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Simple Agents Outperform Experts in Biomedical Imaging Workflow Optimization
Xuefei, null, Wang, null, Horstmann, Kai A., Lin, Ethan, Chen, Jonathan, Farhang, Alexander R., Stiles, Sophia, Sehgal, Atharva, Light, Jonathan, Van Valen, David, Yue, Yisong, Sun, Jennifer J.
Adapting production-level computer vision tools to bespoke scientific datasets is a critical "last mile" bottleneck. Current solutions are impractical: fine-tuning requires large annotated datasets scientists often lack, while manual code adaptation costs scientists weeks to months of effort. W e consider using AI agents to automate this manual coding, and focus on the open question of optimal agent design for this targeted task. W e introduce a systematic evaluation framework for agentic code optimization and use it to study three production-level biomedical imaging pipelines. W e demonstrate that a simple agent framework consistently generates adaptation code that outperforms human-expert solutions. Our analysis reveals that common, complex agent architectures are not universally beneficial, leading to a practical roadmap for agent design.
POrTAL: Plan-Orchestrated Tree Assembly for Lookahead
Conway, Evan, Porfirio, David, Chan, David, Roberts, Mark, Hiatt, Laura M.
Abstract-- Assigning tasks to robots often involves supplying the robot with an overarching goal, such as through natural language, and then relying on the robot to uncover and execute a plan to achieve that goal. In many settings common to human-robot interaction, however, the world is only partially observable to the robot, requiring that it create plans under uncertainty. Although many probabilistic planning algorithms exist for this purpose, these algorithms can be inefficient if executed with the robot's limited computational resources, or may require more steps than expected to achieve the goal. We thereby created a new, lightweight, probabilistic planning algorithm, Plan-Orchestrated Tree Assembly for Lookahead (POrTAL), that combines the strengths of two baseline planning algorithms, FF-Replan and POMCP . In a series of case studies, we demonstrate POrTAL's ability to quickly arrive at solutions that outperform these baselines in terms of number of steps. We additionally demonstrate how POrTAL performs under varying temporal constraints. The ability of modern robots to respond to arbitrary user requests has advanced considerably in recent years. This advancement is in large part due to robots' ability to autonomously plan their own actions. When receiving a goal such as "bring me a cup of coffee," for example, a robot can calculate the minimum number of steps required to achieve this goal: obtain the coffee grinds, proceeding to the coffee maker, load the grinds, and so on. In many scenarios common to human-robot interaction, however, this planning must be performed under considerable uncertainty.
Small Language Models Reshape Higher Education: Courses, Textbooks, and Teaching
While large language models (LLMs) have introduced novel paradigms in science and education, their adoption in higher education is constrained by inherent limitations. These include a tendency to produce inaccuracies and high computational requirements, which compromise the strict demands for accurate and reliable knowledge essential in higher education. Small language models (MiniLMs), by contrast, offer distinct advantages in professional education due to their lightweight nature and precise retrieval capabilities. This research takes "Atmospheric Physics" as an example. We established a specialized corpus and image repository by gathering over 550,000 full-text PDFs from over 130 international well-respected journals in Earth and environmental science. From this collection, we extracted over 100 million high-quality sentence-level corpus and more than 3 million high-resolution academic images. Using MiniLMs, these resources were organized into a high-dimensional vector library for precise retrieval and efficient utilization of extensive educational content. Consequently, we systematically redesigned the courses, textbooks, and teaching strategies for "Atmospheric Physics" based on MiniLMs. The course is designed as a "interdisciplinary-frontier" system, breaking down traditional boundaries between atmospheric science, space science, hydrology, and remote sensing. Teaching materials are transformed from static, lagging text formats into a dynamic digital resource library powered by MiniLM. For teaching methods, we have designed a question-based learning pathway. This paradigm promotes a shift from passive knowledge transfer to active cognitive development. Consequently, this MiniLM-driven "Atmospheric Physics" course demonstrates a specific avenue for "AI for education".
FishDetector-R1: Unified MLLM-Based Framework with Reinforcement Fine-Tuning for Weakly Supervised Fish Detection, Segmentation, and Counting
Liu, Yi, Song, Jingyu, Kallakuri, Vedanth, Skinner, Katherine A.
