In survival analysis, longitudinal information on the health status of a patient can be used to dynamically update the predicted probability that a patient will experience an event of interest. Traditional approaches to dynamic prediction such as joint models become computationally unfeasible with more than a handful of longitudinal covariates, warranting the development of methods that can handle a larger number of longitudinal covariates. We introduce the R package pencal, which implements a Penalized Regression Calibration approach that makes it possible to handle many longitudinal covariates as predictors of survival. pencal uses mixed-effects models to summarize the trajectories of the longitudinal covariates up to a prespecified landmark time, and a penalized Cox model to predict survival based on both baseline covariates and summary measures of the longitudinal covariates. This article illustrates the structure of the R package, provides a step by step example showing how to estimate PRC, compute dynamic predictions of survival and validate performance, and shows how parallelization can be used to significantly reduce computing time.
Deception and persuasion play a critical role in long-horizon dialogues between multiple parties, especially when the interests, goals, and motivations of the participants are not aligned. Such complex tasks pose challenges for current Large Language Models (LLM) as deception and persuasion can easily mislead them, especially in long-horizon multi-party dialogues. To this end, we explore the game of Avalon: The Resistance, a social deduction game in which players must determine each other's hidden identities to complete their team's objective. We introduce an online testbed and a dataset containing 20 carefully collected and labeled games among human players that exhibit long-horizon deception in a cooperative-competitive setting. We discuss the capabilities of LLMs to utilize deceptive long-horizon conversations between six human players to determine each player's goal and motivation. Particularly, we discuss the multimodal integration of the chat between the players and the game's state that grounds the conversation, providing further insights into the true player identities. We find that even current state-of-the-art LLMs do not reach human performance, making our dataset a compelling benchmark to investigate the decision-making and language-processing capabilities of LLMs. Our dataset and online testbed can be found at our project website: //sstepput.github.io/Avalon-NLU/
Regular monitoring of the primary particles and purity profiles of a drug product during development and manufacturing processes is essential for manufacturers to avoid product variability and contamination. Transmission electron microscopy (TEM) imaging helps manufacturers predict how changes affect particle characteristics and purity for virus-based gene therapy vector products and intermediates. Since intact particles can characterize efficacious products, it is beneficial to automate the detection of intact adenovirus against a non-intact-viral background mixed with debris, broken, and artefact particles. In the presence of such particles, detecting intact adenoviruses becomes more challenging. To overcome the challenge, due to such a presence, we developed a software tool for semi-automatic annotation and segmentation of adenoviruses and a software tool for automatic segmentation and detection of intact adenoviruses in TEM imaging systems. The developed semi-automatic tool exploited conventional image analysis techniques while the automatic tool was built based on convolutional neural networks and image analysis techniques. Our quantitative and qualitative evaluations showed outstanding true positive detection rates compared to false positive and negative rates where adenoviruses were nicely detected without mistaking them for real debris, broken adenoviruses, and/or staining artefacts.
The pursuit of autonomous driving technology hinges on the sophisticated integration of perception, decision-making, and control systems. Traditional approaches, both data-driven and rule-based, have been hindered by their inability to grasp the nuance of complex driving environments and the intentions of other road users. This has been a significant bottleneck, particularly in the development of common sense reasoning and nuanced scene understanding necessary for safe and reliable autonomous driving. The advent of Visual Language Models (VLM) represents a novel frontier in realizing fully autonomous vehicle driving. This report provides an exhaustive evaluation of the latest state-of-the-art VLM, \modelnamefull, and its application in autonomous driving scenarios. We explore the model's abilities to understand and reason about driving scenes, make decisions, and ultimately act in the capacity of a driver. Our comprehensive tests span from basic scene recognition to complex causal reasoning and real-time decision-making under varying conditions. Our findings reveal that \modelname demonstrates superior performance in scene understanding and causal reasoning compared to existing autonomous systems. It showcases the potential to handle out-of-distribution scenarios, recognize intentions, and make informed decisions in real driving contexts. However, challenges remain, particularly in direction discernment, traffic light recognition, vision grounding, and spatial reasoning tasks. These limitations underscore the need for further research and development. Project is now available on GitHub for interested parties to access and utilize: \url{//github.com/PJLab-ADG/GPT4V-AD-Exploration}
Summaries of medical text shall be faithful by being consistent and factual with source inputs, which is an important but understudied topic for safety and efficiency in healthcare. In this paper, we investigate and improve faithfulness in summarization on a broad range of medical summarization tasks. Our investigation reveals that current summarization models often produce unfaithful outputs for medical input text. We then introduce FaMeSumm, a framework to improve faithfulness by fine-tuning pre-trained language models based on medical knowledge. FaMeSumm performs contrastive learning on designed sets of faithful and unfaithful summaries, and it incorporates medical terms and their contexts to encourage faithful generation of medical terms. We conduct comprehensive experiments on three datasets in two languages: health question and radiology report summarization datasets in English, and a patient-doctor dialogue dataset in Chinese. Results demonstrate that FaMeSumm is flexible and effective by delivering consistent improvements over mainstream language models such as BART, T5, mT5, and PEGASUS, yielding state-of-the-art performances on metrics for faithfulness and general quality. Human evaluation by doctors also shows that FaMeSumm generates more faithful outputs. Our code is available at //github.com/psunlpgroup/FaMeSumm .
