Learning Collective Variables for Protein Folding with Labeled Data Augmentation through Geodesic Interpolation

In molecular dynamics (MD) simulations, rare events, such as protein folding, are typically studied by means of enhanced sampling techniques, most of which rely on the definition of a collective variable (CV) along which the acceleration occurs. Obtaining an expressive CV is crucial, but often hindered by the lack of information about the particular event, e.g., the transition from unfolded to folded conformation. We propose a simulation-free data augmentation strategy using physics-inspired metrics to generate geodesic interpolations resembling protein folding transitions, thereby improving sampling efficiency without true transition state samples. Leveraging interpolation progress parameters, we introduce a regression-based learning scheme for CV models, which outperforms classifier-based methods when transition state data is limited and noisy

A Survey on Data-Centric Recommender Systems

Recommender systems (RSs) have become an essential tool for mitigating information overload in a range of real-world applications. Recent trends in RSs have revealed a major paradigm shift, moving the spotlight from model-centric innovations to data-centric efforts (e.g., improving data quality and quantity). This evolution has given rise to the concept of data-centric recommender systems (Data-Centric RSs), marking a significant development in the field. This survey provides the first systematic overview of Data-Centric RSs, covering 1) the foundational concepts of recommendation data and Data-Centric RSs; 2) three primary issues of recommendation data; 3) recent research developed to address these issues; and 4) several potential future directions of Data-Centric RSs.

Longitudinal Control Volumes: A Novel Centralized Estimation and Control Framework for Distributed Multi-Agent Sorting Systems

Centralized control of a multi-agent system improves upon distributed control especially when multiple agents share a common task e.g., sorting different materials in a recycling facility. Traditionally, each agent in a sorting facility is tuned individually which leads to suboptimal performance if one agent is less efficient than the others. Centralized control overcomes this bottleneck by leveraging global system state information, but it can be computationally expensive. In this work, we propose a novel framework called Longitudinal Control Volumes (LCV) to model the flow of material in a recycling facility. We then employ a Kalman Filter that incorporates local measurements of materials into a global estimation of the material flow in the system. We utilize a model predictive control algorithm that optimizes the rate of material flow using the global state estimate in real-time. We show that our proposed framework outperforms distributed control methods by 40-100% in simulation and physical experiments.

TSIS: A Supplementary Algorithm to t-SMILES for Fragment-based Molecular Representation

String-based molecular representations, such as SMILES, are a de facto standard for linearly representing molecular information. However, the must be paired symbols and the parsing algorithm result in long grammatical dependencies, making it difficult for even state-of-the-art deep learning models to accurately comprehend the syntax and semantics. Although DeepSMILES and SELFIES have addressed certain limitations, they still struggle with advanced grammar, which makes some strings difficult to read. This study introduces a supplementary algorithm, TSIS (TSID Simplified), to t-SMILES family. Comparative experiments between TSIS and another fragment-based linear solution, SAFE, indicate that SAFE presents challenges in managing long-term dependencies in grammar. TSIS continues to use the tree defined in t-SMILES as its foundational data structure, which sets it apart from the SAFE model. The performance of TSIS models surpasses that of SAFE models, indicating that the tree structure of the t-SMILES family provides certain advantages.

Data-Driven Prediction of Seismic Intensity Distributions Featuring Hybrid Classification-Regression Models

Earthquakes are among the most immediate and deadly natural disasters that humans face. Accurately forecasting the extent of earthquake damage and assessing potential risks can be instrumental in saving numerous lives. In this study, we developed linear regression models capable of predicting seismic intensity distributions based on earthquake parameters: location, depth, and magnitude. Because it is completely data-driven, it can predict intensity distributions without geographical information. The dataset comprises seismic intensity data from earthquakes that occurred in the vicinity of Japan between 1997 and 2020, specifically containing 1,857 instances of earthquakes with a magnitude of 5.0 or greater, sourced from the Japan Meteorological Agency. We trained both regression and classification models and combined them to take advantage of both to create a hybrid model. The proposed model outperformed commonly used Ground Motion Prediction Equations (GMPEs) in terms of the correlation coefficient, F1 score, and MCC. Furthermore, the proposed model can predict even abnormal seismic intensity distributions, a task at conventional GMPEs often struggle.