Analyzing underwater fish imagery is critical for ecological monitoring but remains difficult due to visual degradation and costly annotations. We introduce FishDetector-R1, a unified MLLM-based framework for fish detection, segmentation, and counting under weak supervision. On the DeepFish dataset, our framework achieves substantial gains over baselines, improving AP by 20% and mIoU by 10%, while reducing MAE by 30% and GAME by 35%. These improvements stem from two key components: a novel detect-to-count prompt that enforces spatially consistent detections and counts, and Reinforcement Learning from Verifiable Reward (RLVR) with a complementary scalable paradigm leveraging sparse point labels. Ablation studies further validate the effectiveness of this reward design. Moreover, the improvement generalizes well to other underwater datasets, confirming strong cross-domain robustness. Overall, FishDetector-R1 provides a reliable and scalable solution for accurate marine visual understanding via weak supervision. The project page for FishDetector-R1 is https://umfieldrobotics.github.io/FishDetector-R1.
KidSpeak: A General Multi-purpose LLM for Kids' Speech Recognition and Screening
Sharma, Rohan, Liu, Dancheng, Sun, Jingchen, Zhou, Shijie, Qin, Jiayu, Xiong, Jinjun, Chen, Changyou
With the rapid advancement of conversational and diffusion-based AI, there is a growing adoption of AI in educational services, ranging from grading and assessment tools to personalized learning systems that provide targeted support for students. However, this adaptability has yet to fully extend to the domain of children's speech, where existing models often fail due to their reliance on datasets designed for clear, articulate adult speech. Children, particularly those in early developmental stages or with speech and language pathologies, present unique challenges that current AI models and datasets are ill-equipped to handle. To address this, we introduce KidSpeak, a multi-task speech-enhanced Foundation Model capable of both generative and discriminative tasks specifically tailored to children's speech patterns. Our framework employs a two-stage training process that incorporates phonetic knowledge into the speech encoder, achieving an average accuracy of 87% across four separate tasks. Furthermore, recognizing the limitations of scalable human annotation and existing speech alignment tools, we propose the Flexible and Automatic Speech Aligner (F ASA) and leverage the method to construct high quality datasets for training and evaluation. This novel alignment tool significantly improves the quality of aligned children's speech from noisy data, enhancing data quality by 13.6 compared to human annotations, as demonstrated on the CHILDES dataset. To the best of our knowledge, KidSpeak and F ASA represent the first comprehensive solution designed for speech and language therapy in children, offering both a multi-purpose speech LLM and a robust alignment tool.
Domain-Specific Foundation Model Improves AI-Based Analysis of Neuropathology
Verma, Ruchika, Kandoi, Shrishtee, Afzal, Robina, Chen, Shengjia, Jegminat, Jannes, Karlovich, Michael W., Umphlett, Melissa, Richardson, Timothy E., Clare, Kevin, Hossain, Quazi, Samanamud, Jorge, Faust, Phyllis L., Louis, Elan D., McKee, Ann C., Stein, Thor D., Cherry, Jonathan D., Mez, Jesse, McGoldrick, Anya C., Mora, Dalilah D. Quintana, Nirenberg, Melissa J., Walker, Ruth H., Mendez, Yolfrankcis, Morgello, Susan, Dickson, Dennis W., Murray, Melissa E., Cordon-Cardo, Carlos, Tsankova, Nadejda M., Walker, Jamie M., Dangoor, Diana K., McQuillan, Stephanie, Thorn, Emma L., De Sanctis, Claudia, Li, Shuying, Fuchs, Thomas J., Farrell, Kurt, Crary, John F., Campanella, Gabriele
Foundation models have transformed computational pathology by providing generalizable representations from large-scale histology datasets. However, existing models are predominantly trained on surgical pathology data, which is enriched for non-nervous tissue and overrepresents neoplastic, inflammatory, metabolic, and other non-neurological diseases. Neuropathology represents a markedly different domain of histopathology, characterized by unique cell types (neurons, glia, etc.), distinct cytoarchitecture, and disease-specific pathological features including neurofibrillary tangles, amyloid plaques, Lewy bodies, and pattern-specific neurodegeneration. This domain mismatch may limit the ability of general-purpose foundation models to capture the morphological patterns critical for interpreting neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and cerebellar ataxias. To address this gap, we developed NeuroFM, a foundation model trained specifically on whole-slide images of brain tissue spanning diverse neurodegenerative pathologies. NeuroFM demonstrates superior performance compared to general-purpose models across multiple neuropathology-specific downstream tasks, including mixed dementia disease classification, hippocampal region segmentation, and neurodegenerative ataxia identification encompassing cerebellar essential tremor and spinocerebellar ataxia subtypes. This work establishes that domain-specialized foundation models trained on brain tissue can better capture neuropathology-specific features than models trained on general surgical pathology datasets. By tailoring foundation models to the unique morphological landscape of neurodegenerative diseases, NeuroFM enables more accurate and reliable AI-based analysis for brain disease diagnosis and research, setting a precedent for domain-specific model development in specialized areas of digital pathology.
