Clustering with phylogenetic tools in astrophysics

Phylogenetic approaches are finding more and more applications outside the field of biology. Astrophysics is no exception since an overwhelming amount of multivariate data has appeared in the last twenty years or so. In particular, the diversification of galaxies throughout the evolution of the Universe quite naturally invokes phylogenetic approaches. We have demonstrated that Maximum Parsimony brings useful astrophysical results, and we now proceed toward the analyses of large datasets for galaxies. In this talk I present how we solve the major difficulties for this goal: the choice of the parameters, their discretization, and the analysis of a high number of objects with an unsupervised NP-hard classification technique like cladistics. 1. Introduction How do the galaxy form, and when? How did the galaxy evolve and transform themselves to create the diversity we observe? What are the progenitors to present-day galaxies? To answer these big questions, observations throughout the Universe and the physical modelisation are obvious tools. But between these, there is a key process, without which it would be impossible to extract some digestible information from the complexity of these systems. This is classification. One century ago, galaxies were discovered by Hubble. From images obtained in the visible range of wavelengths, he synthetised his observations through the usual process: classification. With only one parameter (the shape) that is qualitative and determined with the eye, he found four categories: ellipticals, spirals, barred spirals and irregulars. This is the famous Hubble classification. He later hypothetized relationships between these classes, building the Hubble Tuning Fork. The Hubble classification has been refined, notably by de Vaucouleurs, and is still used as the only global classification of galaxies. Even though the physical relationships proposed by Hubble are not retained any more, the Hubble Tuning Fork is nearly always used to represent the classification of the galaxy diversity under its new name the Hubble sequence (e.g. Delgado-Serrano, 2012). Its success is impressive and can be understood by its simplicity, even its beauty, and by the many correlations found between the morphology of galaxies and their other properties. And one must admit that there is no alternative up to now, even though both the Hubble classification and diagram have been recognised to be unsatisfactory. Among the most obvious flaws of this classification, one must mention its monovariate, qualitative, subjective and old-fashioned nature, as well as the difficulty to characterise the morphology of distant galaxies. The first two most significant multivariate studies were by Watanabe et al. (1985) and Whitmore (1984). Since the year 2005, the number of studies attempting to go beyond the Hubble classification has increased largely. Why, despite of this, the Hubble classification and its sequence are still alive and no alternative have yet emerged (Sandage, 2005)? My feeling is that the results of the multivariate analyses are not easily integrated into a one-century old practice of modeling the observations. In addition, extragalactic objects like galaxies, stellar clusters or stars do evolve. Astronomy now provides data on very distant objects, raising the question of the relationships between those and our present day nearby galaxies. Clearly, this is a phylogenetic problem. Astrocladistics 1 aims at exploring the use of phylogenetic tools in astrophysics (Fraix-Burnet et al., 2006a,b). We have proved that Maximum Parsimony (or cladistics) can be applied in astrophysics and provides a new exploration tool of the data (Fraix-Burnet et al., 2009, 2012, Cardone \& Fraix-Burnet, 2013). As far as the classification of galaxies is concerned, a larger number of objects must now be analysed. In this paper, I

An Approach for Thyroid Nodule Analysis Using Thermographic Images

Thyroid cancer is said to be the second most common type of cancer in female individuals and the third in males by 2030, according to projections. In general, detecting cancer in its early stages improves the chance of survival of the individual. Thermography is a diagnostic tool that has been increasingly used to detect cancer and abnormalities, including that of thyroid. Various methods to segment and detect hot regions in thermograms and, consequently, to detect suspicious tissues present in these images have been proposed. It is well known that medical diagnosis yields a great deal of information. Thus, physicians have to comprehensively analyse and evaluate this information in a short period of time, which is infeasible in most cases. In this work, we perform a general review of thermography , focusing on the thyroid analysis. We propose protocols for image acquisiton and an autonomous registration for thyroid images. We also perform analyses of the image data, which include feature extraction, image processing, and a possible approach for classification of healthy or unhealthy patients. In summary, this work presents a pilot project for detection of tumors in our university hospital, which is part of an effort to support preventive medical actions in our endocrinology department. Under some future adjustments, this project will be submitted for approval by the ethics and research committee of Hospital Universitário Antonio Pedro at Universidade Federal Fluminense (HUAP-UFF) and to the Brazilian Ministry of Health Ethical committee under the name: Evaluation of the importance of thermography to aid diagnosis of thyroid nodules of patients in HUAP-UFF (in Portuguese: Avaliação da importância da termografia no auxílio à investigação diagnóstica de nódulos tireoidianos em pacientes acompanhados no HUAP-UFF).

