Foundation models (aka large language models) such as BERT [1] and GPT [2], have demonstrated their stellar performance in learning the complex characteristics and structures of natural languages, making them well-suited for a variety of subsequent applications, such as sentiment analysis, text generation, and translation [3]. These foundation models have recently been adapted to analyze biological sequences as their deep structure and large-scale parameters are well suited for dealing with the intricacy of biological sequences and structures [4, 5, 6, 7, 8, 9, 10, 11]. Biological sequences composed of nucleotides like DNA and RNA, as well as amino acids forming peptides and proteins, are regarded as natural languages of life and can be effectively leveraged by using the technology of foundation models to uncover the underlying patterns and functions they encode [12]. Typically, these foundation models build robust feature representations from biological sequences through a process known as pretraining. Encoder-based models like BERT perform such pretraining by using a method called Masked Language Modeling (MLM), where they predict the actual words of some masked or corrupted ones in given sequences. By pretraining on millions of biological sequences, foundation models gain a comprehensive contextual understanding of the given sequences. Once trained, they only need a few fine-tuning steps to be effectively applicable to specific downstream tasks [13], including prediction of epigenetic marks, gene expressions, protein folding structures, and more.

Natural environments pose significant challenges for autonomous robot navigation, particularly due to their unstructured and ever-changing nature. Hiking trails, with their dynamic conditions influenced by weather, vegetation, and human traffic, represent one such challenge. This work introduces a novel approach to autonomous hiking trail navigation that balances trail adherence with the flexibility to adapt to off-trail routes when necessary. The solution is a Traversability Analysis module that integrates semantic data from camera images with geometric information from LiDAR to create a comprehensive understanding of the surrounding terrain. A planner uses this traversability map to navigate safely, adhering to trails while allowing off-trail movement when necessary to avoid on-trail hazards or for safe off-trail shortcuts. The method is evaluated through simulation to determine the balance between semantic and geometric information in traversability estimation. These simulations tested various weights to assess their impact on navigation performance across different trail scenarios. Weights were then validated through field tests at the West Virginia University Core Arboretum, demonstrating the method's effectiveness in a real-world environment.

Large language models (LLMs) have exhibited remarkable capabilities across various domains and tasks, pushing the boundaries of our knowledge in learning and cognition. The latest model, OpenAI's o1, stands out as the first LLM with an internalized chain-of-thought technique using reinforcement learning strategies. While it has demonstrated surprisingly strong capabilities on various general language tasks, its performance in specialized fields such as medicine remains unknown. To this end, this report provides a comprehensive exploration of o1 on different medical scenarios, examining 3 key aspects: understanding, reasoning, and multilinguality. Specifically, our evaluation encompasses 6 tasks using data from 37 medical datasets, including two newly constructed and more challenging question-answering (QA) tasks based on professional medical quizzes from the New England Journal of Medicine (NEJM) and The Lancet. These datasets offer greater clinical relevance compared to standard medical QA benchmarks such as MedQA, translating more effectively into real-world clinical utility. Our analysis of o1 suggests that the enhanced reasoning ability of LLMs may (significantly) benefit their capability to understand various medical instructions and reason through complex clinical scenarios. Notably, o1 surpasses the previous GPT-4 in accuracy by an average of 6.2% and 6.6% across 19 datasets and two newly created complex QA scenarios. But meanwhile, we identify several weaknesses in both the model capability and the existing evaluation protocols, including hallucination, inconsistent multilingual ability, and discrepant metrics for evaluation. We release our raw data and model outputs at https://ucsc-vlaa.github.io/o1_medicine/ for future research.

Near-sun sky twilight observations allow for the detection of asteroid interior to the orbit of Venus (Aylos), the Earth (Atiras), and comets. We present the results of observations with the Palomar 48-inch telescope (P48)/Zwicky Transient Facility (ZTF) camera in 30 s r-band exposures taken during evening astronomical twilight from 2019 Sep 20 to 2022 March 7 and during morning astronomical twilight sky from 2019 Sep 21 to 2022 Sep 29. More than 46,000 exposures were taken in evening and morning astronomical twilight within 31 to 66 degrees from the Sun with an r-band limiting magnitude between 18.1 and 20.9. The twilight pointings show a slight seasonal dependence in limiting magnitude and ability to point closer towards the Sun, with limiting magnitude slightly improving during summer. In total, the one Aylo, (594913) 'Ayl\'o'chaxnim, and 4 Atiras, 2020 OV1, 2021 BS1, 2021 PB2, and 2021 VR3, were discovered in evening and morning twilight observations. Additional twilight survey discoveries also include 6 long-period comets: C/2020 T2, C/2020 V2, C/2021 D2, C/2021 E3, C/2022 E3, and C/2022 P3, and two short-period comets: P/2021 N1 and P/2022 P2 using deep learning comet detection pipelines. The P48/ZTF twilight survey also recovered 11 known Atiras, one Aylo, three short-period comes, two long-period comets, and one interstellar object. Lastly, the Vera Rubin Observatory will conduct a twilight survey starting in its first year of operations and will cover the sky within 45 degrees of the Sun. Twilight surveys such as those by ZTF and future surveys will provide opportunities for discovering asteroids inside the orbits of Earth and Venus.

