Purpose: This study aims to use a large language model (LLM) to automate the generation of summaries from the CT simulation orders and evaluate its performance. Materials and Methods: A total of 607 CT simulation orders for patients were collected from the Aria database at our institution. A locally hosted Llama 3.1 405B model, accessed via the Application Programming Interface (API) service, was used to extract keywords from the CT simulation orders and generate summaries. The downloaded CT simulation orders were categorized into seven groups based on treatment modalities and disease sites. For each group, a customized instruction prompt was developed collaboratively with therapists to guide the Llama 3.1 405B model in generating summaries. The ground truth for the corresponding summaries was manually derived by carefully reviewing each CT simulation order and subsequently verified by therapists. The accuracy of the LLM-generated summaries was evaluated by therapists using the verified ground truth as a reference. Results: About 98% of the LLM-generated summaries aligned with the manually generated ground truth in terms of accuracy. Our evaluations showed an improved consistency in format and enhanced readability of the LLM-generated summaries compared to the corresponding therapists-generated summaries. This automated approach demonstrated a consistent performance across all groups, regardless of modality or disease site. Conclusions: This study demonstrated the high precision and consistency of the Llama 3.1 405B model in extracting keywords and summarizing CT simulation orders, suggesting that LLMs have great potential to help with this task, reduce the workload of therapists and improve workflow efficiency.

Black-box textual adversarial attacks are challenging due to the lack of model information and the discrete, non-differentiable nature of text. Existing methods often lack versatility for attacking different models, suffer from limited attacking performance due to the inefficient optimization with word saliency ranking, and frequently sacrifice semantic integrity to achieve better attack outcomes. This paper introduces a novel approach to textual adversarial attacks, which we call Cross-Entropy Attacks (CEA), that uses Cross-Entropy optimization to address the above issues. Our CEA approach defines adversarial objectives for both soft-label and hard-label settings and employs CE optimization to identify optimal replacements. Through extensive experiments on document classification and language translation problems, we demonstrate that our attack method excels in terms of attacking performance, imperceptibility, and sentence quality.

With the rapid development of the combination of control technology and the Artificial Intelligence(AI) field, the intelligent control of mobile robots and their applications like industrial manufacturing, logistics sorting, etc. in this field is evolving towards self-learning and adaptation [1]. For example, intelligent control of mobile robots in complex environments can autonomously move in various environments without external assistance [2], which requires navigation [3] and motion planning-related technologies in practical applications. Motion planning is divided into path planning and trajectory planning [4]. Path planning often serves as the crucial step of trajectory planning, its goal is to find the optimal path from a starting point to an endpoint in a given environment. However, path planning in dynamic environments is more practical and challenging [5].

With the rapid advancements in large language model (LLM) technology and the emergence of bioinformatics-specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications. This survey aims to address this need by providing a thorough review of BioLMs, focusing on their evolution, classification, and distinguishing features, alongside a detailed examination of training methodologies, datasets, and evaluation frameworks. We explore the wide-ranging applications of BioLMs in critical areas such as disease diagnosis, drug discovery, and vaccine development, highlighting their impact and transformative potential in bioinformatics. We identify key challenges and limitations inherent in BioLMs, including data privacy and security concerns, interpretability issues, biases in training data and model outputs, and domain adaptation complexities. Finally, we highlight emerging trends and future directions, offering valuable insights to guide researchers and clinicians toward advancing BioLMs for increasingly sophisticated biological and clinical applications.

ChartQA presents significant challenges due to the complex distribution of chart elements and the implicit patterns embedded within the underlying data. In this chapter, we have developed a joint multimodal scene graph for charts, explicitly representing the relationships between chart elements and their associated patterns. Our proposed multimodal scene graph consists of two components: a visual graph and a textual graph, each designed to capture the structural and semantic information within the chart. To unify representations across these different modalities, we introduce a multimodal graph contrastive learning approach that learns unified representations by maximizing similarity between nodes representing the same object across multimodal graphs. The learned graph representations can be seamlessly incorporated into a transformer decoder as a soft prompt. Additionally, given the growing need for Multimodal Large Language Models (MLLMs) in zero-shot scenarios, we have designed Chain-of-Thought (CoT) prompts for MLLMs to reduce hallucinations. We tested both methods on public benchmarks such as ChartQA, OpenCQA, and ChartX, demonstrating improved performance and validating the effectiveness of our proposed methods.

