Uni-ELF: A Multi-Level Representation Learning Framework for Electrolyte Formulation Design

Advancements in lithium battery technology heavily rely on the design and engineering of electrolytes. However, current schemes for molecular design and recipe optimization of electrolytes lack an effective computational-experimental closed loop and often fall short in accurately predicting diverse electrolyte formulation properties. In this work, we introduce Uni-ELF, a novel multi-level representation learning framework to advance electrolyte design. Our approach involves two-stage pretraining: reconstructing three-dimensional molecular structures at the molecular level using the Uni-Mol model, and predicting statistical structural properties (e.g., radial distribution functions) from molecular dynamics simulations at the mixture level. Through this comprehensive pretraining, Uni-ELF is able to capture intricate molecular and mixture-level information, which significantly enhances its predictive capability. As a result, Uni-ELF substantially outperforms state-of-the-art methods in predicting both molecular properties (e.g., melting point, boiling point, synthesizability) and formulation properties (e.g., conductivity, Coulombic efficiency). Moreover, Uni-ELF can be seamlessly integrated into an automatic experimental design workflow. We believe this innovative framework will pave the way for automated AI-based electrolyte design and engineering.

Uni-Mol2: Exploring Molecular Pretraining Model at Scale

In recent years, pretraining models have made significant advancements in the fields of natural language processing (NLP), computer vision (CV), and life sciences. The significant advancements in NLP and CV are predominantly driven by the expansion of model parameters and data size, a phenomenon now recognized as the scaling laws. However, research exploring scaling law in molecular pretraining models remains unexplored. In this work, we present Uni-Mol2 , an innovative molecular pretraining model that leverages a two-track transformer to effectively integrate features at the atomic level, graph level, and geometry structure level. Along with this, we systematically investigate the scaling law within molecular pretraining models, characterizing the power-law correlations between validation loss and model size, dataset size, and computational resources. Consequently, we successfully scale Uni-Mol2 to 1.1 billion parameters through pretraining on 800 million conformations, making it the largest molecular pretraining model to date. Extensive experiments show consistent improvement in the downstream tasks as the model size grows. The Uni-Mol2 with 1.1B parameters also outperforms existing methods, achieving an average 27% improvement on the QM9 and 14% on COMPAS-1D dataset.

DiTFastAttn: Attention Compression for Diffusion Transformer Models

Diffusion Transformers (DiT) excel at image and video generation but face computational challenges due to self-attention's quadratic complexity. We propose DiTFastAttn, a novel post-training compression method to alleviate DiT's computational bottleneck. We identify three key redundancies in the attention computation during DiT inference: 1. spatial redundancy, where many attention heads focus on local information; 2. temporal redundancy, with high similarity between neighboring steps' attention outputs; 3. conditional redundancy, where conditional and unconditional inferences exhibit significant similarity. To tackle these redundancies, we propose three techniques: 1. Window Attention with Residual Caching to reduce spatial redundancy; 2. Temporal Similarity Reduction to exploit the similarity between steps; 3. Conditional Redundancy Elimination to skip redundant computations during conditional generation. To demonstrate the effectiveness of DiTFastAttn, we apply it to DiT, PixArt-Sigma for image generation tasks, and OpenSora for video generation tasks. Evaluation results show that for image generation, our method reduces up to 88\% of the FLOPs and achieves up to 1.6x speedup at high resolution generation.

Uni-Mol Docking V2: Towards Realistic and Accurate Binding Pose Prediction

In recent years, machine learning (ML) methods have emerged as promising alternatives for molecular docking, offering the potential for high accuracy without incurring prohibitive computational costs. However, recent studies have indicated that these ML models may overfit to quantitative metrics while neglecting the physical constraints inherent in the problem. In this work, we present Uni-Mol Docking V2, which demonstrates a remarkable improvement in performance, accurately predicting the binding poses of 77+% of ligands in the PoseBusters benchmark with an RMSD value of less than 2.0 {\AA}, and 75+% passing all quality checks. This represents a significant increase from the 62% achieved by the previous Uni-Mol Docking model. Notably, our Uni-Mol Docking approach generates chemically accurate predictions, circumventing issues such as chirality inversions and steric clashes that have plagued previous ML models. Furthermore, we observe enhanced performance in terms of high-quality predictions (RMSD values of less than 1.0 {\AA} and 1.5 {\AA}) and physical soundness when Uni-Mol Docking is combined with more physics-based methods like Uni-Dock. Our results represent a significant advancement in the application of artificial intelligence for scientific research, adopting a holistic approach to ligand docking that is well-suited for industrial applications in virtual screening and drug design. The code, data and service for Uni-Mol Docking are publicly available for use and further development in https://github.com/dptech-corp/Uni-Mol.

