Unifying Sequences, Structures, and Descriptions for Any-to-Any Protein Generation with the Large Multimodal Model HelixProtX

Proteins are fundamental components of biological systems and can be represented through various modalities, including sequences, structures, and textual descriptions. Despite the advances in deep learning and scientific large language models (LLMs) for protein research, current methodologies predominantly focus on limited specialized tasks -- often predicting one protein modality from another. These approaches restrict the understanding and generation of multimodal protein data. In contrast, large multimodal models have demonstrated potential capabilities in generating any-to-any content like text, images, and videos, thus enriching user interactions across various domains. Integrating these multimodal model technologies into protein research offers significant promise by potentially transforming how proteins are studied. To this end, we introduce HelixProtX, a system built upon the large multimodal model, aiming to offer a comprehensive solution to protein research by supporting any-to-any protein modality generation. Unlike existing methods, it allows for the transformation of any input protein modality into any desired protein modality. The experimental results affirm the advanced capabilities of HelixProtX, not only in generating functional descriptions from amino acid sequences but also in executing critical tasks such as designing protein sequences and structures from textual descriptions. Preliminary findings indicate that HelixProtX consistently achieves superior accuracy across a range of protein-related tasks, outperforming existing state-of-the-art models. By integrating multimodal large models into protein research, HelixProtX opens new avenues for understanding protein biology, thereby promising to accelerate scientific discovery.

EchoMimic: Lifelike Audio-Driven Portrait Animations through Editable Landmark Conditions

The area of portrait image animation, propelled by audio input, has witnessed notable progress in the generation of lifelike and dynamic portraits. Conventional methods are limited to utilizing either audios or facial key points to drive images into videos, while they can yield satisfactory results, certain issues exist. For instance, methods driven solely by audios can be unstable at times due to the relatively weaker audio signal, while methods driven exclusively by facial key points, although more stable in driving, can result in unnatural outcomes due to the excessive control of key point information. In addressing the previously mentioned challenges, in this paper, we introduce a novel approach which we named EchoMimic. EchoMimic is concurrently trained using both audios and facial landmarks. Through the implementation of a novel training strategy, EchoMimic is capable of generating portrait videos not only by audios and facial landmarks individually, but also by a combination of both audios and selected facial landmarks. EchoMimic has been comprehensively compared with alternative algorithms across various public datasets and our collected dataset, showcasing superior performance in both quantitative and qualitative evaluations. Additional visualization and access to the source code can be located on the EchoMimic project page.

BEACON: Benchmark for Comprehensive RNA Tasks and Language Models

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (\textbf{BE}nchm\textbf{A}rk for \textbf{CO}mprehensive R\textbf{N}A Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.

Anomaly Detection of Particle Orbit in Accelerator using LSTM Deep Learning Technology

A stable, reliable, and controllable orbit lock system is crucial to an electron (or ion) accelerator because the beam orbit and beam energy instability strongly affect the quality of the beam delivered to experimental halls. Currently, when the orbit lock system fails operators must manually intervene. This paper develops a Machine Learning based fault detection methodology to identify orbit lock anomalies and notify accelerator operations staff of the off-normal behavior. Our method is unsupervised, so it does not require labeled data. It uses Long-Short Memory Networks (LSTM) Auto Encoder to capture normal patterns and predict future values of monitoring sensors in the orbit lock system. Anomalies are detected when the prediction error exceeds a threshold. We conducted experiments using monitoring data from Jefferson Lab's Continuous Electron Beam Accelerator Facility (CEBAF). The results are promising: the percentage of real anomalies identified by our solution is 68.6%-89.3% using monitoring data of a single component in the orbit lock control system. The accuracy can be as high as 82%.

A Survey on Large Language Model based Autonomous Agents

Autonomous agents have long been a prominent research focus in both academic and industry communities. Previous research in this field often focuses on training agents with limited knowledge within isolated environments, which diverges significantly from human learning processes, and thus makes the agents hard to achieve human-like decisions. Recently, through the acquisition of vast amounts of web knowledge, large language models (LLMs) have demonstrated remarkable potential in achieving human-level intelligence. This has sparked an upsurge in studies investigating LLM-based autonomous agents. In this paper, we present a comprehensive survey of these studies, delivering a systematic review of the field of LLM-based autonomous agents from a holistic perspective. More specifically, we first discuss the construction of LLM-based autonomous agents, for which we propose a unified framework that encompasses a majority of the previous work. Then, we present a comprehensive overview of the diverse applications of LLM-based autonomous agents in the fields of social science, natural science, and engineering. Finally, we delve into the evaluation strategies commonly used for LLM-based autonomous agents. Based on the previous studies, we also present several challenges and future directions in this field. To keep track of this field and continuously update our survey, we maintain a repository of relevant references at https://github.com/Paitesanshi/LLM-Agent-Survey.

