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Conventional biomedical research is increasingly labor-intensive due to the exponential growth of scientific literature and datasets. Artificial intelligence (AI), particularly Large Language Models (LLMs), has the potential to revolutionize this process by automating various steps. Still, significant challenges remain, including the need for multidisciplinary expertise, logicality of experimental design, and performance measurements. This paper introduces BioResearcher, the first end-to-end automated system designed to streamline the entire biomedical research process involving dry lab experiments. BioResearcher employs a modular multi-agent architecture, integrating specialized agents for search, literature processing, experimental design, and programming. By decomposing complex tasks into logically related sub-tasks and utilizing a hierarchical learning approach, BioResearcher effectively addresses the challenges of multidisciplinary requirements and logical complexity. Furthermore, BioResearcher incorporates an LLM-based reviewer for in-process quality control and introduces novel evaluation metrics to assess the quality and automation of experimental protocols. BioResearcher successfully achieves an average execution success rate of 63.07% across eight previously unmet research objectives. The generated protocols averagely outperform typical agent systems by 22.0% on five quality metrics. The system demonstrates significant potential to reduce researchers' workloads and accelerate biomedical discoveries, paving the way for future innovations in automated research systems.

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Automator是蘋果公司為他們的Mac OS X系統開發的一款軟件。 只要通過點擊拖拽鼠標等操作就可以將一系列動作組合成一個工作流,從而幫助你自動的(可重復的)完成一些復雜的工作。Automator還能橫跨很多不同種類的程序,包括:查找器、Safari網絡瀏覽器、iCal、地址簿或者其他的一些程序。它還能和一些第三方的程序一起工作,如微軟的Office、Adobe公司的Photoshop或者Pixelmator等。

Believable proxies of human behavior can empower interactive applications ranging from immersive environments to rehearsal spaces for interpersonal communication to prototyping tools. In this paper, we introduce generative agents--computational software agents that simulate believable human behavior. Generative agents wake up, cook breakfast, and head to work; artists paint, while authors write; they form opinions, notice each other, and initiate conversations; they remember and reflect on days past as they plan the next day. To enable generative agents, we describe an architecture that extends a large language model to store a complete record of the agent's experiences using natural language, synthesize those memories over time into higher-level reflections, and retrieve them dynamically to plan behavior. We instantiate generative agents to populate an interactive sandbox environment inspired by The Sims, where end users can interact with a small town of twenty five agents using natural language. In an evaluation, these generative agents produce believable individual and emergent social behaviors: for example, starting with only a single user-specified notion that one agent wants to throw a Valentine's Day party, the agents autonomously spread invitations to the party over the next two days, make new acquaintances, ask each other out on dates to the party, and coordinate to show up for the party together at the right time. We demonstrate through ablation that the components of our agent architecture--observation, planning, and reflection--each contribute critically to the believability of agent behavior. By fusing large language models with computational, interactive agents, this work introduces architectural and interaction patterns for enabling believable simulations of human behavior.

Within recent times, cybercriminals have curated a variety of organised and resolute cyber attacks within a range of cyber systems, leading to consequential ramifications to private and governmental institutions. Current security-based automation and orchestrations focus on automating fixed purpose and hard-coded solutions, which are easily surpassed by modern-day cyber attacks. Research within Automated Cyber Defence will allow the development and enabling intelligence response by autonomously defending networked systems through sequential decision-making agents. This article comprehensively elaborates the developments within Automated Cyber Defence through a requirement analysis divided into two sub-areas, namely, automated defence and attack agents and Autonomous Cyber Operation (ACO) Gyms. The requirement analysis allows the comparison of automated agents and highlights the importance of ACO Gyms for their continual development. The requirement analysis is also used to critique ACO Gyms with an overall aim to develop them for deploying automated agents within real-world networked systems. Relevant future challenges were addressed from the overall analysis to accelerate development within the area of Automated Cyber Defence.

Designing and generating new data under targeted properties has been attracting various critical applications such as molecule design, image editing and speech synthesis. Traditional hand-crafted approaches heavily rely on expertise experience and intensive human efforts, yet still suffer from the insufficiency of scientific knowledge and low throughput to support effective and efficient data generation. Recently, the advancement of deep learning induces expressive methods that can learn the underlying representation and properties of data. Such capability provides new opportunities in figuring out the mutual relationship between the structural patterns and functional properties of the data and leveraging such relationship to generate structural data given the desired properties. This article provides a systematic review of this promising research area, commonly known as controllable deep data generation. Firstly, the potential challenges are raised and preliminaries are provided. Then the controllable deep data generation is formally defined, a taxonomy on various techniques is proposed and the evaluation metrics in this specific domain are summarized. After that, exciting applications of controllable deep data generation are introduced and existing works are experimentally analyzed and compared. Finally, the promising future directions of controllable deep data generation are highlighted and five potential challenges are identified.

