TREB, a novel tabular imputation framework utilizing BERT, introduces a groundbreaking approach for handling missing values in tabular data. Unlike traditional methods that often overlook the specific demands of imputation, TREB leverages the robust capabilities of BERT to address this critical task. While many BERT-based approaches for tabular data have emerged, they frequently under-utilize the language model's full potential. To rectify this, TREB employs a BERT-based model fine-tuned specifically for the task of imputing real-valued continuous numbers in tabular datasets. The paper comprehensively addresses the unique challenges posed by tabular data imputation, emphasizing the importance of context-based interconnections. The effectiveness of TREB is validated through rigorous evaluation using the California Housing dataset. The results demonstrate its ability to preserve feature interrelationships and accurately impute missing values. Moreover, the authors shed light on the computational efficiency and environmental impact of TREB, quantifying the floating-point operations (FLOPs) and carbon footprint associated with its training and deployment.

Retrieval Augmented Generation (RAG), a paradigm that integrates external contextual information with large language models (LLMs) to enhance factual accuracy and relevance, has emerged as a pivotal area in generative AI. The LLMs used in RAG applications are required to faithfully and completely comprehend the provided context and users' questions, avoid hallucination, handle unanswerable, counterfactual or otherwise low-quality and irrelevant contexts, perform complex multi-hop reasoning and produce reliable citations. In this paper, we introduce SFR-RAG, a small LLM that is instruction-tuned with an emphasis on context-grounded generation and hallucination minimization. We also present ContextualBench, a new evaluation framework compiling multiple popular and diverse RAG benchmarks, such as HotpotQA and TriviaQA, with consistent RAG settings to ensure reproducibility and consistency in model assessments. Experimental results demonstrate that our SFR-RAG-9B model outperforms leading baselines such as Command-R+ (104B) and GPT-4o, achieving state-of-the-art results in 3 out of 7 benchmarks in ContextualBench with significantly fewer parameters. The model is also shown to be resilient to alteration in the contextual information and behave appropriately when relevant context is removed. Additionally, the SFR-RAG model maintains competitive performance in general instruction-following tasks and function-calling capabilities.

This paper investigates gender bias in Large Language Model (LLM)-generated teacher evaluations in higher education setting, focusing on evaluations produced by GPT-4 across six academic subjects. By applying a comprehensive analytical framework that includes Odds Ratio (OR) analysis, Word Embedding Association Test (WEAT), sentiment analysis, and contextual analysis, this paper identified patterns of gender-associated language reflecting societal stereotypes. Specifically, words related to approachability and support were used more frequently for female instructors, while words related to entertainment were predominantly used for male instructors, aligning with the concepts of communal and agentic behaviors. The study also found moderate to strong associations between male salient adjectives and male names, though career and family words did not distinctly capture gender biases. These findings align with prior research on societal norms and stereotypes, reinforcing the notion that LLM-generated text reflects existing biases.

Recent developments in language models have created new opportunities in air traffic control studies. The current focus is primarily on text and language-based use cases. However, these language models may offer a higher potential impact in the air traffic control domain, thanks to their ability to interact with air traffic environments in an embodied agent form. They also provide a language-like reasoning capability to explain their decisions, which has been a significant roadblock for the implementation of automatic air traffic control. This paper investigates the application of a language model-based agent with function-calling and learning capabilities to resolve air traffic conflicts without human intervention. The main components of this research are foundational large language models, tools that allow the agent to interact with the simulator, and a new concept, the experience library. An innovative part of this research, the experience library, is a vector database that stores synthesized knowledge that agents have learned from interactions with the simulations and language models. To evaluate the performance of our language model-based agent, both open-source and closed-source models were tested. The results of our study reveal significant differences in performance across various configurations of the language model-based agents. The best-performing configuration was able to solve almost all 120 but one imminent conflict scenarios, including up to four aircraft at the same time. Most importantly, the agents are able to provide human-level text explanations on traffic situations and conflict resolution strategies.

As large language models achieve increasingly impressive results, questions arise about whether such performance is from generalizability or mere data memorization. Thus, numerous data contamination detection methods have been proposed. However, these approaches are often validated with traditional benchmarks and early-stage LLMs, leaving uncertainty about their effectiveness when evaluating state-of-the-art LLMs on the contamination of more challenging benchmarks. To address this gap and provide a dual investigation of SOTA LLM contamination status and detection method robustness, we evaluate five contamination detection approaches with four state-of-the-art LLMs across eight challenging datasets often used in modern LLM evaluation. Our analysis reveals that (1) Current methods have non-trivial limitations in their assumptions and practical applications; (2) Notable difficulties exist in detecting contamination introduced during instruction fine-tuning with answer augmentation; and (3) Limited consistencies between SOTA contamination detection techniques. These findings highlight the complexity of contamination detection in advanced LLMs and the urgent need for further research on robust and generalizable contamination evaluation. Our code is available at https://github.com/vsamuel2003/data-contamination.