Emergency Computing: An Adaptive Collaborative Inference Method Based on Hierarchical Reinforcement Learning

In achieving effective emergency response, the timely acquisition of environmental information, seamless command data transmission, and prompt decision-making are crucial. This necessitates the establishment of a resilient emergency communication dedicated network, capable of providing communication and sensing services even in the absence of basic infrastructure. In this paper, we propose an Emergency Network with Sensing, Communication, Computation, Caching, and Intelligence (E-SC3I). The framework incorporates mechanisms for emergency computing, caching, integrated communication and sensing, and intelligence empowerment. E-SC3I ensures rapid access to a large user base, reliable data transmission over unstable links, and dynamic network deployment in a changing environment. However, these advantages come at the cost of significant computation overhead. Therefore, we specifically concentrate on emergency computing and propose an adaptive collaborative inference method (ACIM) based on hierarchical reinforcement learning. Experimental results demonstrate our method's ability to achieve rapid inference of AI models with constrained computational and communication resources.

Online Transfer Learning for RSV Case Detection

Transfer learning has become a pivotal technique in machine learning, renowned for its effectiveness in various real-world applications. However, a significant challenge arises when applying this approach to sequential epidemiological data, often characterized by a scarcity of labeled information. To address this challenge, we introduce Predictive Volume-Adaptive Weighting (PVAW), a novel online multi-source transfer learning method. PVAW innovatively implements a dynamic weighting mechanism within an ensemble model, allowing for the automatic adjustment of weights based on the relevance and contribution of each source and target model. We demonstrate the effectiveness of PVAW through its application in analyzing Respiratory Syncytial Virus (RSV) data, collected over multiple seasons at the University of Pittsburgh Medical Center. Our method showcases significant improvements in model performance over existing baselines, highlighting the potential of online transfer learning in handling complex, sequential data. This study not only underscores the adaptability and sophistication of transfer learning in healthcare but also sets a new direction for future research in creating advanced predictive models.

Risk-Sensitive Diffusion: Learning the Underlying Distribution from Noisy Samples

While achieving remarkable performances, we show that diffusion models are fragile to the presence of noisy samples, limiting their potential in the vast amount of settings where, unlike image synthesis, we are not blessed with clean data. Motivated by our finding that such fragility originates from the distribution gaps between noisy and clean samples along the diffusion process, we introduce risk-sensitive SDE, a stochastic differential equation that is parameterized by the risk (i.e., data "dirtiness") to adjust the distributions of noisy samples, reducing misguidance while benefiting from their contained information. The optimal expression for risk-sensitive SDE depends on the specific noise distribution, and we derive its parameterizations that minimize the misguidance of noisy samples for both Gaussian and general non-Gaussian perturbations. We conduct extensive experiments on both synthetic and real-world datasets (e.g., medical time series), showing that our model effectively recovers the clean data distribution from noisy samples, significantly outperforming conditional generation baselines.

Affordable Generative Agents

The emergence of large language models (LLMs) has significantly advanced the simulation of believable interactive agents. However, the substantial cost on maintaining the prolonged agent interactions poses challenge over the deployment of believable LLM-based agents. Therefore, in this paper, we develop Affordable Generative Agents (AGA), a framework for enabling the generation of believable and low-cost interactions on both agent-environment and inter-agents levels. Specifically, for agent-environment interactions, we substitute repetitive LLM inferences with learned policies; while for inter-agent interactions, we model the social relationships between agents and compress auxiliary dialogue information. Extensive experiments on multiple environments show the effectiveness and efficiency of our proposed framework. Also, we delve into the mechanisms of emergent believable behaviors lying in LLM agents, demonstrating that agents can only generate finite behaviors in fixed environments, based upon which, we understand ways to facilitate emergent interaction behaviors. Our code is publicly available at: \url{https://github.com/AffordableGenerativeAgents/Affordable-Generative-Agents}.

A Survey on Graph Condensation

Analytics on large-scale graphs have posed significant challenges to computational efficiency and resource requirements. Recently, Graph condensation (GC) has emerged as a solution to address challenges arising from the escalating volume of graph data. The motivation of GC is to reduce the scale of large graphs to smaller ones while preserving essential information for downstream tasks. For a better understanding of GC and to distinguish it from other related topics, we present a formal definition of GC and establish a taxonomy that systematically categorizes existing methods into three types based on its objective, and classify the formulations to generate the condensed graphs into two categories as modifying the original graphs or synthetic completely new ones. Moreover, our survey includes a comprehensive analysis of datasets and evaluation metrics in this field. Finally, we conclude by addressing challenges and limitations, outlining future directions, and offering concise guidelines to inspire future research in this field.