Low back pain (LBP) is a leading cause of disability globally. Following the onset of LBP and subsequent treatment, adequate patient education is crucial for improving functionality and long-term outcomes. Despite advancements in patient education strategies, significant gaps persist in delivering personalized, evidence-based information to patients with LBP. Recent advancements in large language models (LLMs) and generative artificial intelligence (GenAI) have demonstrated the potential to enhance patient education. However, their application and efficacy in delivering educational content to patients with LBP remain underexplored and warrant further investigation. In this study, we introduce a novel approach utilizing LLMs with Retrieval-Augmented Generation (RAG) and few-shot learning to generate tailored educational materials for patients with LBP. Physical therapists manually evaluated our model responses for redundancy, accuracy, and completeness using a Likert scale. In addition, the readability of the generated education materials is assessed using the Flesch Reading Ease score. The findings demonstrate that RAG-based LLMs outperform traditional LLMs, providing more accurate, complete, and readable patient education materials with less redundancy. Having said that, our analysis reveals that the generated materials are not yet ready for use in clinical practice. This study underscores the potential of AI-driven models utilizing RAG to improve patient education for LBP; however, significant challenges remain in ensuring the clinical relevance and granularity of content generated by these models.

As LLMs evolve, significant effort is spent on manually crafting prompts. While existing prompt optimization methods automate this process, they rely solely on learning from incorrect samples, leading to a sub-optimal performance. Additionally, an unexplored challenge in the literature is prompts effective for prior models may not perform well on newer versions or different languages. We propose the Learning from Contrastive Prompts (LCP) framework to address these gaps, enhancing both prompt optimization and adaptation. LCP employs contrastive learning to generate effective prompts by analyzing patterns in good and bad prompt examples. Our evaluation on the Big-Bench Hard dataset shows that LCP has a win rate of over 76% over existing methods in prompt optimization and demonstrates strong adaptability across different model versions, families, and languages. LCP offers a systematic approach to prompt engineering, reducing manual effort in deploying LLMs across varied contexts.

The usefulness of Large Language Models (LLM) is being continuously tested in various fields. However, their intrinsic linguistic characteristic is still one of the limiting factors when applying these models to exact sciences. In this article, a novel approach to use General Pre-Trained Transformers to assist in the design phase of data acquisition systems will be presented. The solution is packaged in the form of an application that retains the conversational aspects of LLMs, in such a manner that the user must provide details on the desired project in order for the model to draft both a system-level architectural diagram and the block-level specifications, following a Top-Down methodology based on restrictions. To test this tool, two distinct user emulations were used, one of which uses an additional GPT model. In total, 4 different data acquisition projects were used in the testing phase, each with its own measurement requirements: angular position, temperature, acceleration and a fourth project with both pressure and superficial temperature measurements. After 160 test iterations, the study concludes that there is potential for these models to serve adequately as synthesis/assistant tools for data acquisition systems, but there are still technological limitations. The results show coherent architectures and topologies, but that GPTs have difficulties in simultaneously considering all requirements and many times commits theoretical mistakes.

For the planning of radiotherapy treatments for head and neck cancers, Computed Tomography (CT) scans of the patients are typically employed. However, in patients with head and neck cancer, the quality of standard CT scans generated using kilo-Voltage (kVCT) tube potentials is severely degraded by streak artifacts occurring in the presence of metallic implants such as dental fillings. Some radiotherapy devices offer the possibility of acquiring Mega-Voltage CT (MVCT) for daily patient setup verification, due to the higher energy of X-rays used, MVCT scans are almost entirely free from artifacts making them more suitable for radiotherapy treatment planning. In this study, we leverage the advantages of kVCT scans with those of MVCT scans (artifact-free). We propose a deep learning-based approach capable of generating artifact-free MVCT images from acquired kVCT images. The outcome offers the benefits of artifact-free MVCT images with enhanced soft tissue contrast, harnessing valuable information obtained through kVCT technology for precise therapy calibration. Our proposed method employs UNet-inspired model, and is compared with adversarial learning and transformer networks. This first and unique approach achieves remarkable success, with PSNR of 30.02 dB across the entire patient volume and 27.47 dB in artifact-affected regions exclusively. It is worth noting that the PSNR calculation excludes the background, concentrating solely on the region of interest.

The general-utility Markov decision processes (GUMDPs) framework generalizes the MDPs framework by considering objective functions that depend on the frequency of visitation of state-action pairs induced by a given policy. In this work, we contribute with the first analysis on the impact of the number of trials, i.e., the number of randomly sampled trajectories, in infinite-horizon GUMDPs. We show that, as opposed to standard MDPs, the number of trials plays a key-role in infinite-horizon GUMDPs and the expected performance of a given policy depends, in general, on the number of trials. We consider both discounted and average GUMDPs, where the objective function depends, respectively, on discounted and average frequencies of visitation of state-action pairs. First, we study policy evaluation under discounted GUMDPs, proving lower and upper bounds on the mismatch between the finite and infinite trials formulations for GUMDPs. Second, we address average GUMDPs, studying how different classes of GUMDPs impact the mismatch between the finite and infinite trials formulations. Third, we provide a set of empirical results to support our claims, highlighting how the number of trajectories and the structure of the underlying GUMDP influence policy evaluation.

Evaluating the capabilities of Large Language Models (LLMs) to assist teachers and students in educational tasks is receiving increasing attention. In this paper, we assess ChatGPT's capacities to solve and grade real programming exams, from an accredited BSc degree in Computer Science, written in Spanish. Our findings suggest that this AI model is only effective for solving simple coding tasks. Its proficiency in tackling complex problems or evaluating solutions authored by others are far from effective. As part of this research, we also release a new corpus of programming tasks and the corresponding prompts for solving the problems or grading the solutions. This resource can be further exploited by other research teams.