Graphical models or networks describe the statistical dependence among multiple variables and are widely used in biology (e.g., gene regulatory networks). Under appropriate assumptions, directed edges may represent causal relationships. A key feature of a biological network is sparsity, defined by how likely an edge is present, of which we often have some knowledge. However, most existing Bayesian methods use priors for the entire graph, making it difficult to specify the level of sparsity. The few methods that use priors on edges estimate the two directions independently; the sum of the two probabilities can exceed 1. Here, we present baycn (BAYesian Causal Network), a novel approximate Bayesian method that represents a graph in terms of three states of edges: the two directions and edge absence, and specifies priors on these edge states. We design a pseudo Bayesian sampling algorithm for efficient inference. We apply baycn to two genomic problems: i) distinguishing direct and indirect target genes of genetic variants, using these variants as instrumental variables, and ii) inferring combinatorial binding of highly-correlated transcription factors in Drosophila. In both cases and in extensive simulations, our method demonstrates much improved accuracy over existing methods for the whole graph and for individual edges.
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Replaying data is a principal mechanism underlying the stability and data efficiency of off-policy reinforcement learning (RL). We present an effective yet simple framework to extend the use of replays across multiple experiments, minimally adapting the RL workflow for sizeable improvements in controller performance and research iteration times. At its core, Replay Across Experiments (RaE) involves reusing experience from previous experiments to improve exploration and bootstrap learning while reducing required changes to a minimum in comparison to prior work. We empirically show benefits across a number of RL algorithms and challenging control domains spanning both locomotion and manipulation, including hard exploration tasks from egocentric vision. Through comprehensive ablations, we demonstrate robustness to the quality and amount of data available and various hyperparameter choices. Finally, we discuss how our approach can be applied more broadly across research life cycles and can increase resilience by reloading data across random seeds or hyperparameter variations.
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Large language models (LLMs) have been widely recognised as transformative artificial generative intelligence (AGI) technologies due to their capabilities to understand and generate content, including plans with reasoning capabilities. Foundation model based agents derive their autonomy from the capabilities of foundation models, which enable them to autonomously break down a given goal into a set of manageable tasks and orchestrate task execution to meet the goal. Despite the huge efforts put into building foundation model based autonomous agents, the architecture design of the agents has not yet been systematically explored. Also, while there are significant benefits of using autonomous agents for planning and execution, there are serious considerations regarding responsible AI related software quality attributes, such as security and accountability. Therefore, this paper presents a pattern-oriented reference architecture that serves as architecture design guidance and enables responsible-AI-by-design when designing foundation model based autonomous agents. We evaluate the completeness and utility of the proposed reference architecture by mapping it to the architecture of two real-world agents.
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In the classical lossy source coding problem, one encodes long blocks of source symbols that enables the distortion to approach the ultimate Shannon limit. Such a block-coding approach introduces large delays, which is undesirable in many delay-sensitive applications. We consider the zero-delay case, where the goal is to encode and decode a finite-alphabet Markov source without any delay. It has been shown that this problem lends itself to stochastic control techniques, which lead to existence, structural, and general structural approximation results. However, these techniques so far have resulted only in computationally prohibitive algorithmic implementations for code design. To address this problem, we present a reinforcement learning design algorithm and rigorously prove its asymptotic optimality. In particular, we show that a quantized Q-learning algorithm can be used to obtain a near-optimal coding policy for this problem. The proof builds on recent results on quantized Q-learning for weakly Feller controlled Markov chains whose application necessitates the development of supporting technical results on regularity and stability properties, and relating the optimal solutions for discounted and average cost infinite horizon criteria problems. These theoretical results are supported by simulations.
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We characterize the structure and origins of missingness for 159 cross-sectional return predictors and study missing value handling for portfolios constructed using machine learning. Simply imputing with cross-sectional means performs well compared to rigorous expectation-maximization methods. This stems from three facts about predictor data: (1) missingness occurs in large blocks organized by time, (2) cross-sectional correlations are small, and (3) missingness tends to occur in blocks organized by the underlying data source. As a result, observed data provide little information about missing data. Sophisticated imputations introduce estimation noise that can lead to underperformance if machine learning is not carefully applied.
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Our study presents an intermediate-level modeling approach that bridges the gap between complex Agent-Based Models (ABMs) and traditional compartmental models for infectious diseases. We introduce "super-agents" to simulate infection spread in cities, reducing computational complexity while retaining individual-level interactions. This approach leverages real-world mobility data and strategic geospatial tessellations for efficiency. Voronoi Diagram tessellations, based on specific street network locations, outperform standard Census Block Group tessellations, and a hybrid approach balances accuracy and efficiency. Benchmarking against existing ABMs highlights key optimizations. This research improves disease modeling in urban areas, aiding public health strategies in scenarios requiring geographic specificity and high computational efficiency.