Estimating Continuous Muscle Fatigue For Multi-Muscle Coordinated Exercise: A Pilot Study

Assessing the progression of muscle fatigue for daily exercises provides vital indicators for precise rehabilitation, personalized training dose, especially under the context of Metaverse. Assessing fatigue of multi-muscle coordination-involved daily exercises requires the neuromuscular features that represent the fatigue-induced characteristics of spatiotemporal adaptions of multiple muscles and the estimator that captures the time-evolving progression of fatigue. In this paper, we propose to depict fatigue by the features of muscle compensation and spinal module activation changes and estimate continuous fatigue by a physiological rationale model. First, we extract muscle synergy fractionation and the variance of spinal module spikings as features inspired by the prior of fatigue-induced neuromuscular adaptations. Second, we treat the features as observations and develop a Bayesian Gaussian process to capture the time-evolving progression. Third, we solve the issue of lacking supervision information by mathematically formulating the time-evolving characteristics of fatigue as the loss function. Finally, we adapt the metrics that follow the physiological principles of fatigue to quantitatively evaluate the performance. Our extensive experiments present a 0.99 similarity between days, a over 0.7 similarity with other views of fatigue and a nearly 1 weak monotonicity, which outperform other methods. This study would aim the objective assessment of muscle fatigue.

Efficient Multi-order Gated Aggregation Network

Since the recent success of Vision Transformers (ViTs), explorations toward transformer-style architectures have triggered the resurgence of modern ConvNets. In this work, we explore the representation ability of DNNs through the lens of interaction complexities. We empirically show that interaction complexity is an overlooked but essential indicator for visual recognition. Accordingly, a new family of efficient ConvNets, named MogaNet, is presented to pursue informative context mining in pure ConvNet-based models, with preferable complexity-performance trade-offs. In MogaNet, interactions across multiple complexities are facilitated and contextualized by leveraging two specially designed aggregation blocks in both spatial and channel interaction spaces. Extensive studies are conducted on ImageNet classification, COCO object detection, and ADE20K semantic segmentation tasks. The results demonstrate that our MogaNet establishes new state-of-the-art over other popular methods in mainstream scenarios and all model scales. Typically, the lightweight MogaNet-T achieves 80.0\% top-1 accuracy with only 1.44G FLOPs using a refined training setup on ImageNet-1K, surpassing ParC-Net-S by 1.4\% accuracy but saving 59\% (2.04G) FLOPs.

Student-centric Model of Learning Management System Activity and Academic Performance: from Correlation to Causation

In recent years, there is a lot of interest in modeling students' digital traces in Learning Management System (LMS) to understand students' learning behavior patterns including aspects of meta-cognition and self-regulation, with the ultimate goal to turn those insights into actionable information to support students to improve their learning outcomes. In achieving this goal, however, there are two main issues that need to be addressed given the existing literature. Firstly, most of the current work is course-centered (i.e. models are built from data for a specific course) rather than student-centered; secondly, a vast majority of the models are correlational rather than causal. Those issues make it challenging to identify the most promising actionable factors for intervention at the student level where most of the campus-wide academic support is designed for. In this paper, we explored a student-centric analytical framework for LMS activity data that can provide not only correlational but causal insights mined from observational data. We demonstrated this approach using a dataset of 1651 computing major students at a public university in the US during one semester in the Fall of 2019. This dataset includes students' fine-grained LMS interaction logs and administrative data, e.g. demographics and academic performance. In addition, we expand the repository of LMS behavior indicators to include those that can characterize the time-of-the-day of login (e.g. chronotype). Our analysis showed that student login volume, compared with other login behavior indicators, is both strongly correlated and causally linked to student academic performance, especially among students with low academic performance. We envision that those insights will provide convincing evidence for college student support groups to launch student-centered and targeted interventions that are effective and scalable.

Planar Manipulation via Learning Regrasping

Regrasping is important for robots to reorient objects in planar manipulation tasks. Different placements of objects can provide robots with alternative grasp configurations, which are used in complex planar manipulation tasks that require multiple pick-rotate-and-place steps due to the constraints of the environment and robot kinematic constraints. In this work, our goal is to generate diverse placements of objects on the plane using deep neural networks. We propose a pipeline with the stages of orientation generation, position refinement, and placement discrimination to obtain accurate and diverse stable placements based on the perception of point clouds. A large-scale dataset is created for training, including simulated placements and contact information between objects and the plane. The simulation results show that our pipeline outperforms the start-of-the-art, achieving an accuracy rate of 90% and a diversity rate of 80% in simulation on generated placements. Our pipeline is also validated in real-robot experiments. With the generated placements, sequential pick-rotate-and-place steps are calculated for the robot to reorient objects to goal poses that are not reachable within one step. Videos and dataset are available at https://sites.google.com/view/pmvlr2022/.

FaceVerse: a Fine-grained and Detail-controllable 3D Face Morphable Model from a Hybrid Dataset

We present FaceVerse, a fine-grained 3D Neural Face Model, which is built from hybrid East Asian face datasets containing 60K fused RGB-D images and 2K high-fidelity 3D head scan models. A novel coarse-to-fine structure is proposed to take better advantage of our hybrid dataset. In the coarse module, we generate a base parametric model from large-scale RGB-D images, which is able to predict accurate rough 3D face models in different genders, ages, etc. Then in the fine module, a conditional StyleGAN architecture trained with high-fidelity scan models is introduced to enrich elaborate facial geometric and texture details. Note that different from previous methods, our base and detailed modules are both changeable, which enables an innovative application of adjusting both the basic attributes and the facial details of 3D face models. Furthermore, we propose a single-image fitting framework based on differentiable rendering. Rich experiments show that our method outperforms the state-of-the-art methods.