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Jul 29

MicroVQA++: High-Quality Microscopy Reasoning Dataset with Weakly Supervised Graphs for Multimodal Large Language Model

Multimodal Large Language Models are increasingly applied to biomedical imaging, yet scientific reasoning for microscopy remains limited by the scarcity of large-scale, high-quality training data. We introduce MicroVQA++, a three-stage, large-scale and high-quality microscopy VQA corpus derived from the BIOMEDICA archive. Stage one bootstraps supervision from expert-validated figure-caption pairs sourced from peer-reviewed articles. Stage two applies HiCQA-Graph, a novel heterogeneous graph over images, captions, and QAs that fuses NLI-based textual entailment, CLIP-based vision-language alignment, and agent signals to identify and filter inconsistent samples. Stage three uses a MultiModal Large Language Model (MLLM) agent to generate multiple-choice questions (MCQ) followed by human screening. The resulting release comprises a large training split and a human-checked test split whose Bloom's level hard-sample distribution exceeds the MicroVQA benchmark. Our work delivers (i) a quality-controlled dataset that couples expert literature with graph-based filtering and human refinement; (ii) HiCQA-Graph, the first graph that jointly models (image, caption, QA) for cross-modal consistency filtering; (iii) evidence that careful data construction enables 4B-scale MLLMs to reach competitive microscopy reasoning performance (e.g., GPT-5) and achieve state-of-the-art performance among open-source MLLMs. Code and dataset will be released after the review process concludes.

  • 5 authors
·
Nov 14, 2025 2

cuSBF: A Minimizer-Aware Bloom Filter for Genomic Sequence Data on Modern GPUs

Efficient genomic k-mer indexing depends on approximate membership query (AMQ) structures that must deliver high throughput, low false-positive rates (FPR), and modest memory footprints. The Super Bloom filter (SBF) is attractive for this scenario because minimizer-guided sharding and the Findere scheme exploit the redundancy of overlapping k-mers. However, those same features cause high per-k-mer compute cost, severe register pressure, and irregular memory accesses, which hinder an effective GPU implementation. We present cuSBF, an open-source, header-only CUDA library that implements SBF for sequence-native workloads. cuSBF's design merges sectorized shards, cooperative shared-memory tiling, warp-level shard sharing, and segmented warp reductions, turning super-k-mer locality into scalable GPU parallelism. Across real genomic workloads on RTX PRO 6000 Blackwell and GH200 systems, cuSBF achieves the highest throughput among all evaluated sequence-capable baselines. On the RTX PRO 6000, it surpasses the cuCollections blocked Bloom filter baseline by up to 9.1x for insertion and 7.7x for query, while reaching up to 92x and 234x speedups over the multi-threaded CPU Super Bloom reference implementation. It also outperforms GPU-based dynamic AMQs (Cuckoo, Two-Choice, Quotient filters) by 1.5-3400x depending on workload characteristics. A parameter sweep identifies (s = 28, m = 16, H = 4) as Pareto-optimal for k = 31, yielding significantly lower FPR than cuCollections at matched memory budgets. Crucially, cuSBF's architecture-aware design sustains 85% streaming multiprocessor utilization even for out-of-cache filters - proving that sequence locality, not raw bandwidth, is the key to GPU-accelerated genomic indexing.

  • 3 authors
·
Jun 22

Almieyar-Oryx-BloomBench: A Bilingual Multimodal Benchmark for Cognitively Informed Evaluation of Vision-Language Models

Despite the rapid progress of Vision-Language Models (VLMs), the field lacks benchmarks that rigorously diagnose their true reasoning abilities and chart meaningful progress toward human-like multimodal intelligence. Most existing evaluations focus on piecemeal or disconnected tasks, obscuring critical cognitive weaknesses and providing little insight for targeted improvement. To address this gap, we introduce BloomBench, part of the Almieyar benchmarking series, the first cognitively human-grounded, bilingual (English-Arabic) multimodal benchmark for VLMs. Grounded in Bloom's Taxonomy, BloomBench systematically evaluates six levels of cognition (Remember, Understand, Apply, Analyze, Evaluate, Create) through carefully designed image-question-answer tasks. Built with a semi-automated pipeline and validated through a stratified hybrid quality assurance protocol, it ensures scalability, cultural inclusivity, and linguistic fidelity. Leveraging this framework, we conduct a comprehensive study of state-of-the-art VLMs to diagnose their cognitive profiles. Our analysis reveals a sharp cognitive asymmetry: while state-of-the-art models achieve strong performance ceilings in semantic understanding, they struggle substantially with factual recall and creative synthesis. This demonstrates that current general multimodal proficiency masks deeper limitations in specific cognitive layers. Furthermore, our study highlights a critical performance gap between Arabic and English, exposing limitations in current cross-lingual multimodal reasoning. These findings establish a foundation for developing more cognitively aligned and inclusive VLMs. The benchmark framework and dataset is available at: https://github.com/qcri/Almieyar-Oryx-BloomBench.

