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.

On-site scale factor linearity calibration of MEMS triaxial gyroscopes

The calibration of MEMS triaxial gyroscopes is crucial for achieving precise attitude estimation for various wearable health monitoring applications. However, gyroscope calibration poses greater challenges compared to accelerometers and magnetometers. This paper introduces an efficient method for calibrating MEMS triaxial gyroscopes via only a servo motor, making it well-suited for field environments. The core strategy of the method involves utilizing the fact that the dot product of the measured gravity and the rotational speed in a fixed frame remains constant. To eliminate the influence of rotating centrifugal force on the accelerometer, the accelerometer data is measured while stationary. The proposed calibration experiment scheme, which allows gyroscopic measurements when operating each axis at a specific rotation speed, making it easier to evaluate the linearity across a related speed range constituted by a series of rotation speeds. Moreover, solely the classical least squares algorithm proves adequate for estimating the scale factor, notably streamlining the analysis of the calibration process. Extensive numerical simulations were conducted to analyze the proposed method's performance in calibrating a triaxial gyroscope model. Experimental validation was also carried out using a commercially available MEMS inertial measurement unit (LSM9DS1 from Arduino nano 33 BLE SENSE) and a servo motor capable of controlling precise speed. The experimental results effectively demonstrate the efficacy of the proposed calibration approach.

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.

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.

Multi-level protein pre-training with Vabs-Net

In recent years, there has been a surge in the development of 3D structure-based pre-trained protein models, representing a significant advancement over pre-trained protein language models in various downstream tasks. However, most existing structure-based pre-trained models primarily focus on the residue level, i.e., alpha carbon atoms, while ignoring other atoms like side chain atoms. We argue that modeling proteins at both residue and atom levels is important since the side chain atoms can also be crucial for numerous downstream tasks, for example, molecular docking. Nevertheless, we find that naively combining residue and atom information during pre-training typically fails. We identify a key reason is the information leakage caused by the inclusion of atom structure in the input, which renders residue-level pre-training tasks trivial and results in insufficiently expressive residue representations. To address this issue, we introduce a span mask pre-training strategy on 3D protein chains to learn meaningful representations of both residues and atoms. This leads to a simple yet effective approach to learning protein representation suitable for diverse downstream tasks. Extensive experimental results on binding site prediction and function prediction tasks demonstrate our proposed pre-training approach significantly outperforms other methods. Our code will be made public.

Leave No Stone Unturned: Mine Extra Knowledge for Imbalanced Facial Expression Recognition

Facial expression data is characterized by a significant imbalance, with most collected data showing happy or neutral expressions and fewer instances of fear or disgust. This imbalance poses challenges to facial expression recognition (FER) models, hindering their ability to fully understand various human emotional states. Existing FER methods typically report overall accuracy on highly imbalanced test sets but exhibit low performance in terms of the mean accuracy across all expression classes. In this paper, our aim is to address the imbalanced FER problem. Existing methods primarily focus on learning knowledge of minor classes solely from minor-class samples. However, we propose a novel approach to extract extra knowledge related to the minor classes from both major and minor class samples. Our motivation stems from the belief that FER resembles a distribution learning task, wherein a sample may contain information about multiple classes. For instance, a sample from the major class surprise might also contain useful features of the minor class fear. Inspired by that, we propose a novel method that leverages re-balanced attention maps to regularize the model, enabling it to extract transformation invariant information about the minor classes from all training samples. Additionally, we introduce re-balanced smooth labels to regulate the cross-entropy loss, guiding the model to pay more attention to the minor classes by utilizing the extra information regarding the label distribution of the imbalanced training data. Extensive experiments on different datasets and backbones show that the two proposed modules work together to regularize the model and achieve state-of-the-art performance under the imbalanced FER task. Code is available at https://github.com/zyh-uaiaaaa.

Human Machine Co-adaption Interface via Cooperation Markov Decision Process System

This paper aims to develop a new human-machine interface to improve rehabilitation performance from the perspective of both the user (patient) and the machine (robot) by introducing the co-adaption techniques via model-based reinforcement learning. Previous studies focus more on robot assistance, i.e., to improve the control strategy so as to fulfill the objective of Assist-As-Needed. In this study, we treat the full process of robot-assisted rehabilitation as a co-adaptive or mutual learning process and emphasize the adaptation of the user to the machine. To this end, we proposed a Co-adaptive MDPs (CaMDPs) model to quantify the learning rates based on cooperative multi-agent reinforcement learning (MARL) in the high abstraction layer of the systems. We proposed several approaches to cooperatively adjust the Policy Improvement among the two agents in the framework of Policy Iteration. Based on the proposed co-adaptive MDPs, the simulation study indicates the non-stationary problem can be mitigated using various proposed Policy Improvement approaches.

Data Assimilation Predictive GAN (DA-PredGAN): applied to determine the spread of COVID-19

We propose the novel use of a generative adversarial network (GAN) (i) to make predictions in time (PredGAN) and (ii) to assimilate measurements (DA-PredGAN). In the latter case, we take advantage of the natural adjoint-like properties of generative models and the ability to simulate forwards and backwards in time. GANs have received much attention recently, after achieving excellent results for their generation of realistic-looking images. We wish to explore how this property translates to new applications in computational modelling and to exploit the adjoint-like properties for efficient data assimilation. To predict the spread of COVID-19 in an idealised town, we apply these methods to a compartmental model in epidemiology that is able to model space and time variations. To do this, the GAN is set within a reduced-order model (ROM), which uses a low-dimensional space for the spatial distribution of the simulation states. Then the GAN learns the evolution of the low-dimensional states over time. The results show that the proposed methods can accurately predict the evolution of the high-fidelity numerical simulation, and can efficiently assimilate observed data and determine the corresponding model parameters.