Causal Machine Learning (CausalML) is an umbrella term for machine learning methods that formalize the data-generation process as a structural causal model (SCM). This allows one to reason about the effects of changes to this process (i.e., interventions) and what would have happened in hindsight (i.e., counterfactuals). We categorize work in \causalml into five groups according to the problems they tackle: (1) causal supervised learning, (2) causal generative modeling, (3) causal explanations, (4) causal fairness, (5) causal reinforcement learning. For each category, we systematically compare its methods and point out open problems. Further, we review modality-specific applications in computer vision, natural language processing, and graph representation learning. Finally, we provide an overview of causal benchmarks and a critical discussion of the state of this nascent field, including recommendations for future work.

The study of network robustness is a critical tool in the characterization and sense making of complex interconnected systems such as infrastructure, communication and social networks. While significant research has been conducted in all of these areas, gaps in the surveying literature still exist. Answers to key questions are currently scattered across multiple scientific fields and numerous papers. In this survey, we distill key findings across numerous domains and provide researchers crucial access to important information by--(1) summarizing and comparing recent and classical graph robustness measures; (2) exploring which robustness measures are most applicable to different categories of networks (e.g., social, infrastructure; (3) reviewing common network attack strategies, and summarizing which attacks are most effective across different network topologies; and (4) extensive discussion on selecting defense techniques to mitigate attacks across a variety of networks. This survey guides researchers and practitioners in navigating the expansive field of network robustness, while summarizing answers to key questions. We conclude by highlighting current research directions and open problems.

Learning disentanglement aims at finding a low dimensional representation which consists of multiple explanatory and generative factors of the observational data. The framework of variational autoencoder (VAE) is commonly used to disentangle independent factors from observations. However, in real scenarios, factors with semantics are not necessarily independent. Instead, there might be an underlying causal structure which renders these factors dependent. We thus propose a new VAE based framework named CausalVAE, which includes a Causal Layer to transform independent exogenous factors into causal endogenous ones that correspond to causally related concepts in data. We further analyze the model identifiabitily, showing that the proposed model learned from observations recovers the true one up to a certain degree. Experiments are conducted on various datasets, including synthetic and real word benchmark CelebA. Results show that the causal representations learned by CausalVAE are semantically interpretable, and their causal relationship as a Directed Acyclic Graph (DAG) is identified with good accuracy. Furthermore, we demonstrate that the proposed CausalVAE model is able to generate counterfactual data through "do-operation" to the causal factors.

The difficulty of deploying various deep learning (DL) models on diverse DL hardwares has boosted the research and development of DL compilers in the community. Several DL compilers have been proposed from both industry and academia such as Tensorflow XLA and TVM. Similarly, the DL compilers take the DL models described in different DL frameworks as input, and then generate optimized codes for diverse DL hardwares as output. However, none of the existing survey has analyzed the unique design of the DL compilers comprehensively. In this paper, we perform a comprehensive survey of existing DL compilers by dissecting the commonly adopted design in details, with emphasis on the DL oriented multi-level IRs, and frontend/backend optimizations. Specifically, we provide a comprehensive comparison among existing DL compilers from various aspects. In addition, we present detailed analysis of the multi-level IR design and compiler optimization techniques. Finally, several insights are highlighted as the potential research directions of DL compiler. This is the first survey paper focusing on the unique design of DL compiler, which we hope can pave the road for future research towards the DL compiler.

Embedding entities and relations into a continuous multi-dimensional vector space have become the dominant method for knowledge graph embedding in representation learning. However, most existing models ignore to represent hierarchical knowledge, such as the similarities and dissimilarities of entities in one domain. We proposed to learn a Domain Representations over existing knowledge graph embedding models, such that entities that have similar attributes are organized into the same domain. Such hierarchical knowledge of domains can give further evidence in link prediction. Experimental results show that domain embeddings give a significant improvement over the most recent state-of-art baseline knowledge graph embedding models.

The design of deep graph models still remains to be investigated and the crucial part is how to explore and exploit the knowledge from different hops of neighbors in an efficient way. In this paper, we propose a novel RNN-like deep graph neural network architecture by incorporating AdaBoost into the computation of network; and the proposed graph convolutional network called AdaGCN~(AdaBoosting Graph Convolutional Network) has the ability to efficiently extract knowledge from high-order neighbors and integrate knowledge from different hops of neighbors into the network in an AdaBoost way. We also present the architectural difference between AdaGCN and existing graph convolutional methods to show the benefits of our proposal. Finally, extensive experiments demonstrate the state-of-the-art prediction performance and the computational advantage of our approach AdaGCN.

Knowledge representation learning (KRL) aims to represent entities and relations in knowledge graph in low-dimensional semantic space, which have been widely used in massive knowledge-driven tasks. In this article, we introduce the reader to the motivations for KRL, and overview existing approaches for KRL. Afterwards, we extensively conduct and quantitative comparison and analysis of several typical KRL methods on three evaluation tasks of knowledge acquisition including knowledge graph completion, triple classification, and relation extraction. We also review the real-world applications of KRL, such as language modeling, question answering, information retrieval, and recommender systems. Finally, we discuss the remaining challenges and outlook the future directions for KRL. The codes and datasets used in the experiments can be found in //github.com/thunlp/OpenKE.

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