This paper establishes the nearly optimal rate of approximation for deep neural networks (DNNs) when applied to Korobov functions, effectively overcoming the curse of dimensionality. The approximation results presented in this paper are measured with respect to $L_p$ norms and $H^1$ norms. Our achieved approximation rate demonstrates a remarkable "super-convergence" rate, outperforming traditional methods and any continuous function approximator. These results are non-asymptotic, providing error bounds that consider both the width and depth of the networks simultaneously.
Recently, graph neural networks have been gaining a lot of attention to simulate dynamical systems due to their inductive nature leading to zero-shot generalizability. Similarly, physics-informed inductive biases in deep-learning frameworks have been shown to give superior performance in learning the dynamics of physical systems. There is a growing volume of literature that attempts to combine these two approaches. Here, we evaluate the performance of thirteen different graph neural networks, namely, Hamiltonian and Lagrangian graph neural networks, graph neural ODE, and their variants with explicit constraints and different architectures. We briefly explain the theoretical formulation highlighting the similarities and differences in the inductive biases and graph architecture of these systems. We evaluate these models on spring, pendulum, gravitational, and 3D deformable solid systems to compare the performance in terms of rollout error, conserved quantities such as energy and momentum, and generalizability to unseen system sizes. Our study demonstrates that GNNs with additional inductive biases, such as explicit constraints and decoupling of kinetic and potential energies, exhibit significantly enhanced performance. Further, all the physics-informed GNNs exhibit zero-shot generalizability to system sizes an order of magnitude larger than the training system, thus providing a promising route to simulate large-scale realistic systems.
Understanding causality helps to structure interventions to achieve specific goals and enables predictions under interventions. With the growing importance of learning causal relationships, causal discovery tasks have transitioned from using traditional methods to infer potential causal structures from observational data to the field of pattern recognition involved in deep learning. The rapid accumulation of massive data promotes the emergence of causal search methods with brilliant scalability. Existing summaries of causal discovery methods mainly focus on traditional methods based on constraints, scores and FCMs, there is a lack of perfect sorting and elaboration for deep learning-based methods, also lacking some considers and exploration of causal discovery methods from the perspective of variable paradigms. Therefore, we divide the possible causal discovery tasks into three types according to the variable paradigm and give the definitions of the three tasks respectively, define and instantiate the relevant datasets for each task and the final causal model constructed at the same time, then reviews the main existing causal discovery methods for different tasks. Finally, we propose some roadmaps from different perspectives for the current research gaps in the field of causal discovery and point out future research directions.
Graph neural networks generalize conventional neural networks to graph-structured data and have received widespread attention due to their impressive representation ability. In spite of the remarkable achievements, the performance of Euclidean models in graph-related learning is still bounded and limited by the representation ability of Euclidean geometry, especially for datasets with highly non-Euclidean latent anatomy. Recently, hyperbolic space has gained increasing popularity in processing graph data with tree-like structure and power-law distribution, owing to its exponential growth property. In this survey, we comprehensively revisit the technical details of the current hyperbolic graph neural networks, unifying them into a general framework and summarizing the variants of each component. More importantly, we present various HGNN-related applications. Last, we also identify several challenges, which potentially serve as guidelines for further flourishing the achievements of graph learning in hyperbolic spaces.
Deep neural networks have revolutionized many machine learning tasks in power systems, ranging from pattern recognition to signal processing. The data in these tasks is typically represented in Euclidean domains. Nevertheless, there is an increasing number of applications in power systems, where data are collected from non-Euclidean domains and represented as the graph-structured data with high dimensional features and interdependency among nodes. The complexity of graph-structured data has brought significant challenges to the existing deep neural networks defined in Euclidean domains. Recently, many studies on extending deep neural networks for graph-structured data in power systems have emerged. In this paper, a comprehensive overview of graph neural networks (GNNs) in power systems is proposed. Specifically, several classical paradigms of GNNs structures (e.g., graph convolutional networks, graph recurrent neural networks, graph attention networks, graph generative networks, spatial-temporal graph convolutional networks, and hybrid forms of GNNs) are summarized, and key applications in power systems such as fault diagnosis, power prediction, power flow calculation, and data generation are reviewed in detail. Furthermore, main issues and some research trends about the applications of GNNs in power systems are discussed.
We propose a novel attention gate (AG) model for medical imaging that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules of cascaded convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN architectures such as the U-Net model with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed Attention U-Net architecture is evaluated on two large CT abdominal datasets for multi-class image segmentation. Experimental results show that AGs consistently improve the prediction performance of U-Net across different datasets and training sizes while preserving computational efficiency. The code for the proposed architecture is publicly available.