Evaluating the Utility of Personal Health Records in Personalized Health AI

Patient-managed Personal Health Records (PHRs) promises to empower patients to better understand their health; but information in the record is complex, potentially hindering insights. In this study, we assess the potential of large language models (LLMs, Gemini 3.0 Flash) to provide helpful answers to user health queries, when provided clinical data from PHRs as context. A total of 2,257 user queries were drawn from 3 different distributions to represent patient questions: shorter web search queries, longer questions derived from templates of chatbot conversations, and questions patients asked to their healthcare team (patient calls). Queries were matched with de-identified PHRs (from a pool of 1,945). Gemini responses were generated (1) without PHR context; (2) with a basic summary of demographics, conditions, and medications; (3) with full, extensive clinical notes. For evaluation, we leveraged an existing rating framework (SHARP), and developed a new framework for specific error modes when interpreting PHRs. Evaluation was performed using autoraters for the full set, and with clinician ratings for a subset (n=95), with both sets of raters knowing the full PHR context. We see significant improvements in the helpfulness of answers to all question types with PHR data (p < 0.001, paired t-test). We also observe potential gains in safety, accuracy, relevance and personalization of answers. Our PHR evaluation framework further identifies gaps in LLM understanding of particular aspects of complex PHRs, such as temporal disorientation, and rare but meaningful confabulations. These results suggest potential for PHR data to help people with a wide range of user needs; and provide a framework for monitoring for gaps in LLM answers based on PHR context. This study motivates further work to assess and realize potential benefits to users from understanding their health records.

From Learning Resources to Competencies: LLM-Based Tagging with Evidence and Graph Constraints

Linking learning resources to a structured competency framework is key to enabling competency-based search and curriculum analytics in Learning Management Systems (LMS). However, manual tagging is labor-intensive, and fully automatic methods often lack transparency. In this paper, we present an end-to-end alignment pipeline that uses a large language model (LLM) as a constrained, evidence-producing tagger. LMS resources -both instructional content and assessments -are first segmented into meaningful pedagogical fragments. For each fragment, a small set of candidate competencies is retrieved from structured competency profiles enriched with graph-based context. The LLM then selects the most relevant competencies from this set and provides supporting evidence spans from the fragment text. These predictions are refined using the structure of the competency graph and aggregated at the resource level. We evaluate our approach on a dataset built from the Computer Science department's competency referential at the Université de Technologie de Compiègne (UTC), covering 22 competencies across multiple course materials. Our LLM+BM25+Graph (LBG) pipeline achieves strong results, with a micro-F1 of 0.57 and macro-F1 of 0.50 at the fragment level, 0.51 macro-F1 at the resource level, and an MRR of 0.82outperforming zero-shot and few-shot LLM variants, retrieval/similarity baselines, and supervised classifiers -while also producing more mechanically traceable evidence spans to support human auditing and educational analysis.

