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Nov 10

Training, learning and inference: unified dynamics of neural systems

We define an atomic generation fact f=(u,tau,omega,z;rho), recording the origin, realized transformation, concrete occurrence, generated result and relation role. Compiled into a Generation-Fact Graph (GFG), these facts provide an AI-native, compilable scientific fact substrate preserving generation histories. We establish a GFG-based recursive scientific process in which analysis, intervention, replay and validation form facts for later cycles. Using nanoGPT, we establish unified training-learning dynamics. Training is the evolution of a parameter-optimizer system with state and memory: each actual training action enters the receiving state and produces a finite-amplitude nonlinear functional response conditioned by that state and target-specific update geometry. Learning is the persistent reorganization of distributed functional support by these responses; capability formation, maintenance, decline or recovery becomes observable when target-specific states are evaluated against their readout boundaries. Three primary coordinates - target-boundary state, target-specific update geometry and parameter-Adam receiving state - yield a second-order predictor operating before post-update outputs are read. On held-out runs, it achieved 91.43% accuracy and 91.49% macro-averaged recall across four transitions. We further establish inference as a frozen projection of training-learning dynamics. Component gating and rollback show causal recruitment and non-additive combination of query-conditioned support formed during training, deriving organizational conditions realized by Attention. Controlled feedback indicates possible double-edged reinforcement effects. ResNet/CIFAR-100 and diffusion/CIFAR-10 experiments confirm receiving-state-conditioned responses, persistent support reorganization and frozen inference projection beyond nanoGPT.

  • 1 authors
·
Aug 20 2

Enhancing Domain-Specific Retrieval-Augmented Generation: Synthetic Data Generation and Evaluation using Reasoning Models

Retrieval-Augmented Generation (RAG) systems face significant performance gaps when applied to technical domains requiring precise information extraction from complex documents. Current evaluation methodologies relying on document-level metrics inadequately capture token-resolution retrieval accuracy that is critical for domain-related documents. We propose a framework combining granular evaluation metrics with synthetic data generation to optimize domain-specific RAG performance. First, we introduce token-aware metrics Precision Omega and Intersection-over-Union (IoU) that quantify context preservation versus information density trade-offs inherent in technical texts. Second, we develop a reasoning model-driven pipeline using instruction-tuned LLMs (DeepSeek-R1, DeepSeek-R1 distilled variants, and Phi-4) to generate context-anchored QA pairs with discontinuous reference spans across three specialized corpora: SEC 10-K filings (finance), biomedical abstracts (PubMed), and APT threat reports (cybersecurity). Our empirical analysis reveals critical insights: smaller chunks (less than 10 tokens) improve precision by 31-42% (IoU = 0.071 vs. baseline 0.053) at recall costs (-18%), while domain-specific embedding strategies yield 22% variance in optimal chunk sizing (5-20 tokens). The DeepSeek-R1-Distill-Qwen-32B model demonstrates superior concept alignment (+14% mean IoU over alternatives), though no configuration universally dominates. Financial texts favor larger chunks for risk factor coverage (Recall = 0.81 at size = 20), whereas cybersecurity content benefits from atomic segmentation, Precision Omega = 0.28 at size = 5. Our code is available on https://github.com/aryan-jadon/Synthetic-Data-Generation-and-Evaluation-using-Reasoning-Model

  • 3 authors
·
Feb 21, 2025

From Terminology to Diagrams: Visual-Instruction Generation for Scientific Diagram Understanding

