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Dongbo Wang

Publications and source records attributed to Dongbo Wang.

9 recordsLinked to original sources

G-Power: Architecture-level GPU Power Modeling with Aggregated Knowledge Foundations from Known GPUs

Graphics Processing Units (GPUs) have been serving as critical computation resources for large-scale parallel computations. With increasing chip complexity, power efficiency has become an important design objective for modern GPUs. GPU power optimization relies on fast power evaluation, requiring architecture-level GPU power model. However, because of the time-consuming power label collection, only simple microbenchmarks are adopted for training. The limitation of microbenchmarks as training data incurs low accuracy for existing architecture-level GPU power models like AccelWattch. To address the limitation of microbenchmarks as training data, we propose G-Power, an architecture-level GPU power modeling framework that utilizes additional known GPU chips to provide additional knowledge. G-Power utilizes the aggregated knowledge foundation from additional known GPU chips and then performs fine-tuning on our target GPU. To provide foundations with additional known GPU chips and capture the similarity to utilize these foundations for fine-tuning, G-Power adopts a three-phase algorithm consisting of 1) pre-training with additional known chips, 2) attention-inspired aggregation, and 3) fine-tuning on our target GPU. We evaluate G-Power on four modern NVIDIA GPUs, demonstrating high accuracy. G-Power can achieve a low MAPE of 14% and a high correlation coefficient R of 0.88 on average, which are 22% lower MAPE and 0.36 higher R than AccelWattch.

cs.AR

Interpretable structural-semantic decoding reveals language-like organisation of regulatory information in DNA

Decoding how linear DNA encodes regulatory information remains a central challenge. Existing decoding approaches lack interpretability and struggle to reveal the underlying coding principles. Here, we present the interpretability-first, structural artificial intelligence (AI) framework for DNA (ISAF4DNA), which uses state-aware symbolic encoding and couples structural unit discovery with semantic validation to form a closed-loop structural-semantic decoder. When applied to N6-methyladenine (6mA) datasets from 63 species, ISAF4DNA reveals a language-like organization of regulatory information: (i) a conserved motif-derivation pathway AT -> GAT/ATC -> GATC; (ii) two forms of redundant syntax: anchor-type structures with a conserved core and selective flanks, and fuzzy-type clusters composed of distributed units with positional tolerance; and (iii) differential deployment trends between prokaryotes and multicellular eukaryotes. Together, these observations motivate the development of a testable framework, EpigenoLinguistics, that treats motifs as lexical units, redundancy as syntax, and deployment as pragmatics. This framework advances the ``DNA as language'' concept from a metaphor to a falsifiable framework with supporting evidence, thereby bridging biology and computational linguistics. ISAF4DNA advances the application of AI techniques in biology from black-box predictions to mechanism-level signals, augments database annotations, and guides regulatory-element design, with principles extensible to other modifications.

q-bio.OT

A DNA-Centric Mechanism for Protein Targeting in 6mA Methylation

How DNA-binding proteins locate specific genomic targets remains a central challenge in molecular biology. Traditional protein-centric approaches, which rely on wet-lab experiments and visualization techniques, often lack genome-wide resolution and fail to capture physiological dynamics in living cells. Here, we introduce a DNA-centric strategy that leverages in vivo N6-methyladenine (6mA) data to decode the logic of protein-DNA recognition. By integrating linguistically inspired modeling with machine learning, we reveal two distinct search modes: a protein-driven diffusion mechanism and a DNA sequence-driven mechanism, wherein specific motifs function as protein traps. We further reconstruct high-resolution interaction landscapes at the level of individual sequences and trace the evolutionary trajectories of recognition motifs across species. This framework addresses fundamental limitations of protein-centered approaches and positions DNA itself as an intrinsic reporter of protein-binding behavior.

q-bio.QM

Can reasoning models comprehend mathematical problems in Chinese ancient texts? An empirical study based on data from Suanjing Shishu

This study addresses the challenges in intelligent processing of Chinese ancient mathematical classics by constructing Guji_MATH, a benchmark for evaluating classical texts based on Suanjing Shishu. It systematically assesses the mathematical problem-solving capabilities of mainstream reasoning models under the unique linguistic constraints of classical Chinese. Through machine-assisted annotation and manual verification, 538 mathematical problems were extracted from 8 canonical texts, forming a structured dataset centered on the "Question-Answer-Solution" framework, supplemented by problem types and difficulty levels. Dual evaluation modes--closed-book (autonomous problem-solving) and open-book (reproducing classical solution methods)--were designed to evaluate the performance of six reasoning models on ancient Chinese mathematical problems. Results indicate that reasoning models can partially comprehend and solve these problems, yet their overall performance remains inferior to benchmarks on modern mathematical tasks. Enhancing models' classical Chinese comprehension and cultural knowledge should be prioritized for optimization. This study provides methodological support for mining mathematical knowledge from ancient texts and disseminating traditional culture, while offering new perspectives for evaluating cross-linguistic and cross-cultural capabilities of reasoning models.

cs.CL

Fusing Bidirectional Chains of Thought and Reward Mechanisms A Method for Enhancing Question-Answering Capabilities of Large Language Models for Chinese Intangible Cultural Heritage