Large language models (LLMs) excel at few-shot in-context learning (ICL) without requiring parameter updates. However, as the number of ICL demonstrations increases from a few to many, performance tends to plateau and eventually decline. We identify two primary causes for this trend: the suboptimal negative log-likelihood (NLL) optimization objective and the incremental data noise. To address these issues, we introduce DrICL, a novel optimization method that enhances model performance through Differentiated Learning and advantage-based Reweighting objectives. Globally, DrICL utilizes differentiated learning to optimize the NLL objective, ensuring that many-shot performance surpasses zero-shot levels. Locally, it dynamically adjusts the weighting of many-shot demonstrations by leveraging cumulative advantages inspired by reinforcement learning, thereby improving generalization. This approach allows the model to handle varying numbers of shots effectively, mitigating the impact of noisy data. Recognizing the lack of multi-task datasets with diverse many-shot distributions, we develop the Many-Shot ICL Benchmark (ICL-50)-a large-scale benchmark of 50 tasks that cover shot numbers from 1 to 350 within sequences of up to 8,000 tokens-for fine-tuning purposes. ICL-50 facilitates the evaluation of many-shot ICL strategies across seven prominent NLP tasks and 50 distinct datasets. Experimental results demonstrate that LLMs enhanced with DrICL achieve significant improvements in many-shot setups across various tasks, including both in-domain and out-of-domain scenarios. We release the code and benchmark dataset hoping to facilitate further research in many-shot ICL.

Question answering over temporal knowledge graphs (TKGs) is crucial for understanding evolving facts and relationships, yet its development is hindered by limited datasets and difficulties in generating custom QA pairs. We propose a novel categorization framework based on timeline-context relationships, along with \textbf{TimelineKGQA}, a universal temporal QA generator applicable to any TKGs. The code is available at: \url{https://github.com/PascalSun/TimelineKGQA} as an open source Python package.

Bayesian Optimization (BO) is a sample-efficient black-box optimizer commonly used in search spaces where hyperparameters are independent. However, in many practical AutoML scenarios, there will be dependencies among hyperparameters, forming a conditional search space, which can be partitioned into structurally distinct subspaces. The structure and dimensionality of hyperparameter configurations vary across these subspaces, challenging the application of BO. Some previous BO works have proposed solutions to develop multiple Gaussian Process models in these subspaces. However, these approaches tend to be inefficient as they require a substantial number of observations to guarantee each GP's performance and cannot capture relationships between hyperparameters across different subspaces. To address these issues, this paper proposes a novel approach to model the response surfaces of all subspaces in one, which can model the relationships between hyperparameters elegantly via a self-attention mechanism. Concretely, we design a structure-aware hyperparameter embedding to preserve the structural information. Then, we introduce an attention-based deep feature extractor, capable of projecting configurations with different structures from various subspaces into a unified feature space, where the response surfaces can be formulated using a single standard Gaussian Process. The empirical results on a simulation function, various real-world tasks, and HPO-B benchmark demonstrate that our proposed approach improves the efficacy and efficiency of BO within conditional search spaces.

Purpose: We present an updated study evaluating the performance of large language models (LLMs) in answering radiation oncology physics questions, focusing on the recently released models. Methods: A set of 100 multiple choice radiation oncology physics questions, previously created by a well-experienced physicist, was used for this study. The answer options of the questions were randomly shuffled to create "new" exam sets. Five LLMs (OpenAI o1-preview, GPT-4o, LLaMA 3.1 (405B), Gemini 1.5 Pro, and Claude 3.5 Sonnet) with the versions released before September 30, 2024, were queried using these new exam sets. To evaluate their deductive reasoning capabilities, the correct answers in the questions were replaced with "None of the above." Then, the explaining-first and step-by-step instruction prompts were used to test if this strategy improved their reasoning capabilities. The performance of the LLMs was compared with the answers from medical physicists. Results: All models demonstrated expert-level performance on these questions, with o1-preview even surpassing medical physicists with a majority vote. When replacing the correct answers with "None of the above," all models exhibited a considerable decline in performance, suggesting room for improvement. The explaining-first and step-by-step instruction prompts helped enhance the reasoning capabilities of the LLaMA 3.1 (405B), Gemini 1.5 Pro, and Claude 3.5 Sonnet models. Conclusion: These recently released LLMs demonstrated expert-level performance in answering radiation oncology physics questions, exhibiting great potential to assist in radiation oncology physics training and education.

Low-rank adaptation (LoRA) reduces the computational and memory demands of fine-tuning large language models (LLMs) by approximating updates with low-rank matrices. However, low-rank approximation in two-dimensional space fails to capture high-dimensional structures within the target matrix. Recently, tensor decomposition methods have been explored for fine-tuning LLMs, leveraging their ability to extract structured information. Yet, these approaches primarily rely on random initialization, and the impact of initialization on tensor adaptation remains underexplored. In this paper, we reveal that random initialization significantly diverges from the validation loss achieved by full fine-tuning. To address this, we propose Weight-Decomposed Tensor Adaptation (DoTA), which leverages the Matrix Product Operator (MPO) decomposition of pre-trained weights for effective initialization in fine-tuning LLMs. Additionally, we introduce QDoTA, a quantized version of DoTA designed for 4-bit quantization. Experiments on commonsense and arithmetic reasoning tasks show that DoTA outperforms random initialization methods with fewer parameters. QDoTA further reduces memory consumption and achieves comparable performance to DoTA on commonsense reasoning tasks. We will release our code to support future research.