Vision-language models (VLMs) have demonstrated strong performance in visual question answering with natural images. However, they continue to struggle with scientific diagrams, which are designed to convey functional or relational meaning rather than literal scenes. We therefore introduce a framework for generating large-scale diagram-grounded instruction data by leveraging terminology derived from scientific curricula. Our approach systematically extracts domain concepts, synthesizes atomic facts, retrieves relevant diagrams from the web, and generates multimodal supervision in the form of diagram captions and multiple-choice questions. Using this pipeline, we construct SciGram, a dataset of over 194K diagrams and 1.4M visual instructions across life, earth, and physical sciences. Despite relying on noisy web data and synthetic annotations, models fine-tuned on SciGram achieve substantial improvements on diagram-centric benchmarks, including TQA, ScienceQA, and AI2D, outperforming or matching state-of-the-art VLMs while using fewer training instances. Furthermore, augmenting existing models such as LLaVA OneVision with SciGram establishes new state-of-the-art performance on diagram question answering. Our results highlight the effectiveness of terminology-grounded instruction generation as a general strategy for improving vision-language reasoning in scientific domains. To support future research in scientific diagram understanding, we release both the SciGram dataset and models.

  • 2 authors
·
Aug 31

AtomicRAG: Atom-Entity Graphs for Retrieval-Augmented Generation

Recent GraphRAG methods integrate graph structures into text indexing and retrieval, using knowledge graph triples to connect text chunks, thereby improving retrieval coverage and precision. However, we observe that treating text chunks as the basic unit of knowledge representation rigidly groups multiple atomic facts together, limiting the flexibility and adaptability needed to support diverse retrieval scenarios. Additionally, triple-based entity linking is sensitive to relation-extraction errors, which can lead to missing or incorrect reasoning paths and ultimately hurt retrieval accuracy. To address these issues, we propose the Atom-Entity Graph, a more precise and reliable architecture for knowledge representation and indexing. In our approach, knowledge is stored as knowledge atoms, namely individual, self-contained units of factual information, rather than coarse-grained text chunks. This allows knowledge elements to be flexibly reassembled without mutual interference, thereby enabling seamless alignment with diverse query perspectives. Edges between entities simply indicate whether a relationship exists. By combining personalized PageRank with relevance-based filtering, we maintain accurate entity connections and improve the reliability of reasoning. Theoretical analysis and experiments on five public benchmarks show that the proposed AtomicRAG algorithm outperforms strong RAG baselines in retrieval accuracy and reasoning robustness. Code: https://github.com/7HHHHH/AtomicRAG.

  • 8 authors
·
Feb 9

Unveiling and Bridging the Functional Perception Gap in MLLMs: Atomic Visual Alignment and Hierarchical Evaluation via PET-Bench

While Multimodal Large Language Models (MLLMs) have demonstrated remarkable proficiency in tasks such as abnormality detection and report generation for anatomical modalities, their capability in functional imaging remains largely unexplored. In this work, we identify and quantify a fundamental functional perception gap: the inability of current vision encoders to decode functional tracer biodistribution independent of morphological priors. Identifying Positron Emission Tomography (PET) as the quintessential modality to investigate this disconnect, we introduce PET-Bench, the first large-scale functional imaging benchmark comprising 52,308 hierarchical QA pairs from 9,732 multi-site, multi-tracer PET studies. Extensive evaluation of 19 state-of-the-art MLLMs reveals a critical safety hazard termed the Chain-of-Thought (CoT) hallucination trap. We observe that standard CoT prompting, widely considered to enhance reasoning, paradoxically decouples linguistic generation from visual evidence in PET, producing clinically fluent but factually ungrounded diagnoses. To resolve this, we propose Atomic Visual Alignment (AVA), a simple fine-tuning strategy that enforces the mastery of low-level functional perception prior to high-level diagnostic reasoning. Our results demonstrate that AVA effectively bridges the perception gap, transforming CoT from a source of hallucination into a robust inference tool and improving diagnostic accuracy by up to 14.83%. Code and data are available at https://github.com/yezanting/PET-Bench.

