Deep learning (DL) and machine learning (ML) models have shown promise in drug response prediction (DRP), yet their ability to generalize across datasets remains an open question, raising concerns about their real-world applicability. Due to the lack of standardized benchmarking approaches, model evaluations and comparisons often rely on inconsistent datasets and evaluation criteria, making it difficult to assess true predictive capabilities. In this work, we introduce a benchmarking framework for evaluating cross-dataset prediction generalization in DRP models. Our framework incorporates five publicly available drug screening datasets, six standardized DRP models, and a scalable workflow for systematic evaluation. To assess model generalization, we introduce a set of evaluation metrics that quantify both absolute performance (e.g., predictive accuracy across datasets) and relative performance (e.g., performance drop compared to within-dataset results), enabling a more comprehensive assessment of model transferability. Our results reveal substantial performance drops when models are tested on unseen datasets, underscoring the importance of rigorous generalization assessments. While several models demonstrate relatively strong cross-dataset generalization, no single model consistently outperforms across all datasets. Furthermore, we identify CTRPv2 as the most effective source dataset for training, yielding higher generalization scores across target datasets. By sharing this standardized evaluation framework with the community, our study aims to establish a rigorous foundation for model comparison, and accelerate the development of robust DRP models for real-world applications.

The rapid development of artificial intelligence has brought about substantial advancements in the field. One promising direction is the integration of Large Language Models (LLMs) with structured knowledge-based systems. This approach aims to enhance AI capabilities by combining the generative language understanding of LLMs with the precise knowledge representation of structured systems. This survey explores the synergy between LLMs and knowledge bases, focusing on real-world applications and addressing associated technical, operational, and ethical challenges. Through a comprehensive literature review, the study identifies critical issues and evaluates existing solutions. The paper highlights the benefits of integrating generative AI with knowledge bases, including improved data contextualization, enhanced model accuracy, and better utilization of knowledge resources. The findings provide a detailed overview of the current state of research, identify key gaps, and offer actionable recommendations. These insights contribute to advancing AI technologies and support their practical deployment across various sectors.

Autonomous vehicles have been rapidly developed as demand that provides safety and efficiency in transportation systems. As autonomous vehicles are designed based on open-source operating and computing systems, there are numerous resources aimed at building an operating platform composed of Ubuntu, Autoware, and Robot Operating System (ROS). However, no explicit guidelines exist to help scholars perform trouble-shooting due to incompatibility between the Autoware platform and Ubuntu operating systems installed in autonomous driving systems-equipped vehicles (i.e., Chrysler Pacifica). The paper presents an overview of integrating the Autoware platform into the autonomous vehicle's interface based on lessons learned from trouble-shooting processes for resolving incompatible issues. The trouble-shooting processes are presented based on resolving the incompatibility and integration issues of Ubuntu 20.04, Autoware.AI, and ROS Noetic software installed in an autonomous driving systems-equipped vehicle. Specifically, the paper focused on common incompatibility issues and code-solving protocols involving Python compatibility, Compute Unified Device Architecture (CUDA) installation, Autoware installation, and simulation in Autoware.AI. The objective of the paper is to provide an explicit and detail-oriented presentation to showcase how to address incompatibility issues among an autonomous vehicle's operating interference. The lessons and experience presented in the paper will be useful for researchers who encountered similar issues and could follow up by performing trouble-shooting activities and implementing ADS-related projects in the Ubuntu, Autoware, and ROS operating systems.

The year 2023 marked a significant surge in the exploration of applying large language model (LLM) chatbots, notably ChatGPT, across various disciplines. We surveyed the applications of ChatGPT in bioinformatics and biomedical informatics throughout the year, covering omics, genetics, biomedical text mining, drug discovery, biomedical image understanding, bioinformatics programming, and bioinformatics education. Our survey delineates the current strengths and limitations of this chatbot in bioinformatics and offers insights into potential avenues for future developments.

Pursuit-evasion games (PEGs) model interactions between a team of pursuers and an evader in graph-based environments such as urban street networks. Recent advancements have demonstrated the effectiveness of the pre-training and fine-tuning paradigm in PSRO to improve scalability in solving large-scale PEGs. However, these methods primarily focus on specific PEGs with fixed initial conditions that may vary substantially in real-world scenarios, which significantly hinders the applicability of the traditional methods. To address this issue, we introduce Grasper, a GeneRAlist purSuer for Pursuit-Evasion pRoblems, capable of efficiently generating pursuer policies tailored to specific PEGs. Our contributions are threefold: First, we present a novel architecture that offers high-quality solutions for diverse PEGs, comprising critical components such as (i) a graph neural network (GNN) to encode PEGs into hidden vectors, and (ii) a hypernetwork to generate pursuer policies based on these hidden vectors. As a second contribution, we develop an efficient three-stage training method involving (i) a pre-pretraining stage for learning robust PEG representations through self-supervised graph learning techniques like GraphMAE, (ii) a pre-training stage utilizing heuristic-guided multi-task pre-training (HMP) where heuristic-derived reference policies (e.g., through Dijkstra's algorithm) regularize pursuer policies, and (iii) a fine-tuning stage that employs PSRO to generate pursuer policies on designated PEGs. Finally, we perform extensive experiments on synthetic and real-world maps, showcasing Grasper's significant superiority over baselines in terms of solution quality and generalizability. We demonstrate that Grasper provides a versatile approach for solving pursuit-evasion problems across a broad range of scenarios, enabling practical deployment in real-world situations.