Persistent AI Agents in Academic Research: A Single-Investigator Implementation Case Study

Background: Large language models are typically evaluated as models, benchmarks, or short conversational episodes. Less is known about what happens when an agent is embedded persistently in a real academic research environment with durable memory, local files, external tools, scheduled routines, delegated roles, and explicit safety protocols. Methods: A structured self-observed implementation case study was conducted from January 31 to May 25, 2026. The unit of analysis was the persistent human-agent environment: researcher, agent runtime, memory layer, tools, repositories, scheduled jobs, specialized agent roles, and governance rules. Outcomes were organized using PARE-M (Persistent Agentic Research Environment Measurement), a measurement framework covering architecture, utilization, artifact production, resource use, reproducibility, and governance. Results: Recoverable main-agent telemetry contained 75,671 de-duplicated records across 96 active days, with 8,059 user-role and 23,710 assistant-role messages. The workspace included 502 memory-related files, 17 configured agent directories, and 57 skill files. Active system time was 579.7 hours (30-minute capped-gap estimate). Memory-derived records identified 482 output-proxy events and 889 failure, verification, correction, or protocol-proxy events. A strict May 2026 trajectory subset captured 627 model-completed events and 73.95 million recorded tokens, of which 82.9% were cache reads. Conclusions: The workflow was cache-dominant, suggesting that persistent agentic environments may shift the economic unit from cost per token to cost per completed artifact. Future evaluations should use artifact-level denominators, reproducible parsing rules, correction taxonomies, and independent coding of governance events.

Practical Anonymous Two-Party Gradient Boosting Decision Tree

Structured data is well handled by gradient-boosted decision trees (GBDT), which are usually trained on vertically partitioned features across mutually distrustful parties. High speed and interpretability make GBDTs popular in finance and healthcare, where neural networks may fall short. Enabling secure computation for GBDTs poses unique challenges, requiring secure record alignment for comparison. Relying on private set intersection (PSI) is a de facto approach. Mistaking PSI for a safety measure actually exposes which record identifiers (IDs) are shared between the datasets. Although circuit-PSI could help, it is costly for generic uses. New ideas are needed to efficiently train in a "dark forest". Aiming to hide the IDs, we initiate the study of anonymous GBDT training on split data held by two parties. Dual circuit-PSI in our design lets the parties alternate as receiver to run pick-then-sum over local features. Via oblivious programmable pseudorandom functions, we propagate circuit-PSI outputs as shared state across runs. Avoiding universal alignment, we resolve the neglected dilemma that ID hiding incurs a cost that scales with domain size. Next, we halve the cost of ciphertext packing used to convert single-instruction multiple-data homomorphic encryption from (ring) learning with errors in prior secure GBDT (Usenix Security' 23) and related secure machine-learning computations. Comparative experiments show our protocol remains competitive with leaky approaches in efficiency. Enabling ID-hiding aggregation, our techniques can extend to other vertically partitioned analytics.

MinerU-Popo: Universal Post-Processing Model for Structured Document Parsing

VLM-based OCR models have become the de facto choice for document parsing, as they can accurately extract page-level elements (e.g., paragraphs within individual pages) together with their bounding boxes and textual content. However, downstream applications such as RAG require coherent document-level information, whereas these models often break cross-page continuity and fail to recover disrupted structures, such as paragraphs and tables truncated by page boundaries. Such relationships are not confined to a single page; instead, they require joint analysis of titles, paragraphs, tables, and images spanning multiple pages. A natural solution is therefore to reuse existing OCR outputs and reconstruct document-level logical structures through post-processing. To this end, we propose MinerU-Popo, a lightweight and universal framework for POst-Processing OCR outputs, which converts page-level results from diverse parsers into coherent document-level structures. MinerU-Popo decomposes the problem into four focused subtasks: text truncation recovery, table truncation recovery, title hierarchy reconstruction, and image-text association. To address these effectively, we build a task-oriented data engine with task-specific input filtering, and use the generated data (30K) to fine-tune a lightweight post-processing model (Qwen3-VL-4B). To support long documents, we introduce dynamic chunking with overlap-based synchronization, which aligns chunk-level outputs from the fine-tuned model and preserves global consistency. Finally, we assemble the aligned outputs into a tree-structured document representation, further enriched with node chunking and summaries for downstream retrieval and analysis. Empirical results show MinerU-Popo improves title-hierarchy TEDS by at least 20% across all five tested OCR models, improves RAG accuracy and reduces per-query latency.