  • 17 authors
·
Jan 6

HALoGEN: Fantastic LLM Hallucinations and Where to Find Them

Despite their impressive ability to generate high-quality and fluent text, generative large language models (LLMs) also produce hallucinations: statements that are misaligned with established world knowledge or provided input context. However, measuring hallucination can be challenging, as having humans verify model generations on-the-fly is both expensive and time-consuming. In this work, we release HALoGEN, a comprehensive hallucination benchmark consisting of: (1) 10,923 prompts for generative models spanning nine domains including programming, scientific attribution, and summarization, and (2) automatic high-precision verifiers for each use case that decompose LLM generations into atomic units, and verify each unit against a high-quality knowledge source. We use this framework to evaluate ~150,000 generations from 14 language models, finding that even the best-performing models are riddled with hallucinations (sometimes up to 86% of generated atomic facts depending on the domain). We further define a novel error classification for LLM hallucinations based on whether they likely stem from incorrect recollection of training data (Type A errors), or incorrect knowledge in training data (Type B errors), or are fabrication (Type C errors). We hope our framework provides a foundation to enable the principled study of why generative models hallucinate, and advances the development of trustworthy large language models.

  • 4 authors
·
Jan 14, 2025 2

ZoomCap: Evidence-Routed Visual Zooming for Recoverable Visual Information Transfer

Detailed captions transfer visual information into vision-language model supervision, but quality is easily conflated with length: long single-pass outputs still miss small objects, text, and spatial relations or promote uncertain observations into confident claims. We formulate fine-grained captioning as recoverable visual information transfer, in which a teacher acquires missing evidence under a finite observation budget and converts it into reusable supervision. ZoomCap uses a draft caption to route conditional knowledge retrieval, OCR-sensitive reading, coverage-gap recovery, and adaptive visual zooming, allocating deeper crops only to the most complex eligible region, deriving spatial relations from grounded geometry, and fusing non-duplicate evidence. We also introduce FactCycle, which scores caption-derived atomic claims on two blind anchors--source image (truthfulness) and reconstruction (realizability)--separating fabrication from generator loss claim by claim; human and multi-judge comparisons complement this fact-level view. Against Qwen3.5-397B-A17B captions, ZoomCap achieves an 81.9% human tie-adjusted preference score with a teacher over 10x smaller, and FactCycle counts 52.4 transferred claims per image vs. 31.5 for ScaleCap. The evidence also transfers: in continual pre-training, ZoomCap-450K improves the 11-benchmark average by 1.31-2.38 points over the strongest competing corpus and Ling-Tiny-VL-v3 gains 1.4 points on a production document/OCR monitor suite (1.5 on perception) at 60B tokens; in medical pre-training, 2.64M ZoomCap-captioned images improve five VQA benchmarks by 3.04 points (vs. 1.76 for same-image Gemini-3.1-Pro captions).

  • 8 authors
·
Oct 14

Spectroscopic measurements and models of energy deposition in the substrate of quantum circuits by natural ionizing radiation

Naturally occurring background radiation is a source of correlated decoherence events in superconducting qubits that will challenge error-correction schemes. To characterize the radiation environment in an unshielded laboratory, we performed broadband, spectroscopic measurements of background events in silicon substrates located inside a millikelvin refrigerator, an environment representative of superconducting qubit systems. We measured the background spectra in silicon substrates of two thicknesses, 0.5 mm and 1.5 mm, and obtained the average event rate and the integrated power deposition. In a 25 mm^2 area and the thinner substrate, these values are 0.023 events per second and 4.9 keV/s, counting events that deposit at least 40 keV. We find the background spectrum to be nearly featureless. Its intensity decreases by a factor of 40,000 between 100 keV and 3 MeV for silicon substrates 0.5 mm thick. We find the cryogenic measurements to be in good agreement with predictions based on measurements of the terrestrial gamma-ray flux, published models of cosmic-ray fluxes, a crude model of the cryostat, and radiation-transport simulations. No free parameters are required to predict the background spectra in the silicon substrates. The good agreement between measurements and predictions allow assessment of the relative contributions of terrestrial and cosmic background sources and their dependence on substrate thickness. Our spectroscopic measurements are performed with superconducting microresonators that transduce deposited energy to a readily detectable electrical signal. We find that gamma-ray emissions from radioisotopes are responsible for the majority of events depositing E<1.5 MeV, while nucleons among the cosmic-ray secondary particles cause most events that deposit more energy. These results suggest several paths to reducing the impact of background radiation on quantum circuits.

  • 19 authors
·
Oct 10, 2024