Policy-Space Response Oracles (PSRO) as a general algorithmic framework has achieved state-of-the-art performance in learning equilibrium policies of two-player zero-sum games. However, the hand-crafted hyperparameter value selection in most of the existing works requires extensive domain knowledge, forming the main barrier to applying PSRO to different games. In this work, we make the first attempt to investigate the possibility of self-adaptively determining the optimal hyperparameter values in the PSRO framework. Our contributions are three-fold: (1) Using several hyperparameters, we propose a parametric PSRO that unifies the gradient descent ascent (GDA) and different PSRO variants. (2) We propose the self-adaptive PSRO (SPSRO) by casting the hyperparameter value selection of the parametric PSRO as a hyperparameter optimization (HPO) problem where our objective is to learn an HPO policy that can self-adaptively determine the optimal hyperparameter values during the running of the parametric PSRO. (3) To overcome the poor performance of online HPO methods, we propose a novel offline HPO approach to optimize the HPO policy based on the Transformer architecture. Experiments on various two-player zero-sum games demonstrate the superiority of SPSRO over different baselines.

E-health allows smart devices and medical institutions to collaboratively collect patients' data, which is trained by Artificial Intelligence (AI) technologies to help doctors make diagnosis. By allowing multiple devices to train models collaboratively, federated learning is a promising solution to address the communication and privacy issues in e-health. However, applying federated learning in e-health faces many challenges. First, medical data is both horizontally and vertically partitioned. Since single Horizontal Federated Learning (HFL) or Vertical Federated Learning (VFL) techniques cannot deal with both types of data partitioning, directly applying them may consume excessive communication cost due to transmitting a part of raw data when requiring high modeling accuracy. Second, a naive combination of HFL and VFL has limitations including low training efficiency, unsound convergence analysis, and lack of parameter tuning strategies. In this paper, we provide a thorough study on an effective integration of HFL and VFL, to achieve communication efficiency and overcome the above limitations when data is both horizontally and vertically partitioned. Specifically, we propose a hybrid federated learning framework with one intermediate result exchange and two aggregation phases. Based on this framework, we develop a Hybrid Stochastic Gradient Descent (HSGD) algorithm to train models. Then, we theoretically analyze the convergence upper bound of the proposed algorithm. Using the convergence results, we design adaptive strategies to adjust the training parameters and shrink the size of transmitted data. Experimental results validate that the proposed HSGD algorithm can achieve the desired accuracy while reducing communication cost, and they also verify the effectiveness of the adaptive strategies.

The latest development in artificial intelligence (AI), chatbots, the product of generative AI, has captivated the public in the last two years. But it similarly poses an unprecedented challenge and can have potentially unwanted effects on our lives. OpenAI released the chatbot ChatGPT on November 30, 2022. The overwhelming response of the public towards ChatGPT usage pushed Google to release Bard, ChatGPT's rival, and Microsoft to release AI-powered Bing. But the recent GPT-4 topped the list as it has more capabilities than any other existing chatbot. Being LLM-based, these chatbots create synthetic media with the intention of creating better content, enhanced quality, or professional voices. The capabilities of such chatbots raise questions on the ethical use of AI. In the meantime, deepfakes, which are high-quality AI-generated fake videos, have been circulating online. Synthetically generated deepfake videos have exceeded acceptable limits in terms of reality distortion.

Process-Based Modeling (PBM) and Machine Learning (ML) are often perceived as distinct paradigms in the geosciences. Here we present differentiable geoscientific modeling as a powerful pathway toward dissolving the perceived barrier between them and ushering in a paradigm shift. For decades, PBM offered benefits in interpretability and physical consistency but struggled to efficiently leverage large datasets. ML methods, especially deep networks, presented strong predictive skills yet lacked the ability to answer specific scientific questions. While various methods have been proposed for ML-physics integration, an important underlying theme -- differentiable modeling -- is not sufficiently recognized. Here we outline the concepts, applicability, and significance of differentiable geoscientific modeling (DG). "Differentiable" refers to accurately and efficiently calculating gradients with respect to model variables, critically enabling the learning of high-dimensional unknown relationships. DG refers to a range of methods connecting varying amounts of prior knowledge to neural networks and training them together, capturing a different scope than physics-guided machine learning and emphasizing first principles. Preliminary evidence suggests DG offers better interpretability and causality than ML, improved generalizability and extrapolation capability, and strong potential for knowledge discovery, while approaching the performance of purely data-driven ML. DG models require less training data while scaling favorably in performance and efficiency with increasing amounts of data. With DG, geoscientists may be better able to frame and investigate questions, test hypotheses, and discover unrecognized linkages.

Abstract: Conventional training methods for artificial neural network (ANN) models never achieve zero error rate systematically for large data. A new training method consists of three steps: first create an auxiliary data from conventionally trained parameters which correspond exactly to a global minimum for the loss function of the cloned data; second create a one-parameter homotopy (hybrid) of the auxiliary data and the original data; and third train the model for the hybrid data iteratively from the auxiliary data end of the homotopy parameter to the original data end while maintaining the zero-error training rate at every iteration. This continuation method is guaranteed to converge numerically by a theorem which converts the ANN training problem into a continuation problem for fixed points of a parameterized transformation in the training parameter space to which the Uniform Contraction Mapping Theorem from dynamical systems applies. By definition, to train an ANN model is to find the global minimum of its loss function with the 100% accuracy rate. The theoretical solution to this problem was established by [3, 7] in 1989 for finite points classification with sufficiently many parameters.