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Lion (Evolved Sign Momentum), a new optimizer discovered through program search, has shown promising results in training large AI models. It performs comparably or favorably to AdamW but with greater memory efficiency. As we can expect from the results of a random search program, Lion incorporates elements from several existing algorithms, including signed momentum, decoupled weight decay, Polak, and Nesterov momentum, but does not fit into any existing category of theoretically grounded optimizers. Thus, even though Lion appears to perform well as a general-purpose optimizer for a wide range of tasks, its theoretical basis remains uncertain. This lack of theoretical clarity limits opportunities to further enhance and expand Lion's efficacy. This work aims to demystify Lion. Based on both continuous-time and discrete-time analysis, we demonstrate that Lion is a theoretically novel and principled approach for minimizing a general loss function $f(x)$ while enforcing a bound constraint $\|x\|_\infty \leq 1/\lambda$. Lion achieves this through the incorporation of decoupled weight decay, where $\lambda$ represents the weight decay coefficient. Our analysis is made possible by the development of a new Lyapunov function for the Lion updates. It applies to a broader family of Lion-$\kappa$ algorithms, where the $\text{sign}(\cdot)$ operator in Lion is replaced by the subgradient of a convex function $\kappa$, leading to the solution of a general composite optimization problem of $\min_x f(x) + \kappa^*(x)$. Our findings provide valuable insights into the dynamics of Lion and pave the way for further improvements and extensions of Lion-related algorithms.
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Advancements in artificial intelligence (AI) over the last decade demonstrate that machines can exhibit communicative behavior and influence how humans think, feel, and behave. In fact, the recent development of ChatGPT has shown that large language models (LLMs) can be leveraged to generate high-quality communication content at scale and across domains, suggesting that they will be increasingly used in practice. However, many questions remain about how knowing the source of the messages influences recipients' evaluation of and preference for AI-generated messages compared to human-generated messages. This paper investigated this topic in the context of vaping prevention messaging. In Study 1, which was pre-registered, we examined the influence of source disclosure on people's evaluation of AI-generated health prevention messages compared to human-generated messages. We found that source disclosure (i.e., labeling the source of a message as AI vs. human) significantly impacted the evaluation of the messages but did not significantly alter message rankings. In a follow-up study (Study 2), we examined how the influence of source disclosure may vary by the participants' negative attitudes towards AI. We found a significant moderating effect of negative attitudes towards AI on message evaluation, but not for message selection. However, for those with moderate levels of negative attitudes towards AI, source disclosure decreased the preference for AI-generated messages. Overall, the results of this series of studies showed a slight bias against AI-generated messages once the source was disclosed, adding to the emerging area of study that lies at the intersection of AI and communication.
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Artificial intelligence (AI) for reaction condition optimization has become an important topic in the pharmaceutical industry, given that a data-driven AI model can assist drug discovery and accelerate reaction design. However, existing AI models lack the chemical insights and real-time knowledge acquisition abilities of experienced human chemists. This paper proposes a Large Language Model (LLM) empowered AI agent to bridge this gap. We put forth a novel three-phase paradigm and applied advanced intelligence-enhancement methods like in-context learning and multi-LLM debate so that the AI agent can borrow human insight and update its knowledge by searching the latest chemical literature. Additionally, we introduce a novel Coarse-label Contrastive Learning (CCL) based chemical fingerprint that greatly enhances the agent's performance in optimizing the reaction condition. With the above efforts, the proposed AI agent can autonomously generate the optimal reaction condition recommendation without any human interaction. Further, the agent is highly professional in terms of chemical reactions. It demonstrates close-to-human performance and strong generalization capability in both dry-lab and wet-lab experiments. As the first attempt in the chemical AI agent, this work goes a step further in the field of "AI for chemistry" and opens up new possibilities for computer-aided synthesis planning.
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Counterfactual reasoning, a fundamental aspect of human cognition, involves contemplating alternatives to established facts or past events, significantly enhancing our abilities in planning and decision-making. In light of the advancements in current multi-modal large language models, we explore their effectiveness in counterfactual reasoning. To facilitate this investigation, we introduce a novel dataset, C-VQA, specifically designed to test the counterfactual reasoning capabilities of modern multi-modal large language models. This dataset is constructed by infusing original questions with counterfactual presuppositions, spanning various types such as numerical and boolean queries. It encompasses a mix of real and synthetic data, representing a wide range of difficulty levels. Our thorough evaluations of contemporary vision-language models using this dataset have revealed substantial performance drops, with some models showing up to a 40% decrease, highlighting a significant gap between current models and human-like vision reasoning capabilities. We hope our dataset will serve as a vital benchmark for evaluating the counterfactual reasoning capabilities of models. Code and dataset are publicly available at https://bzhao.me/C-VQA/.
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