VLegal-Bench: Cognitively Grounded Benchmark for Vietnamese Legal Reasoning of Large Language Models

The rapid advancement of large language models (LLMs) has enabled new possibilities for applying artificial intelligence within the legal domain. Nonetheless, the complexity, hierarchical organization, and frequent revisions of Vietnamese legislation pose considerable challenges for evaluating how well these models interpret and utilize legal knowledge. To address this gap, the Vietnamese Legal Benchmark (VLegal-Bench) is introduced, the first comprehensive benchmark designed to systematically assess LLMs on Vietnamese legal tasks. Informed by Bloom's cognitive taxonomy, VLegal-Bench encompasses multiple levels of legal understanding through tasks designed to reflect practical usage scenarios. The benchmark comprises 10,450 samples generated through a rigorous annotation pipeline, where legal experts label and cross-validate each instance using our annotation system to ensure every sample is grounded in authoritative legal documents and mirrors real-world legal assistant workflows, including general legal questions and answers, retrieval-augmented generation, multi-step reasoning, and scenario-based problem solving tailored to Vietnamese law. By providing a standardized, transparent, and cognitively informed evaluation framework, VLegal-Bench establishes a solid foundation for assessing LLM performance in Vietnamese legal contexts and supports the development of more reliable, interpretable, and ethically aligned AI-assisted legal systems. To facilitate access and reproducibility, we provide a public landing page for this benchmark at https://vilegalbench.cmcai.vn/.

  • 9 authors
·
Dec 16, 2025

Towards Autonomous Mathematics Research

Recent advances in foundational models have yielded reasoning systems capable of achieving a gold-medal standard at the International Mathematical Olympiad. The transition from competition-level problem-solving to professional research, however, requires navigating vast literature and constructing long-horizon proofs. In this work, we introduce Aletheia, a math research agent that iteratively generates, verifies, and revises solutions end-to-end in natural language. Specifically, Aletheia is powered by an advanced version of Gemini Deep Think for challenging reasoning problems, a novel inference-time scaling law that extends beyond Olympiad-level problems, and intensive tool use to navigate the complexities of mathematical research. We demonstrate the capability of Aletheia from Olympiad problems to PhD-level exercises and most notably, through several distinct milestones in AI-assisted mathematics research: (a) a research paper (Feng26) generated by AI without any human intervention in calculating certain structure constants in arithmetic geometry called eigenweights; (b) a research paper (LeeSeo26) demonstrating human-AI collaboration in proving bounds on systems of interacting particles called independent sets; and (c) an extensive semi-autonomous evaluation (Feng et al., 2026a) of 700 open problems on Bloom's Erdos Conjectures database, including autonomous solutions to four open questions. In order to help the public better understand the developments pertaining to AI and mathematics, we suggest codifying standard levels quantifying autonomy and novelty of AI-assisted results. We conclude with reflections on human-AI collaboration in mathematics.

google Google
·
Feb 10 1

Instruction Tuning with Human Curriculum

The dominant paradigm for instruction tuning is the random-shuffled training of maximally diverse instruction-response pairs. This paper explores the potential benefits of applying a structured cognitive learning approach to instruction tuning in contemporary large language models like ChatGPT and GPT-4. Unlike the previous conventional randomized instruction dataset, we propose a highly structured synthetic dataset that mimics the progressive and organized nature of human education. We curate our dataset by aligning it with educational frameworks, incorporating meta information including its topic and cognitive rigor level for each sample. Our dataset covers comprehensive fine-grained topics spanning diverse educational stages (from middle school to graduate school) with various questions for each topic to enhance conceptual depth using Bloom's taxonomy-a classification framework distinguishing various levels of human cognition for each concept. The results demonstrate that this cognitive rigorous training approach yields significant performance enhancements - +3.06 on the MMLU benchmark and an additional +1.28 on AI2 Reasoning Challenge (hard set) - compared to conventional randomized training, all while avoiding additional computational costs. This research highlights the potential of leveraging human learning principles to enhance the capabilities of language models in comprehending and responding to complex instructions and tasks.

  • 3 authors
·
Oct 14, 2023

OpenLearnLM Benchmark: A Unified Framework for Evaluating Knowledge, Skill, and Attitude in Educational Large Language Models

Large Language Models are increasingly deployed as educational tools, yet existing benchmarks focus on narrow skills and lack grounding in learning sciences. We introduce OpenLearnLM Benchmark, a theory-grounded framework evaluating LLMs across three dimensions derived from educational assessment theory: Knowledge (curriculum-aligned content and pedagogical understanding), Skills (scenario-based competencies organized through a four-level center-role-scenario-subscenario hierarchy), and Attitude (alignment consistency and deception resistance). Our benchmark comprises 124K+ items spanning multiple subjects, educational roles, and difficulty levels based on Bloom's taxonomy. The Knowledge domain prioritizes authentic assessment items from established benchmarks, while the Attitude domain adapts Anthropic's Alignment Faking methodology to detect behavioral inconsistency under varying monitoring conditions. Evaluation of seven frontier models reveals distinct capability profiles: Claude-Opus-4.5 excels in practical skills despite lower content knowledge, while Grok-4.1-fast leads in knowledge but shows alignment concerns. Notably, no single model dominates all dimensions, validating the necessity of multi-axis evaluation. OpenLearnLM provides an open, comprehensive framework for advancing LLM readiness in authentic educational contexts.

  • 14 authors
·
Jan 19