The rapid development of large language models (LLMs) has provided significant support and opportunities for the advancement of domain-specific LLMs. However, fine-tuning these large models using Intangible Cultural Heritage (ICH) data inevitably faces challenges such as bias, incorrect knowledge inheritance, and catastrophic forgetting. To address these issues, we propose a novel training method that integrates a bidirectional chains of thought and a reward mechanism. This method is built upon ICH-Qwen, a large language model specifically designed for the field of intangible cultural heritage. The proposed method enables the model to not only perform forward reasoning but also enhances the accuracy of the generated answers by utilizing reverse questioning and reverse reasoning to activate the model's latent knowledge. Additionally, a reward mechanism is introduced during training to optimize the decision-making process. This mechanism improves the quality of the model's outputs through structural and content evaluations with different weighting schemes. We conduct comparative experiments on ICH-Qwen, with results demonstrating that our method outperforms 0-shot, step-by-step reasoning, knowledge distillation, and question augmentation methods in terms of accuracy, Bleu-4, and Rouge-L scores on the question-answering task. Furthermore, the paper highlights the effectiveness of combining the bidirectional chains of thought and reward mechanism through ablation experiments. In addition, a series of generalizability experiments are conducted, with results showing that the proposed method yields improvements on various domain-specific datasets and advanced models in areas such as Finance, Wikidata, and StrategyQA. This demonstrates that the method is adaptable to multiple domains and provides a valuable approach for model training in future applications across diverse fields.

cs.CL

ICH-Qwen: A Large Language Model Towards Chinese Intangible Cultural Heritage

The intangible cultural heritage (ICH) of China, a cultural asset transmitted across generations by various ethnic groups, serves as a significant testament to the evolution of human civilization and holds irreplaceable value for the preservation of historical lineage and the enhancement of cultural self-confidence. However, the rapid pace of modernization poses formidable challenges to ICH, including threats damage, disappearance and discontinuity of inheritance. China has the highest number of items on the UNESCO Intangible Cultural Heritage List, which is indicative of the nation's abundant cultural resources and emphasises the pressing need for ICH preservation. In recent years, the rapid advancements in large language modelling have provided a novel technological approach for the preservation and dissemination of ICH. This study utilises a substantial corpus of open-source Chinese ICH data to develop a large language model, ICH-Qwen, for the ICH domain. The model employs natural language understanding and knowledge reasoning capabilities of large language models, augmented with synthetic data and fine-tuning techniques. The experimental results demonstrate the efficacy of ICH-Qwen in executing tasks specific to the ICH domain. It is anticipated that the model will provide intelligent solutions for the protection, inheritance and dissemination of intangible cultural heritage, as well as new theoretical and practical references for the sustainable development of intangible cultural heritage. Furthermore, it is expected that the study will open up new paths for digital humanities research.

cs.CL

Language-Inspired Modeling Reveals Redundant Encoding of N4-acetylcytidine(ac4C) Modifications in mRNA

The ac4C modification on mRNA has been demonstrated to be associated with various diseases; however, its molecular mechanism remains unclear. The wet lab experiments produced relatively rough data, which lack precise ac4C modification sites, and extracting valuable information from such data remains a challenge. In this study, we integrate linguistics, traditional machine learning, and deep learning, establishing a link between the understanding of mRNA data and natural language processing (NLP). Through our analysis, we successfully revealed key information about ac4C in mRNA and uncovered the information storage mechanism of ac4C redundancy on a single sequence. This redundant information storage method in mRNA facilitates the transmission of ac4C information and promotes the enrichment of ac4C.

q-bio.OT

GujiBERT and GujiGPT: Construction of Intelligent Information Processing Foundation Language Models for Ancient Texts

In the context of the rapid development of large language models, we have meticulously trained and introduced the GujiBERT and GujiGPT language models, which are foundational models specifically designed for intelligent information processing of ancient texts. These models have been trained on an extensive dataset that encompasses both simplified and traditional Chinese characters, allowing them to effectively handle various natural language processing tasks related to ancient books, including but not limited to automatic sentence segmentation, punctuation, word segmentation, part-of-speech tagging, entity recognition, and automatic translation. Notably, these models have exhibited exceptional performance across a range of validation tasks using publicly available datasets. Our research findings highlight the efficacy of employing self-supervised methods to further train the models using classical text corpora, thus enhancing their capability to tackle downstream tasks. Moreover, it is worth emphasizing that the choice of font, the scale of the corpus, and the initial model selection all exert significant influence over the ultimate experimental outcomes. To cater to the diverse text processing preferences of researchers in digital humanities and linguistics, we have developed three distinct categories comprising a total of nine model variations. We believe that by sharing these foundational language models specialized in the domain of ancient texts, we can facilitate the intelligent processing and scholarly exploration of ancient literary works and, consequently, contribute to the global dissemination of China's rich and esteemed traditional culture in this new era.

cs.CL

SsciBERT: A Pre-trained Language Model for Social Science Texts

The academic literature of social sciences records human civilization and studies human social problems. With its large-scale growth, the ways to quickly find existing research on relevant issues have become an urgent demand for researchers. Previous studies, such as SciBERT, have shown that pre-training using domain-specific texts can improve the performance of natural language processing tasks. However, the pre-trained language model for social sciences is not available so far. In light of this, the present research proposes a pre-trained model based on the abstracts published in the Social Science Citation Index (SSCI) journals. The models, which are available on GitHub (https://github.com/S-T-Full-Text-Knowledge-Mining/SSCI-BERT), show excellent performance on discipline classification, abstract structure-function recognition, and named entity recognition tasks with the social sciences literature.

cs.CL