Genomic question answering often requires complex reasoning and integration across diverse biomedical sources. GeneGPT addressed this challenge by combining domain-specific APIs with OpenAI's code-davinci-002 large language model to enable natural language interaction with genomic databases. However, its reliance on a proprietary model limits scalability, increases operational costs, and raises concerns about data privacy and generalization. In this work, we revisit and reproduce GeneGPT in a pilot study using open source models, including Llama 3.1, Qwen2.5, and Qwen2.5 Coder, within a monolithic architecture; this allows us to identify the limitations of this approach. Building on this foundation, we then develop OpenBioLLM, a modular multi-agent framework that extends GeneGPT by introducing agent specialization for tool routing, query generation, and response validation. This enables coordinated reasoning and role-based task execution. OpenBioLLM matches or outperforms GeneGPT on over 90% of the benchmark tasks, achieving average scores of 0.849 on Gene-Turing and 0.830 on GeneHop, while using smaller open-source models without additional fine-tuning or tool-specific pretraining. OpenBioLLM's modular multi-agent design reduces latency by 40-50% across benchmark tasks, significantly improving efficiency without compromising model capability. The results of our comprehensive evaluation highlight the potential of open-source multi-agent systems for genomic question answering. Code and resources are available at https://github.com/ielab/OpenBioLLM.

Multimodal Large Language Models (MLLMs) have seen rapid advances in recent years and are now being applied to visual document understanding tasks. They are expected to process a wide range of document images across languages, including Japanese. Understanding documents from images requires models to read what are written in them. Since some Japanese documents are written vertically, support for vertical writing is essential. However, research specifically focused on vertically written Japanese text remains limited. In this study, we evaluate the reading capability of existing MLLMs on vertically written Japanese text. First, we generate a synthetic Japanese OCR dataset by rendering Japanese texts into images, and use it for both model fine-tuning and evaluation. This dataset includes Japanese text in both horizontal and vertical writing. We also create an evaluation dataset sourced from the real-world document images containing vertically written Japanese text. Using these datasets, we demonstrate that the existing MLLMs perform worse on vertically written Japanese text than on horizontally written Japanese text. Furthermore, we show that training MLLMs on our synthesized Japanese OCR dataset results in improving the performance of models that previously could not handle vertical writing. The datasets and code are publicly available https://github.com/llm-jp/eval_vertical_ja.

Human-like agents have long been one of the goals in pursuing artificial intelligence. Although reinforcement learning (RL) has achieved superhuman performance in many domains, relatively little attention has been focused on designing human-like RL agents. As a result, many reward-driven RL agents often exhibit unnatural behaviors compared to humans, raising concerns for both interpretability and trustworthiness. To achieve human-like behavior in RL, this paper first formulates human-likeness as trajectory optimization, where the objective is to find an action sequence that closely aligns with human behavior while also maximizing rewards, and adapts the classic receding-horizon control to human-like learning as a tractable and efficient implementation. To achieve this, we introduce Macro Action Quantization (MAQ), a human-like RL framework that distills human demonstrations into macro actions via Vector-Quantized VAE. Experiments on D4RL Adroit benchmarks show that MAQ significantly improves human-likeness, increasing trajectory similarity scores, and achieving the highest human-likeness rankings among all RL agents in the human evaluation study. Our results also demonstrate that MAQ can be easily integrated into various off-the-shelf RL algorithms, opening a promising direction for learning human-like RL agents. Our code is available at https://rlg.iis.sinica.edu.tw/papers/MAQ.

Abstract--COVID-19 is a respiratory disease that caused a global pandemic in 2019. It is highly infectious and has the following symptoms: fever or chills, cough, shortness of breath, fatigue, muscle or body aches, headache, the new loss of taste or smell, sore throat, congestion or runny nose, nausea or vomiting, and diarrhea. These symptoms vary in severity; some people with many risk factors have been known to have lengthy hospital stays or die from the disease. In this paper, we analyze patients' electronic health records (EHR) to predict the severity of their COVID-19 infection using the length of stay (LOS) as our measurement of severity. This is an imbalanced classification problem, as many people have a shorter LOS rather than a longer one. T o combat this problem, we synthetically create alternate oversampled training data sets. Once we have this oversampled data, we run it through an Artificial Neural Network (ANN), which during training has its hyperparameters tuned by using bayesian optimization. We select the model with the best F1 score and then evaluate it and discuss it. COVID-19 is defined by the Centers for Disease Control and Prevention (CDC) as "a respiratory disease caused by SARS-CoV -2, a coronavirus discovered in 2019. The virus spreads mainly from person to person through respiratory droplets produced when an infected person coughs, sneezes, or talks" [1]. Furthermore, they add, "For people who have symptoms, illness can range from mild to severe. Adults 65 years and older and people of any age with underlying medical conditions are at higher risk for severe illness" [1].In 2019 this novel coronavirus was first detected. The highly infectious nature of this disease, combined with the respiratory nature of the infection, caused a pandemic. Along with being highly contagious, COVID-19 also has an extensive range of symptoms such as fever or chills, cough, shortness of breath, fatigue, muscle or body aches, headache, the new loss of taste or smell, sore throat, congestion or runny nose, nausea or vomiting, and diarrhea [2]. Along with a long list of symptoms, COVID-19 has many risk factors, which may increase the severity of the infection.

