The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. While modern biological pre-trained models have achieved great success in analyzing these macromolecules individually, their interconnected nature remains under-explored. In this paper, we follow the guidance of the central dogma to redesign both the data and model pipeline and offer a comprehensive framework, Life-Code, that spans different biological functions. As for data flow, we propose a unified pipeline to integrate multi-omics data by reverse-transcribing RNA and reverse-translating amino acids into nucleotide-based sequences. As for the model, we design a codon tokenizer and a hybrid long-sequence architecture to encode the interactions of both coding and non-coding regions with masked modeling pre-training. To model the translation and folding process with coding sequences, Life-Code learns protein structures of the corresponding amino acids by knowledge distillation from off-the-shelf protein language models. Such designs enable Life-Code to capture complex interactions within genetic sequences, providing a more comprehensive understanding of multi-omics with the central dogma. Extensive Experiments show that Life-Code achieves state-of-the-art performance on various tasks across three omics, highlighting its potential for advancing multi-omics analysis and interpretation.

Recently, large foundation models, including large language models (LLMs) and large vision-language models (LVLMs), have become essential tools in critical fields such as law, finance, and healthcare. As these models increasingly integrate into our daily life, it is necessary to conduct moral evaluation to ensure that their outputs align with human values and remain within moral boundaries. Previous works primarily focus on LLMs, proposing moral datasets and benchmarks limited to text modality. However, given the rapid development of LVLMs, there is still a lack of multimodal moral evaluation methods. To bridge this gap, we introduce M$^3$oralBench, the first MultiModal Moral Benchmark for LVLMs. M$^3$oralBench expands the everyday moral scenarios in Moral Foundations Vignettes (MFVs) and employs the text-to-image diffusion model, SD3.0, to create corresponding scenario images. It conducts moral evaluation across six moral foundations of Moral Foundations Theory (MFT) and encompasses tasks in moral judgement, moral classification, and moral response, providing a comprehensive assessment of model performance in multimodal moral understanding and reasoning. Extensive experiments on 10 popular open-source and closed-source LVLMs demonstrate that M$^3$oralBench is a challenging benchmark, exposing notable moral limitations in current models. Our benchmark is publicly available.

Tracking the 6DoF pose of unknown objects in monocular RGB video sequences is crucial for robotic manipulation. However, existing approaches typically rely on accurate depth information, which is non-trivial to obtain in real-world scenarios. Although depth estimation algorithms can be employed, geometric inaccuracy can lead to failures in RGBD-based pose tracking methods. To address this challenge, we introduce GSGTrack, a novel RGB-based pose tracking framework that jointly optimizes geometry and pose. Specifically, we adopt 3D Gaussian Splatting to create an optimizable 3D representation, which is learned simultaneously with a graph-based geometry optimization to capture the object's appearance features and refine its geometry. However, the joint optimization process is susceptible to perturbations from noisy pose and geometry data. Thus, we propose an object silhouette loss to address the issue of pixel-wise loss being overly sensitive to pose noise during tracking. To mitigate the geometric ambiguities caused by inaccurate depth information, we propose a geometry-consistent image pair selection strategy, which filters out low-confidence pairs and ensures robust geometric optimization. Extensive experiments on the OnePose and HO3D datasets demonstrate the effectiveness of GSGTrack in both 6DoF pose tracking and object reconstruction.

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.

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%.

In recent years, AI-assisted drug design methods have been proposed to generate molecules given the pockets' structures of target proteins. Most of them are atom-level-based methods, which consider atoms as basic components and generate atom positions and types. In this way, however, it is hard to generate realistic fragments with complicated structures. To solve this, we propose D3FG, a functional-group-based diffusion model for pocket-specific molecule generation and elaboration. D3FG decomposes molecules into two categories of components: functional groups defined as rigid bodies and linkers as mass points. And the two kinds of components can together form complicated fragments that enhance ligand-protein interactions. To be specific, in the diffusion process, D3FG diffuses the data distribution of the positions, orientations, and types of the components into a prior distribution; In the generative process, the noise is gradually removed from the three variables by denoisers parameterized with designed equivariant graph neural networks. In the experiments, our method can generate molecules with more realistic 3D structures, competitive affinities toward the protein targets, and better drug properties. Besides, D3FG as a solution to a new task of molecule elaboration, could generate molecules with high affinities based on existing ligands and the hotspots of target proteins.

User behavior analysis is crucial in human-centered AI applications. In this field, the collection of sufficient and high-quality user behavior data has always been a fundamental yet challenging problem. An intuitive idea to address this problem is automatically simulating the user behaviors. However, due to the subjective and complex nature of human cognitive processes, reliably simulating the user behavior is difficult. Recently, large language models (LLM) have obtained remarkable successes, showing great potential to achieve human-like intelligence. We argue that these models present significant opportunities for reliable user simulation, and have the potential to revolutionize traditional study paradigms in user behavior analysis. In this paper, we take recommender system as an example to explore the potential of using LLM for user simulation. Specifically, we regard each user as an LLM-based autonomous agent, and let different agents freely communicate, behave and evolve in a virtual simulator called RecAgent. For comprehensively simulation, we not only consider the behaviors within the recommender system (\emph{e.g.}, item browsing and clicking), but also accounts for external influential factors, such as, friend chatting and social advertisement. Our simulator contains at most 1000 agents, and each agent is composed of a profiling module, a memory module and an action module, enabling it to behave consistently, reasonably and reliably. In addition, to more flexibly operate our simulator, we also design two global functions including real-human playing and system intervention. To evaluate the effectiveness of our simulator, we conduct extensive experiments from both agent and system perspectives. In order to advance this direction, we have released our project at {https://github.com/RUC-GSAI/YuLan-Rec}.

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.

Extrinsic manipulation, a technique that enables robots to leverage extrinsic resources for object manipulation, presents practical yet challenging scenarios. Particularly in the context of extrinsic manipulation on a supporting plane, regrasping becomes essential for achieving the desired final object poses. This process involves sequential operation steps and stable placements of objects, which provide grasp space for the robot. To address this challenge, we focus on predicting diverse placements of objects on the plane using deep neural networks. A framework that comprises orientation generation, placement refinement, and placement discrimination stages is proposed, leveraging point clouds to obtain precise and diverse stable placements. To facilitate training, a large-scale dataset is constructed, encompassing stable object placements and contact information between objects. Through extensive experiments, our approach is demonstrated to outperform the start-of-the-art, achieving an accuracy rate of 90.4\% and a diversity rate of 81.3\% in predicted placements. Furthermore, we validate the effectiveness of our approach through real-robot experiments, demonstrating its capability to compute sequential pick-and-place steps based on the predicted placements for regrasping objects to goal poses that are not readily attainable within a single step. Videos and dataset are available at https://sites.google.com/view/pmvlr2022/.

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.