Automating Exploratory Proteomics Research via Language Models

With the development of artificial intelligence, its contribution to science is evolving from simulating a complex problem to automating entire research processes and producing novel discoveries. Achieving this advancement requires both specialized general models grounded in real-world scientific data and iterative, exploratory frameworks that mirror human scientific methodologies. In this paper, we present PROTEUS, a fully automated system for scientific discovery from raw proteomics data. PROTEUS uses large language models (LLMs) to perform hierarchical planning, execute specialized bioinformatics tools, and iteratively refine analysis workflows to generate high-quality scientific hypotheses. The system takes proteomics datasets as input and produces a comprehensive set of research objectives, analysis results, and novel biological hypotheses without human intervention. We evaluated PROTEUS on 12 proteomics datasets collected from various biological samples (e.g. immune cells, tumors) and different sample types (single-cell and bulk), generating 191 scientific hypotheses. These were assessed using both automatic LLM-based scoring on 5 metrics and detailed reviews from human experts. Results demonstrate that PROTEUS consistently produces reliable, logically coherent results that align well with existing literature while also proposing novel, evaluable hypotheses. The system's flexible architecture facilitates seamless integration of diverse analysis tools and adaptation to different proteomics data types. By automating complex proteomics analysis workflows and hypothesis generation, PROTEUS has the potential to considerably accelerate the pace of scientific discovery in proteomics research, enabling researchers to efficiently explore large-scale datasets and uncover biological insights.

Few-shot Open Relation Extraction with Gaussian Prototype and Adaptive Margin

Few-shot relation extraction with none-of-the-above (FsRE with NOTA) aims at predicting labels in few-shot scenarios with unknown classes. FsRE with NOTA is more challenging than the conventional few-shot relation extraction task, since the boundaries of unknown classes are complex and difficult to learn. Meta-learning based methods, especially prototype-based methods, are the mainstream solutions to this task. They obtain the classification boundary by learning the sample distribution of each class. However, their performance is limited because few-shot overfitting and NOTA boundary confusion lead to misclassification between known and unknown classes. To this end, we propose a novel framework based on Gaussian prototype and adaptive margin named GPAM for FsRE with NOTA, which includes three modules, semi-factual representation, GMM-prototype metric learning and decision boundary learning. The first two modules obtain better representations to solve the few-shot problem through debiased information enhancement and Gaussian space distance measurement. The third module learns more accurate classification boundaries and prototypes through adaptive margin and negative sampling. In the training procedure of GPAM, we use contrastive learning loss to comprehensively consider the effects of range and margin on the classification of known and unknown classes to ensure the model's stability and robustness. Sufficient experiments and ablations on the FewRel dataset show that GPAM surpasses previous prototype methods and achieves state-of-the-art performance.

ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery

The advancements of language language models (LLMs) have piqued growing interest in developing LLM-based language agents to automate scientific discovery end-to-end, which has sparked both excitement and skepticism about the true capabilities of such agents. In this work, we argue that for an agent to fully automate scientific discovery, it must be able to complete all essential tasks in the workflow. Thus, we call for rigorous assessment of agents on individual tasks in a scientific workflow before making bold claims on end-to-end automation. To this end, we present ScienceAgentBench, a new benchmark for evaluating language agents for data-driven scientific discovery. To ensure the scientific authenticity and real-world relevance of our benchmark, we extract 102 tasks from 44 peer-reviewed publications in four disciplines and engage nine subject matter experts to validate them. We unify the target output for every task to a self-contained Python program file and employ an array of evaluation metrics to examine the generated programs, execution results, and costs. Each task goes through multiple rounds of manual validation by annotators and subject matter experts to ensure its annotation quality and scientific plausibility. We also propose two effective strategies to mitigate data contamination concerns. Using our benchmark, we evaluate five open-weight and proprietary LLMs, each with three frameworks: direct prompting, OpenHands, and self-debug. Given three attempts for each task, the best-performing agent can only solve 32.4% of the tasks independently and 34.3% with expert-provided knowledge. These results underscore the limited capacities of current language agents in generating code for data-driven discovery, let alone end-to-end automation for scientific research.

