Deep learning-driven pulmonary arteries and veins segmentation reveals demography-associated pulmonary vasculature anatomy

Pulmonary artery-vein segmentation is crucial for diagnosing pulmonary diseases and surgical planning, and is traditionally achieved by Computed Tomography Pulmonary Angiography (CTPA). However, concerns regarding adverse health effects from contrast agents used in CTPA have constrained its clinical utility. In contrast, identifying arteries and veins using non-contrast CT, a conventional and low-cost clinical examination routine, has long been considered impossible. Here we propose a High-abundant Pulmonary Artery-vein Segmentation (HiPaS) framework achieving accurate artery-vein segmentation on both non-contrast CT and CTPA across various spatial resolutions. HiPaS first performs spatial normalization on raw CT scans via a super-resolution module, and then iteratively achieves segmentation results at different branch levels by utilizing the low-level vessel segmentation as a prior for high-level vessel segmentation. We trained and validated HiPaS on our established multi-centric dataset comprising 1,073 CT volumes with meticulous manual annotation. Both quantitative experiments and clinical evaluation demonstrated the superior performance of HiPaS, achieving a dice score of 91.8% and a sensitivity of 98.0%. Further experiments demonstrated the non-inferiority of HiPaS segmentation on non-contrast CT compared to segmentation on CTPA. Employing HiPaS, we have conducted an anatomical study of pulmonary vasculature on 10,613 participants in China (five sites), discovering a new association between pulmonary vessel abundance and sex and age: vessel abundance is significantly higher in females than in males, and slightly decreases with age, under the controlling of lung volumes (p < 0.0001). HiPaS realizing accurate artery-vein segmentation delineates a promising avenue for clinical diagnosis and understanding pulmonary physiology in a non-invasive manner.

Parameter Efficient Quasi-Orthogonal Fine-Tuning via Givens Rotation

With the increasingly powerful performances and enormous scales of Pretrained Language Models (PLMs), promoting parameter efficiency in fine-tuning has become a crucial need for effective and efficient adaptation to various downstream tasks. One representative line of fine-tuning methods is Orthogonal Fine-tuning (OFT), which rigorously preserves the angular distances within the parameter space to preserve the pretrained knowledge. Despite the empirical effectiveness, OFT still suffers low parameter efficiency at $\mathcal{O}(d^2)$ and limited capability of downstream adaptation. Inspired by Givens rotation, in this paper, we proposed quasi-Givens Orthogonal Fine-Tuning (qGOFT) to address the problems. We first use $\mathcal{O}(d)$ Givens rotations to accomplish arbitrary orthogonal transformation in $SO(d)$ with provable equivalence, reducing parameter complexity from $\mathcal{O}(d^2)$ to $\mathcal{O}(d)$. Then we introduce flexible norm and relative angular adjustments under soft orthogonality regularization to enhance the adaptation capability of downstream semantic deviations. Extensive experiments on various tasks and PLMs validate the effectiveness of our methods.

Selecting Query-bag as Pseudo Relevance Feedback for Information-seeking Conversations

Information-seeking dialogue systems are widely used in e-commerce systems, with answers that must be tailored to fit the specific settings of the online system. Given the user query, the information-seeking dialogue systems first retrieve a subset of response candidates, then further select the best response from the candidate set through re-ranking. Current methods mainly retrieve response candidates based solely on the current query, however, incorporating similar questions could introduce more diverse content, potentially refining the representation and improving the matching process. Hence, in this paper, we proposed a Query-bag based Pseudo Relevance Feedback framework (QB-PRF), which constructs a query-bag with related queries to serve as pseudo signals to guide information-seeking conversations. Concretely, we first propose a Query-bag Selection module (QBS), which utilizes contrastive learning to train the selection of synonymous queries in an unsupervised manner by leveraging the representations learned from pre-trained VAE. Secondly, we come up with a Query-bag Fusion module (QBF) that fuses synonymous queries to enhance the semantic representation of the original query through multidimensional attention computation. We verify the effectiveness of the QB-PRF framework on two competitive pretrained backbone models, including BERT and GPT-2. Experimental results on two benchmark datasets show that our framework achieves superior performance over strong baselines.

Harnessing Multi-Role Capabilities of Large Language Models for Open-Domain Question Answering

Open-domain question answering (ODQA) has emerged as a pivotal research spotlight in information systems. Existing methods follow two main paradigms to collect evidence: (1) The \textit{retrieve-then-read} paradigm retrieves pertinent documents from an external corpus; and (2) the \textit{generate-then-read} paradigm employs large language models (LLMs) to generate relevant documents. However, neither can fully address multifaceted requirements for evidence. To this end, we propose LLMQA, a generalized framework that formulates the ODQA process into three basic steps: query expansion, document selection, and answer generation, combining the superiority of both retrieval-based and generation-based evidence. Since LLMs exhibit their excellent capabilities to accomplish various tasks, we instruct LLMs to play multiple roles as generators, rerankers, and evaluators within our framework, integrating them to collaborate in the ODQA process. Furthermore, we introduce a novel prompt optimization algorithm to refine role-playing prompts and steer LLMs to produce higher-quality evidence and answers. Extensive experimental results on widely used benchmarks (NQ, WebQ, and TriviaQA) demonstrate that LLMQA achieves the best performance in terms of both answer accuracy and evidence quality, showcasing its potential for advancing ODQA research and applications.

