Yuqi Zhou

Sunhao Dai, Yuqi Zhou, Liang Pang et al.

Recently, the emergence of large language models (LLMs) has revolutionized the paradigm of information retrieval (IR) applications, especially in web search, by generating vast amounts of human-like texts on the Internet. As a result, IR systems in the LLM era are facing a new challenge: the indexed documents are now not only written by human beings but also automatically generated by the LLMs. How these LLM-generated documents influence the IR systems is a pressing and still unexplored question. In this work, we conduct a quantitative evaluation of IR models in scenarios where both human-written and LLM-generated texts are involved. Surprisingly, our findings indicate that neural retrieval models tend to rank LLM-generated documents higher. We refer to this category of biases in neural retrievers towards the LLM-generated content as the \textbf{source bias}. Moreover, we discover that this bias is not confined to the first-stage neural retrievers, but extends to the second-stage neural re-rankers. Then, in-depth analyses from the perspective of text compression indicate that LLM-generated texts exhibit more focused semantics with less noise, making it easier for neural retrieval models to semantic match. To mitigate the source bias, we also propose a plug-and-play debiased constraint for the optimization objective, and experimental results show its effectiveness. Finally, we discuss the potential severe concerns stemming from the observed source bias and hope our findings can serve as a critical wake-up call to the IR community and beyond. To facilitate future explorations of IR in the LLM era, the constructed two new benchmarks are available at https://github.com/KID-22/Source-Bias.

Yifan Zhao, Liangchen Li, Yuqi Zhou et al.

Macro lens has the advantages of high resolution and large magnification, and 3D modeling of small and detailed objects can provide richer information. However, defocus blur in macrophotography is a long-standing problem that heavily hinders the clear imaging of the captured objects and high-quality 3D reconstruction of them. Traditional image deblurring methods require a large number of images and annotations, and there is currently no multi-view 3D reconstruction method for macrophotography. In this work, we propose a joint deblurring and 3D reconstruction method for macrophotography. Starting from multi-view blurry images captured, we jointly optimize the clear 3D model of the object and the defocus blur kernel of each pixel. The entire framework adopts a differentiable rendering method to self-supervise the optimization of the 3D model and the defocus blur kernel. Extensive experiments show that from a small number of multi-view images, our proposed method can not only achieve high-quality image deblurring but also recover high-fidelity 3D appearance.

Huixue Zhou, Robin Austin, Sheng-Chieh Lu et al.

Objective: Our study aimed to construct an exhaustive Complementary and Integrative Health (CIH) Lexicon (CIHLex) to better represent the often underrepresented physical and psychological CIH approaches in standard terminologies. We also intended to apply advanced Natural Language Processing (NLP) models such as Bidirectional Encoder Representations from Transformers (BERT) and GPT-3.5 Turbo for CIH named entity recognition, evaluating their performance against established models like MetaMap and CLAMP. Materials and Methods: We constructed the CIHLex by integrating various resources, compiling and integrating data from biomedical literature and relevant knowledge bases. The Lexicon encompasses 198 unique concepts with 1090 corresponding unique terms. We matched these concepts to the Unified Medical Language System (UMLS). Additionally, we developed and utilized BERT models and compared their efficiency in CIH named entity recognition to that of other models such as MetaMap, CLAMP, and GPT3.5-turbo. Results: From the 198 unique concepts in CIHLex, 62.1% could be matched to at least one term in the UMLS. Moreover, 75.7% of the mapped UMLS Concept Unique Identifiers (CUIs) were categorized as "Therapeutic or Preventive Procedure." Among the models applied to CIH named entity recognition, BLUEBERT delivered the highest macro average F1-score of 0.90, surpassing other models. Conclusion: Our CIHLex significantly augments representation of CIH approaches in biomedical literature. Demonstrating the utility of advanced NLP models, BERT notably excelled in CIH entity recognition. These results highlight promising strategies for enhancing standardization and recognition of CIH terminology in biomedical contexts.

Dalton Schutte, Jake Vasilakes, Anu Bompelli et al.

OBJECTIVE: Leverage existing biomedical NLP tools and DS domain terminology to produce a novel and comprehensive knowledge graph containing dietary supplement (DS) information for discovering interactions between DS and drugs, or Drug-Supplement Interactions (DSI). MATERIALS AND METHODS: We created SemRepDS (an extension of SemRep), capable of extracting semantic relations from abstracts by leveraging a DS-specific terminology (iDISK) containing 28,884 DS terms not found in the UMLS. PubMed abstracts were processed using SemRepDS to generate semantic relations, which were then filtered using a PubMedBERT-based model to remove incorrect relations before generating our knowledge graph (SuppKG). Two pathways are used to identify potential DS-Drug interactions which are then evaluated by medical professionals for mechanistic plausibility. RESULTS: Comparison analysis found that SemRepDS returned 206.9% more DS relations and 158.5% more DS entities than SemRep. The fine-tuned BERT model obtained an F1 score of 0.8605 and removed 43.86% of the relations, improving the precision of the relations by 26.4% compared to pre-filtering. SuppKG consists of 2,928 DS-specific nodes. Manual review of findings identified 44 (88%) proposed DS-Gene-Drug and 32 (64%) proposed DS-Gene1-Function-Gene2-Drug pathways to be mechanistically plausible. DISCUSSION: The additional relations extracted using SemRepDS generated SuppKG that was used to find plausible DSI not found in the current literature. By the nature of the SuppKG, these interactions are unlikely to have been found using SemRep without the expanded DS terminology. CONCLUSION: We successfully extend SemRep to include DS information and produce SuppKG which can be used to find potential DS-Drug interactions.