Deep reinforcement learning with symmetric data augmentation applied for aircraft lateral attitude tracking control

Symmetry is an essential property in some dynamical systems that can be exploited for state transition prediction and control policy optimization. This paper develops two symmetry-integrated Reinforcement Learning (RL) algorithms based on standard Deep Deterministic Policy Gradient (DDPG),which leverage environment symmetry to augment explored transition samples of a Markov Decision Process(MDP). The firstly developed algorithm is named as Deep Deterministic Policy Gradient with Symmetric Data Augmentation (DDPG-SDA), which enriches dataset of standard DDPG algorithm by symmetric data augmentation method under symmetry assumption of a dynamical system. To further improve sample utilization efficiency, the second developed RL algorithm incorporates one extra critic network, which is independently trained with augmented dataset. A two-step approximate policy iteration method is proposed to integrate training for two critic networks and one actor network. The resulting RL algorithm is named as Deep Deterministic Policy Gradient with Symmetric Critic Augmentation (DDPG-SCA). Simulation results demonstrate enhanced sample efficiency and tracking performance of developed two RL algorithms in aircraft lateral tracking control task.

Learning Physical Simulation with Message Passing Transformer

Machine learning methods for physical simulation have achieved significant success in recent years. We propose a new universal architecture based on Graph Neural Network, the Message Passing Transformer, which incorporates a Message Passing framework, employs an Encoder-Processor-Decoder structure, and applies Graph Fourier Loss as loss function for model optimization. To take advantage of the past message passing state information, we propose Hadamard-Product Attention to update the node attribute in the Processor, Hadamard-Product Attention is a variant of Dot-Product Attention that focuses on more fine-grained semantics and emphasizes on assigning attention weights over each feature dimension rather than each position in the sequence relative to others. We further introduce Graph Fourier Loss (GFL) to balance high-energy and low-energy components. To improve time performance, we precompute the graph's Laplacian eigenvectors before the training process. Our architecture achieves significant accuracy improvements in long-term rollouts for both Lagrangian and Eulerian dynamical systems over current methods.

Enhancing Human-Robot Collaborative Assembly in Manufacturing Systems Using Large Language Models

The development of human-robot collaboration has the ability to improve manufacturing system performance by leveraging the unique strengths of both humans and robots. On the shop floor, human operators contribute with their adaptability and flexibility in dynamic situations, while robots provide precision and the ability to perform repetitive tasks. However, the communication gap between human operators and robots limits the collaboration and coordination of human-robot teams in manufacturing systems. Our research presents a human-robot collaborative assembly framework that utilizes a large language model for enhancing communication in manufacturing environments. The framework facilitates human-robot communication by integrating voice commands through natural language for task management. A case study for an assembly task demonstrates the framework's ability to process natural language inputs and address real-time assembly challenges, emphasizing adaptability to language variation and efficiency in error resolution. The results suggest that large language models have the potential to improve human-robot interaction for collaborative manufacturing assembly applications.

Neural Fluidic System Design and Control with Differentiable Simulation

We present a novel framework to explore neural control and design of complex fluidic systems with dynamic solid boundaries. Our system features a fast differentiable Navier-Stokes solver with solid-fluid interface handling, a low-dimensional differentiable parametric geometry representation, a control-shape co-design algorithm, and gym-like simulation environments to facilitate various fluidic control design applications. Additionally, we present a benchmark of design, control, and learning tasks on high-fidelity, high-resolution dynamic fluid environments that pose challenges for existing differentiable fluid simulators. These tasks include designing the control of artificial hearts, identifying robotic end-effector shapes, and controlling a fluid gate. By seamlessly incorporating our differentiable fluid simulator into a learning framework, we demonstrate successful design, control, and learning results that surpass gradient-free solutions in these benchmark tasks.