Recent advances in generative AI for music have achieved remarkable fidelity and stylistic diversity, yet these systems often fail to align with nuanced human preferences due to the specific loss functions they use. This paper advocates for the systematic application of preference alignment techniques to music generation, addressing the fundamental gap between computational optimization and human musical appreciation. Drawing on recent breakthroughs including MusicRL's large-scale preference learning, multi-preference alignment frameworks like diffusion-based preference optimization in DiffRhythm+, and inference-time optimization techniques like Text2midi-InferAlign, we discuss how these techniques can address music's unique challenges: temporal coherence, harmonic consistency, and subjective quality assessment. We identify key research challenges including scalability to long-form compositions, reliability amongst others in preference modelling. Looking forward, we envision preference-aligned music generation enabling transformative applications in interactive composition tools and personalized music services. This work calls for sustained interdisciplinary research combining advances in machine learning, music-theory to create music AI systems that truly serve human creative and experiential needs.

While intelligent tutoring systems (ITSs) can use information from past students to personalize instruction, each new student is unique. Moreover, the education problem is inherently difficult because the learning process is only partially observable. We therefore develop a dynamic, time-series environment to simulate a classroom setting, with student-teacher interventions - including tutoring sessions, lectures, and exams. In particular, we design the simulated environment to allow for varying levels of probing interventions that can gather more information. Then, we develop reinforcement learning ITSs that combine learning the individual state of students while pulling from population information through the use of probing interventions. These interventions can reduce the difficulty of student estimation, but also introduce a cost-benefit decision to find a balance between probing enough to get accurate estimates and probing so often that it becomes disruptive to the student. We compare the efficacy of standard RL algorithms with several greedy rules-based heuristic approaches to find that they provide different solutions, but with similar results. We also highlight the difficulty of the problem with increasing levels of hidden information, and the boost that we get if we allow for probing interventions. We show the flexibility of both heuristic and RL policies with regards to changing student population distributions, finding that both are flexible, but RL policies struggle to help harder classes. Finally, we test different course structures with non-probing policies and we find that our policies are able to boost the performance of quiz and midterm structures more than we can in a finals-only structure, highlighting the benefit of having additional information.

The ionosphere is a critical component of near-Earth space, shaping GNSS accuracy, high-frequency communications, and aviation operations. For these reasons, accurate forecasting and modeling of ionospheric variability has become increasingly relevant. To address this gap, we present IonCast, a suite of deep learning models that include a GraphCast-inspired model tailored for ionospheric dynamics. IonCast leverages spatiotemporal learning to forecast global Total Electron Content (TEC), integrating diverse physical drivers and observational datasets. Validating on held-out storm-time and quiet conditions highlights improved skill compared to persistence. By unifying heterogeneous data with scalable graph-based spatiotemporal learning, IonCast demonstrates how machine learning can augment physical understanding of ionospheric variability and advance operational space weather resilience.

Accurate prediction of project duration and cost remains one of the most challenging aspects of project management, particularly in resource-constrained and interdependent task networks. Traditional analytical techniques such as the Critical Path Method (CPM) and Program Evaluation and Review Technique (PERT) rely on simplified and often static assumptions regarding task interdependencies and resource performance. This study proposes a novel resource-based predictive framework that integrates network representations of project activities with graph neural networks (GNNs) to capture structural and contextual relationships among tasks, resources, and time-cost dynamics. The model represents the project as a heterogeneous activity-resource graph in which nodes denote activities and resources, and edges encode temporal and resource dependencies. We evaluate multiple learning paradigms, including GraphSAGE and Temporal Graph Networks, on both synthetic and benchmark project datasets. Experimental results show that the proposed GNN framework achieves an average 23 to 31 percent reduction in mean absolute error compared to traditional regression and tree-based methods, while improving the coefficient of determination R2 from approximately 0.78 to 0.91 for large and complex project networks. Furthermore, the learned embeddings provide interpretable insights into resource bottlenecks and critical dependencies, enabling more explainable and adaptive scheduling decisions.

UAV swarms have emerged as transformative systems for complex missions including wildfire surveillance ( Julian and Kochenderfer 2019), intelligence surveillance and reconnaissance ( Kolar 2020), situational awareness ( Scharre 2018), and cooperative interception ( Balhance et al. 2017). In these applications, trajectory optimization is the cornerstone for ensuring both mission success and operational s afety ( Sezer 2022; Qian et al. 2020; Sanchez-Lopez et al. 2020). Over the past decade, trajectory optimization techniques hav e evolved from sophisticated single-agent formulations to distributed multi-agent frameworks, driven by the increasing scale and complexity of swarm-based missions ( Saravanos et al. 2023). For individual UAV trajectory optimization, a variety of numerical m ethods have demonstrated strong performance. Pseudospectral methods achieve high-accuracy solution s by discretizing continuous-time problems ( Chai et al. 2017), while sequential quadratic programming (SQP) ( Hong et al. 2021) and sequential convex programming (SCP) ( Deligiannis et al. 2019) provide flexible tools for handling nonlinear dynamics and constraint s.

Knowledge distillation (KD) methods can transfer knowledge of a parameter-heavy teacher model to a light-weight student model. The status quo for feature KD methods is to utilize loss functions based on logits (i.e., pre-softmax class scores) and intermediate layer features (i.e., latent representations). Unlike previous approaches, we propose a feature KD framework for training the student's backbone using feature-based losses exclusively (i.e., without logit-based losses such as cross entropy). Leveraging recent discoveries about the geometry of latent representations, we introduce a knowledge quality metric for identifying which teacher layers provide the most effective knowledge for distillation. Experiments on three image classification datasets with four diverse student-teacher pairs, spanning convolutional neural networks and vision transformers, demonstrate our KD method achieves state-of-the-art performance, delivering top-1 accuracy boosts of up to 15% over standard approaches. We publically share our code to facilitate future work at https://github.com/Thegolfingocto/KD_wo_CE.