A self-driving lab for solution-processed electrochromic thin films
Dahms, Selma, Torresi, Luca, Bandesha, Shahbaz Tareq, Hansmann, Jan, Rรถhm, Holger, Colsmann, Alexander, Schott, Marco, Friederich, Pascal
Solution-processed electrochromic materials offer high potential for energy-efficient smart windows and displays. Their performance varies with material choice and processing conditions. Electrochromic thin film electrodes require a smooth, defect-free coating for optimal contrast between bleached and colored states. The complexity of optimizing the spin-coated electrochromic thin layer poses challenges for rapid development. This study demonstrates the use of self-driving laboratories to accelerate the development of electrochromic coatings by coupling automation with machine learning. Our system combines automated data acquisition, image processing, spectral analysis, and Bayesian optimization to explore processing parameters efficiently. This approach not only increases throughput but also enables a pointed search for optimal processing parameters. The approach can be applied to various solution-processed materials, highlighting the potential of self-driving labs in enhancing materials discovery and process optimization.
Adaptive Dataset Quantization: A New Direction for Dataset Pruning
This paper addresses the challenges of storage and communication costs for large-scale datasets in resource-constrained edge devices by proposing a novel dataset quantization approach to reduce intra-sample redundancy. Unlike traditional dataset pruning and distillation methods that focus on inter-sample redundancy, the proposed method compresses each image by reducing redundant or less informative content within samples while preserving essential features. It first applies linear symmetric quantization to obtain an initial quantization range and scale for each sample. Then, an adaptive quantization allocation algorithm is introduced to distribute different quantization ratios for samples with varying precision requirements, maintaining a constant total compression ratio. The main contributions include: (1) being the first to use limited bits to represent datasets for storage reduction; (2) introducing a dataset-level quantization algorithm with adaptive ratio allocation; and (3) validating the method's effectiveness through extensive experiments on CIFAR-10, CIFAR-100, and ImageNet-1K. Results show that the method maintains model training performance while achieving significant dataset compression, outperforming traditional quantization and dataset pruning baselines under the same compression ratios.
AI-Generated Compromises for Coalition Formation: Modeling, Simulation, and a Textual Case Study
Briman, Eyal, Shapiro, Ehud, Talmon, Nimrod
The challenge of finding compromises between agent proposals is fundamental to AI sub-fields such as argumentation, mediation, and negotiation. Building on this tradition, Elkind et al. (2021) introduced a process for coalition formation that seeks majority-supported proposals preferable to the status quo, using a metric space where each agent has an ideal point. The crucial step in this iterative process involves identifying compromise proposals around which agent coalitions can unite. How to effectively find such compromise proposals, however, remains an open question. We address this gap by formalizing a holistic model that encompasses agent bounded rationality and uncertainty and developing AI models to generate such compromise proposals. We focus on the domain of collaboratively writing text documents -- e.g., to enable the democratic creation of a community constitution. We apply NLP (Natural Language Processing) techniques and utilize LLMs (Large Language Models) to create a semantic metric space for text and develop algorithms to suggest suitable compromise points. To evaluate the effectiveness of our algorithms, we simulate various coalition formation processes and demonstrate the potential of AI to facilitate large-scale democratic text editing, such as collaboratively drafting a constitution, an area where traditional tools are limited.
FlockVote: LLM-Empowered Agent-Based Modeling for Simulating U.S. Presidential Elections
Zhou, Lingfeng, Xu, Yi, Wang, Zhenyu, Wang, Dequan
Modeling complex human behavior, such as voter decisions in national elections, is a long-standing challenge for computational social science. Traditional agent-based models (ABMs) are limited by oversimplified rules, while large-scale statistical models often lack interpretability. We introduce FlockVote, a novel framework that uses Large Language Models (LLMs) to build a "computational laboratory" of LLM agents for political simulation. Each agent is instantiated with a high-fidelity demographic profile and dynamic contextual information (e.g. candidate policies), enabling it to perform nuanced, generative reasoning to simulate a voting decision. We deploy this framework as a testbed on the 2024 U.S. Presidential Election, focusing on seven key swing states. Our simulation's macro-level results successfully replicate the real-world outcome, demonstrating the high fidelity of our "virtual society". The primary contribution is not only the prediction, but also the framework's utility as an interpretable research tool. FlockVote moves beyond black-box outputs, allowing researchers to probe agent-level rationale and analyze the stability and sensitivity of LLM-driven social simulations.