TheaterGen: Character Management with LLM for Consistent Multi-turn Image Generation

Recent advances in diffusion models can generate high-quality and stunning images from text. However, multi-turn image generation, which is of high demand in real-world scenarios, still faces challenges in maintaining semantic consistency between images and texts, as well as contextual consistency of the same subject across multiple interactive turns. To address this issue, we introduce TheaterGen, a training-free framework that integrates large language models (LLMs) and text-to-image (T2I) models to provide the capability of multi-turn image generation. Within this framework, LLMs, acting as a "Screenwriter", engage in multi-turn interaction, generating and managing a standardized prompt book that encompasses prompts and layout designs for each character in the target image. Based on these, Theatergen generate a list of character images and extract guidance information, akin to the "Rehearsal". Subsequently, through incorporating the prompt book and guidance information into the reverse denoising process of T2I diffusion models, Theatergen generate the final image, as conducting the "Final Performance". With the effective management of prompt books and character images, TheaterGen significantly improves semantic and contextual consistency in synthesized images. Furthermore, we introduce a dedicated benchmark, CMIGBench (Consistent Multi-turn Image Generation Benchmark) with 8000 multi-turn instructions. Different from previous multi-turn benchmarks, CMIGBench does not define characters in advance. Both the tasks of story generation and multi-turn editing are included on CMIGBench for comprehensive evaluation. Extensive experimental results show that TheaterGen outperforms state-of-the-art methods significantly. It raises the performance bar of the cutting-edge Mini DALLE 3 model by 21% in average character-character similarity and 19% in average text-image similarity.

A Mobile Additive Manufacturing Robot Framework for Smart Manufacturing Systems

Recent technological innovations in the areas of additive manufacturing and collaborative robotics have paved the way toward realizing the concept of on-demand, personalized production on the shop floor. Additive manufacturing process can provide the capability of printing highly customized parts based on various customer requirements. Autonomous, mobile systems provide the flexibility to move custom parts around the shop floor to various manufacturing operations, as needed by product requirements. In this work, we proposed a mobile additive manufacturing robot framework for merging an additive manufacturing process system with an autonomous mobile base. Two case studies showcase the potential benefits of the proposed mobile additive manufacturing framework. The first case study overviews the effect that a mobile system can have on a fused deposition modeling process. The second case study showcases how integrating a mobile additive manufacturing machine can improve the throughput of the manufacturing system. The major findings of this study are that the proposed mobile robotic AM has increased throughput by taking advantage of the travel time between operations/processing sites. It is particularly suited to perform intermittent operations (e.g., preparing feedstock) during the travel time of the robotic AM. One major implication of this study is its application in manufacturing structural components (e.g., concrete construction, and feedstock preparation during reconnaissance missions) in remote or extreme terrains with on-site or on-demand feedstocks.

Resolution-Agnostic Neural Compression for High-Fidelity Portrait Video Conferencing via Implicit Radiance Fields

Video conferencing has caught much more attention recently. High fidelity and low bandwidth are two major objectives of video compression for video conferencing applications. Most pioneering methods rely on classic video compression codec without high-level feature embedding and thus can not reach the extremely low bandwidth. Recent works instead employ model-based neural compression to acquire ultra-low bitrates using sparse representations of each frame such as facial landmark information, while these approaches can not maintain high fidelity due to 2D image-based warping. In this paper, we propose a novel low bandwidth neural compression approach for high-fidelity portrait video conferencing using implicit radiance fields to achieve both major objectives. We leverage dynamic neural radiance fields to reconstruct high-fidelity talking head with expression features, which are represented as frame substitution for transmission. The overall system employs deep model to encode expression features at the sender and reconstruct portrait at the receiver with volume rendering as decoder for ultra-low bandwidth. In particular, with the characteristic of neural radiance fields based model, our compression approach is resolution-agnostic, which means that the low bandwidth achieved by our approach is independent of video resolution, while maintaining fidelity for higher resolution reconstruction. Experimental results demonstrate that our novel framework can (1) construct ultra-low bandwidth video conferencing, (2) maintain high fidelity portrait and (3) have better performance on high-resolution video compression than previous works.