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.

Ada3D : Exploiting the Spatial Redundancy with Adaptive Inference for Efficient 3D Object Detection

Voxel-based methods have achieved state-of-the-art performance for 3D object detection in autonomous driving. However, their significant computational and memory costs pose a challenge for their application to resource-constrained vehicles. One reason for this high resource consumption is the presence of a large number of redundant background points in Lidar point clouds, resulting in spatial redundancy in both 3D voxel and dense BEV map representations. To address this issue, we propose an adaptive inference framework called Ada3D, which focuses on exploiting the input-level spatial redundancy. Ada3D adaptively filters the redundant input, guided by a lightweight importance predictor and the unique properties of the Lidar point cloud. Additionally, we utilize the BEV features' intrinsic sparsity by introducing the Sparsity Preserving Batch Normalization. With Ada3D, we achieve 40% reduction for 3D voxels and decrease the density of 2D BEV feature maps from 100% to 20% without sacrificing accuracy. Ada3D reduces the model computational and memory cost by 5x, and achieves 1.52x/1.45x end-to-end GPU latency and 1.5x/4.5x GPU peak memory optimization for the 3D and 2D backbone respectively.

Revisiting Data Augmentation in Model Compression: An Empirical and Comprehensive Study

The excellent performance of deep neural networks is usually accompanied by a large number of parameters and computations, which have limited their usage on the resource-limited edge devices. To address this issue, abundant methods such as pruning, quantization and knowledge distillation have been proposed to compress neural networks and achieved significant breakthroughs. However, most of these compression methods focus on the architecture or the training method of neural networks but ignore the influence from data augmentation. In this paper, we revisit the usage of data augmentation in model compression and give a comprehensive study on the relation between model sizes and their optimal data augmentation policy. To sum up, we mainly have the following three observations: (A) Models in different sizes prefer data augmentation with different magnitudes. Hence, in iterative pruning, data augmentation with varying magnitudes leads to better performance than data augmentation with a consistent magnitude. (B) Data augmentation with a high magnitude may significantly improve the performance of large models but harm the performance of small models. Fortunately, small models can still benefit from strong data augmentations by firstly learning them with "additional parameters" and then discard these "additional parameters" during inference. (C) The prediction of a pre-trained large model can be utilized to measure the difficulty of data augmentation. Thus it can be utilized as a criterion to design better data augmentation policies. We hope this paper may promote more research on the usage of data augmentation in model compression.

CORSD: Class-Oriented Relational Self Distillation

Knowledge distillation conducts an effective model compression method while holding some limitations:(1) the feature based distillation methods only focus on distilling the feature map but are lack of transferring the relation of data examples; (2) the relational distillation methods are either limited to the handcrafted functions for relation extraction, such as L2 norm, or weak in inter- and intra- class relation modeling. Besides, the feature divergence of heterogeneous teacher-student architectures may lead to inaccurate relational knowledge transferring. In this work, we propose a novel training framework named Class-Oriented Relational Self Distillation (CORSD) to address the limitations. The trainable relation networks are designed to extract relation of structured data input, and they enable the whole model to better classify samples by transferring the relational knowledge from the deepest layer of the model to shallow layers. Besides, auxiliary classifiers are proposed to make relation networks capture class-oriented relation that benefits classification task. Experiments demonstrate that CORSD achieves remarkable improvements. Compared to baseline, 3.8%, 1.5% and 4.5% averaged accuracy boost can be observed on CIFAR100, ImageNet and CUB-200-2011, respectively.

Uni-QSAR: an Auto-ML Tool for Molecular Property Prediction

Recently deep learning based quantitative structure-activity relationship (QSAR) models has shown surpassing performance than traditional methods for property prediction tasks in drug discovery. However, most DL based QSAR models are restricted to limited labeled data to achieve better performance, and also are sensitive to model scale and hyper-parameters. In this paper, we propose Uni-QSAR, a powerful Auto-ML tool for molecule property prediction tasks. Uni-QSAR combines molecular representation learning (MRL) of 1D sequential tokens, 2D topology graphs, and 3D conformers with pretraining models to leverage rich representation from large-scale unlabeled data. Without any manual fine-tuning or model selection, Uni-QSAR outperforms SOTA in 21/22 tasks of the Therapeutic Data Commons (TDC) benchmark under designed parallel workflow, with an average performance improvement of 6.09\%. Furthermore, we demonstrate the practical usefulness of Uni-QSAR in drug discovery domains.