This paper presents RNAdiffusion, a latent diffusion model for generating and optimizing discrete RNA sequences. RNA is a particularly dynamic and versatile molecule in biological processes. RNA sequences exhibit high variability and diversity, characterized by their variable lengths, flexible three-dimensional structures, and diverse functions. We utilize pretrained BERT-type models to encode raw RNAs into token-level biologically meaningful representations. A Q-Former is employed to compress these representations into a fixed-length set of latent vectors, with an autoregressive decoder trained to reconstruct RNA sequences from these latent variables. We then develop a continuous diffusion model within this latent space. To enable optimization, we train reward networks to estimate functional properties of RNA from the latent variables. We employ gradient-based guidance during the backward diffusion process, aiming to generate RNA sequences that are optimized for higher rewards. Empirical experiments confirm that RNAdiffusion generates non-coding RNAs that align with natural distributions across various biological indicators. We fine-tuned the diffusion model on untranslated regions (UTRs) of mRNA and optimize sample sequences for protein translation efficiencies. Our guided diffusion model effectively generates diverse UTR sequences with high Mean Ribosome Loading (MRL) and Translation Efficiency (TE), surpassing baselines. These results hold promise for studies on RNA sequence-function relationships, protein synthesis, and enhancing therapeutic RNA design.

The advent of foundation models (FMs) such as large language models (LLMs) has led to a cultural shift in data science, both in medicine and beyond. This shift involves moving away from specialized predictive models trained for specific, well-defined domain questions to generalist FMs pre-trained on vast amounts of unstructured data, which can then be adapted to various clinical tasks and questions. As a result, the standard data science workflow in medicine has been fundamentally altered; the foundation model lifecycle (FMLC) now includes distinct upstream and downstream processes, in which computational resources, model and data access, and decision-making power are distributed among multiple stakeholders. At their core, FMs are fundamentally statistical models, and this new workflow challenges the principles of Veridical Data Science (VDS), hindering the rigorous statistical analysis expected in transparent and scientifically reproducible data science practices. We critically examine the medical FMLC in light of the core principles of VDS: predictability, computability, and stability (PCS), and explain how it deviates from the standard data science workflow. Finally, we propose recommendations for a reimagined medical FMLC that expands and refines the PCS principles for VDS including considering the computational and accessibility constraints inherent to FMs.

Pre-trained large language models(LLMs) have attracted increasing attention in biomedical domains due to their success in natural language processing. However, the complex traits and heterogeneity of multi-sources genomics data pose significant challenges when adapting these models to the bioinformatics and biomedical field. To address these challenges, we present GP-GPT, the first specialized large language model for genetic-phenotype knowledge representation and genomics relation analysis. Our model is fine-tuned in two stages on a comprehensive corpus composed of over 3,000,000 terms in genomics, proteomics, and medical genetics, derived from multiple large-scale validated datasets and scientific publications. GP-GPT demonstrates proficiency in accurately retrieving medical genetics information and performing common genomics analysis tasks, such as genomics information retrieval and relationship determination. Comparative experiments across domain-specific tasks reveal that GP-GPT outperforms state-of-the-art LLMs, including Llama2, Llama3 and GPT-4. These results highlight GP-GPT's potential to enhance genetic disease relation research and facilitate accurate and efficient analysis in the fields of genomics and medical genetics. Our investigation demonstrated the subtle changes of bio-factor entities' representations in the GP-GPT, which suggested the opportunities for the application of LLMs to advancing gene-phenotype research.

The rapid development of LLMs brings both convenience and potential threats. As costumed and private LLMs are widely applied, model copyright protection has become important. Text watermarking is emerging as a promising solution to AI-generated text detection and model protection issues. However, current text watermarks have largely ignored the critical need for injecting different watermarks for different users, which could help attribute the watermark to a specific individual. In this paper, we explore the personalized text watermarking scheme for LLM copyright protection and other scenarios, ensuring accountability and traceability in content generation. Specifically, we propose a novel text watermarking method PersonaMark that utilizes sentence structure as the hidden medium for the watermark information and optimizes the sentence-level generation algorithm to minimize disruption to the model's natural generation process. By employing a personalized hashing function to inject unique watermark signals for different users, personalized watermarked text can be obtained. Since our approach performs on sentence level instead of token probability, the text quality is highly preserved. The injection process of unique watermark signals for different users is time-efficient for a large number of users with the designed multi-user hashing function. As far as we know, we achieved personalized text watermarking for the first time through this. We conduct an extensive evaluation of four different LLMs in terms of perplexity, sentiment polarity, alignment, readability, etc. The results demonstrate that our method maintains performance with minimal perturbation to the model's behavior, allows for unbiased insertion of watermark information, and exhibits strong watermark recognition capabilities.

Recent advancements in event-based zero-shot object recognition have demonstrated promising results. However, these methods heavily depend on extensive training and are inherently constrained by the characteristics of CLIP. To the best of our knowledge, this research is the first study to explore the understanding capabilities of large language models (LLMs) for event-based visual content. We demonstrate that LLMs can achieve event-based object recognition without additional training or fine-tuning in conjunction with CLIP, effectively enabling pure zero-shot event-based recognition. Particularly, we evaluate the ability of GPT-4o / 4turbo and two other open-source LLMs to directly recognize event-based visual content. Extensive experiments are conducted across three benchmark datasets, systematically assessing the recognition accuracy of these models. The results show that LLMs, especially when enhanced with well-designed prompts, significantly improve event-based zero-shot recognition performance. Notably, GPT-4o outperforms the compared models and exceeds the recognition accuracy of state-of-the-art event-based zero-shot methods on N-ImageNet by five orders of magnitude. The implementation of this paper is available at \url{https://github.com/ChrisYu-Zz/Pure-event-based-recognition-based-LLM}.