field of computer-aided synthesis planning (CASP) has seen rapid advancements in recent years, achieving significant progress across various algorithmic benchmarks. However, chemists often encounter numerous infeasible reactions when using CASP in practice. This article delves into common errors associated with CASP and introduces a product prediction model aimed at enhancing the accuracy of single-step models. While the product prediction model reduces the number of single-step reactions, it integrates multiple single-step models to maintain the overall reaction count and increase reaction diversity. Based on manual analysis and large-scale testing, the product prediction model, combined with the multi-model ensemble approach, has been proven to offer higher feasibility and greater diversity.

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.

End-to-End Crystal Structure Prediction from Powder X-Ray Diffraction

Powder X-ray diffraction (PXRD) is a crucial means for crystal structure determination. Such determination often involves external database matching to find a structural analogue and Rietveld refinement to obtain finer structure. However, databases may be incomplete and Rietveld refinement often requires intensive trial-and-error efforts from trained experimentalists, which remains ineffective in practice. To settle these issues, we propose XtalNet, the first end-to-end deep learning-based framework capable of ab initio generation of crystal structures that accurately match given PXRD patterns. The model employs contrastive learning and Diffusion-based conditional generation to enable the simultaneous execution of two tasks: crystal structure retrieval based on PXRD patterns and conditional structure generations. To validate the effectiveness of XtalNet, we curate a much more challenging and practical dataset hMOF-100, XtalNet performs well on this dataset, reaching 96.3\% top-10 hit ratio on the database retrieval task and 95.0\% top-10 match rate on the ranked structure generation task.

Node-Aligned Graph-to-Graph Generation for Retrosynthesis Prediction

Single-step retrosynthesis is a crucial task in organic chemistry and drug design, requiring the identification of required reactants to synthesize a specific compound. with the advent of computer-aided synthesis planning, there is growing interest in using machine-learning techniques to facilitate the process. Existing template-free machine learning-based models typically utilize transformer structures and represent molecules as ID sequences. However, these methods often face challenges in fully leveraging the extensive topological information of the molecule and aligning atoms between the production and reactants, leading to results that are not as competitive as those of semi-template models. Our proposed method, Node-Aligned Graph-to-Graph (NAG2G), also serves as a transformer-based template-free model but utilizes 2D molecular graphs and 3D conformation information. Furthermore, our approach simplifies the incorporation of production-reactant atom mapping alignment by leveraging node alignment to determine a specific order for node generation and generating molecular graphs in an auto-regressive manner node-by-node. This method ensures that the node generation order coincides with the node order in the input graph, overcoming the difficulty of determining a specific node generation order in an auto-regressive manner. Our extensive benchmarking results demonstrate that the proposed NAG2G can outperform the previous state-of-the-art baselines in various metrics.

A Human-Machine Joint Learning Framework to Boost Endogenous BCI Training

Brain-computer interfaces (BCIs) provide a direct pathway from the brain to external devices and have demonstrated great potential for assistive and rehabilitation technologies. Endogenous BCIs based on electroencephalogram (EEG) signals, such as motor imagery (MI) BCIs, can provide some level of control. However, mastering spontaneous BCI control requires the users to generate discriminative and stable brain signal patterns by imagery, which is challenging and is usually achieved over a very long training time (weeks/months). Here, we propose a human-machine joint learning framework to boost the learning process in endogenous BCIs, by guiding the user to generate brain signals towards an optimal distribution estimated by the decoder, given the historical brain signals of the user. To this end, we firstly model the human-machine joint learning process in a uniform formulation. Then a human-machine joint learning framework is proposed: 1) for the human side, we model the learning process in a sequential trial-and-error scenario and propose a novel ``copy/new'' feedback paradigm to help shape the signal generation of the subject toward the optimal distribution; 2) for the machine side, we propose a novel adaptive learning algorithm to learn an optimal signal distribution along with the subject's learning process. Specifically, the decoder reweighs the brain signals generated by the subject to focus more on ``good'' samples to cope with the learning process of the subject. Online and psuedo-online BCI experiments with 18 healthy subjects demonstrated the advantages of the proposed joint learning process over co-adaptive approaches in both learning efficiency and effectiveness.

ACE-HetEM for ab initio Heterogenous Cryo-EM 3D Reconstruction

Due to the extremely low signal-to-noise ratio (SNR) and unknown poses (projection angles and image translation) in cryo-EM experiments, reconstructing 3D structures from 2D images is very challenging. On top of these challenges, heterogeneous cryo-EM reconstruction also has an additional requirement: conformation classification. An emerging solution to this problem is called amortized inference, implemented using the autoencoder architecture or its variants. Instead of searching for the correct image-to-pose/conformation mapping for every image in the dataset as in non-amortized methods, amortized inference only needs to train an encoder that maps images to appropriate latent spaces representing poses or conformations. Unfortunately, standard amortized-inference-based methods with entangled latent spaces have difficulty learning the distribution of conformations and poses from cryo-EM images. In this paper, we propose an unsupervised deep learning architecture called "ACE-HetEM" based on amortized inference. To explicitly enforce the disentanglement of conformation classifications and pose estimations, we designed two alternating training tasks in our method: image-to-image task and pose-to-pose task. Results on simulated datasets show that ACE-HetEM has comparable accuracy in pose estimation and produces even better reconstruction resolution than non-amortized methods. Furthermore, we show that ACE-HetEM is also applicable to real experimental datasets.

Deep Learning Applications Based on WISE Infrared Data: Classification of Stars, Galaxies and Quasars

The Wide-field Infrared Survey Explorer (WISE) has detected hundreds of millions of sources over the entire sky. However, classifying them reliably is a great challenge due to degeneracies in WISE multicolor space and low detection levels in its two longest-wavelength bandpasses. In this paper, the deep learning classification network, IICnet (Infrared Image Classification network), is designed to classify sources from WISE images to achieve a more accurate classification goal. IICnet shows good ability on the feature extraction of the WISE sources. Experiments demonstrates that the classification results of IICnet are superior to some other methods; it has obtained 96.2% accuracy for galaxies, 97.9% accuracy for quasars, and 96.4% accuracy for stars, and the Area Under Curve (AUC) of the IICnet classifier can reach more than 99%. In addition, the superiority of IICnet in processing infrared images has been demonstrated in the comparisons with VGG16, GoogleNet, ResNet34, MobileNet, EfficientNetV2, and RepVGG-fewer parameters and faster inference. The above proves that IICnet is an effective method to classify infrared sources.