Keyphrase Generative Representation of Youth Crisis Conversations Beyond Static Taxonomies

Crisis Responders (CRs) rapidly assess thousands of youth SMS conversations each year to identify mental health concerns and guide support. Yet youth distress is increasingly expressed through evolving and context-specific language that often does not fit fixed-label taxonomies. This work analyzed 703,975 de-identified Kids Help Phone conversations (2018-2023) and expanded KHP's 19-label issue taxonomy into a 39-label hierarchical schema. We then introduce Keyphrase Generative Representation (KGR), a constrained LLM generating concise, conversation-specific keyphrases, evaluated across 129 conversations and 387 expert annotations. The expanded taxonomy achieved expert consensus reliability, with an accuracy of 0.96, and expert review found that 81% of keyphrases accurately reflected content and 74% improved clarity. KGR surfaced identity-linked themes absent from the fixed taxonomy, including immigration problems and caregiver burden, and supported a topic-retrieval workflow that increased accuracy from 0.25 to 0.70 (+0.45) over the manual analyst process. KGR marks a shift toward hybrid, interpretable generative representations that extend crisis response beyond static taxonomies to surface emerging and culturally grounded patterns of youth distress.

MobileMoE: Scaling On-Device Mixture of Experts

Mixture-of-Experts (MoE) has become the de facto architecture for hundred-billion-parameter language models, yet its advantages at sub-billion scales for on-device deployment remain largely unexplored. To close this gap, we present MobileMoE, a family of on-device MoE language models with sub-billion active parameters (0.3-0.9B active and 1.3-5.3B total) that establish a new Pareto frontier for on-device LLMs. We first formulate an on-device MoE scaling law that jointly optimizes MoE architecture under mobile memory and compute constraints, identifying an on-device sweet spot - moderate sparsity with fine-grained and shared experts - that is simultaneously memory and compute-optimal. Building on the derived architectures, we train MobileMoE with a four-stage recipe covering pre-training, mid-training, instruction fine-tuning, and quantization-aware training, all on open-source datasets. Across 14 benchmarks, MobileMoE matches or exceeds leading on-device dense LLMs with 2-4$\times$ fewer inference FLOPs, and matches or surpasses the state-of-the-art MoE OLMoE-1B-7B with up to 60% fewer parameters. To bridge the last mile to mobile deployment, we provide the first efficient MoE inference on commodity smartphones with comprehensive on-device profiling. At comparable INT4 weight memory, MobileMoE-S delivers $1.8$-$3.8\times$ faster prefill and $2.2$-$3.4\times$ faster decode than the dense baseline MobileLLM-Pro.

MechRL: Reinforcement Learning Agents Perform Circuit Discovery for Mechanistic Interpretability

Mechanistic interpretability has identified small sets of attention heads that implement specific behaviours in transformer language models, but recovering these circuits typically requires a bespoke analytical pipeline for each new task. We recast circuit discovery as a reinforcement-learning problem. An agent operates over the 144 attention heads of GPT-2 small as a discrete action space; each action triggers a zero-ablation and a contrastive reward that subtracts the ablation's damage to general next-token prediction from its damage to the target task. A single PPO policy, trained on two tasks (induction and IOI) in a vectorised multi-task environment, attains the per-episode oracle on both training tasks and on a held-out third task (docstring completion). Its preferred heads coincide with the canonical heads of established literature on precisely the axes those papers identify as causally non-redundant under single-head ablation; the categories they identify as redundant are correctly de-prioritised by the agent. On the held-out task, best-of-five planning recovers 96\% of the oracle ceiling with no task signal supplied at evaluation. These results indicate that reinforcement learning over causal interventions is a viable, transferable substrate for identifying the single-head bottlenecks of mechanistic circuits, complementary to existing path-patching approaches.