Masked Thought: Simply Masking Partial Reasoning Steps Can Improve Mathematical Reasoning Learning of Language Models

In reasoning tasks, even a minor error can cascade into inaccurate results, leading to suboptimal performance of large language models in such domains. Earlier fine-tuning approaches sought to mitigate this by leveraging more precise supervisory signals from human labeling, larger models, or self-sampling, although at a high cost. Conversely, we develop a method that avoids external resources, relying instead on introducing perturbations to the input. Our training approach randomly masks certain tokens within the chain of thought, a technique we found to be particularly effective for reasoning tasks. When applied to fine-tuning with GSM8K, this method achieved a 5% improvement in accuracy over standard supervised fine-tuning with a few codes modified and no additional labeling effort. Furthermore, it is complementary to existing methods. When integrated with related data augmentation methods, it leads to an average improvement of 3% improvement in GSM8K accuracy and 1% improvement in MATH accuracy across five datasets of various quality and size, as well as two base models. We further investigate the mechanisms behind this improvement through case studies and quantitative analysis, suggesting that our approach may provide superior support for the model in capturing long-distance dependencies, especially those related to questions. This enhancement could deepen understanding of premises in questions and prior steps. Our code is available at Github.

Rethinking Scientific Summarization Evaluation: Grounding Explainable Metrics on Facet-aware Benchmark

The summarization capabilities of pretrained and large language models (LLMs) have been widely validated in general areas, but their use in scientific corpus, which involves complex sentences and specialized knowledge, has been less assessed. This paper presents conceptual and experimental analyses of scientific summarization, highlighting the inadequacies of traditional evaluation methods, such as $n$-gram, embedding comparison, and QA, particularly in providing explanations, grasping scientific concepts, or identifying key content. Subsequently, we introduce the Facet-aware Metric (FM), employing LLMs for advanced semantic matching to evaluate summaries based on different aspects. This facet-aware approach offers a thorough evaluation of abstracts by decomposing the evaluation task into simpler subtasks.Recognizing the absence of an evaluation benchmark in this domain, we curate a Facet-based scientific summarization Dataset (FD) with facet-level annotations. Our findings confirm that FM offers a more logical approach to evaluating scientific summaries. In addition, fine-tuned smaller models can compete with LLMs in scientific contexts, while LLMs have limitations in learning from in-context information in scientific domains. This suggests an area for future enhancement of LLMs.

LLM Agents for Psychology: A Study on Gamified Assessments

Psychological measurement is essential for mental health, self-understanding, and personal development. Traditional methods, such as self-report scales and psychologist interviews, often face challenges with engagement and accessibility. While game-based and LLM-based tools have been explored to improve user interest and automate assessment, they struggle to balance engagement with generalizability. In this work, we propose PsychoGAT (Psychological Game AgenTs) to achieve a generic gamification of psychological assessment. The main insight is that powerful LLMs can function both as adept psychologists and innovative game designers. By incorporating LLM agents into designated roles and carefully managing their interactions, PsychoGAT can transform any standardized scales into personalized and engaging interactive fiction games. To validate the proposed method, we conduct psychometric evaluations to assess its effectiveness and employ human evaluators to examine the generated content across various psychological constructs, including depression, cognitive distortions, and personality traits. Results demonstrate that PsychoGAT serves as an effective assessment tool, achieving statistically significant excellence in psychometric metrics such as reliability, convergent validity, and discriminant validity. Moreover, human evaluations confirm PsychoGAT's enhancements in content coherence, interactivity, interest, immersion, and satisfaction.

Leveraging Professional Radiologists' Expertise to Enhance LLMs' Evaluation for Radiology Reports

In radiology, Artificial Intelligence (AI) has significantly advanced report generation, but automatic evaluation of these AI-produced reports remains challenging. Current metrics, such as Conventional Natural Language Generation (NLG) and Clinical Efficacy (CE), often fall short in capturing the semantic intricacies of clinical contexts or overemphasize clinical details, undermining report clarity. To overcome these issues, our proposed method synergizes the expertise of professional radiologists with Large Language Models (LLMs), like GPT-3.5 and GPT-4 1. Utilizing In-Context Instruction Learning (ICIL) and Chain of Thought (CoT) reasoning, our approach aligns LLM evaluations with radiologist standards, enabling detailed comparisons between human and AI generated reports. This is further enhanced by a Regression model that aggregates sentence evaluation scores. Experimental results show that our "Detailed GPT-4 (5-shot)" model achieves a 0.48 score, outperforming the METEOR metric by 0.19, while our "Regressed GPT-4" model shows even greater alignment with expert evaluations, exceeding the best existing metric by a 0.35 margin. Moreover, the robustness of our explanations has been validated through a thorough iterative strategy. We plan to publicly release annotations from radiology experts, setting a new standard for accuracy in future assessments. This underscores the potential of our approach in enhancing the quality assessment of AI-driven medical reports.

PepHarmony: A Multi-View Contrastive Learning Framework for Integrated Sequence and Structure-Based Peptide Encoding

Recent advances in protein language models have catalyzed significant progress in peptide sequence representation. Despite extensive exploration in this field, pre-trained models tailored for peptide-specific needs remain largely unaddressed due to the difficulty in capturing the complex and sometimes unstable structures of peptides. This study introduces a novel multi-view contrastive learning framework PepHarmony for the sequence-based peptide encoding task. PepHarmony innovatively combines both sequence- and structure-level information into a sequence-level encoding module through contrastive learning. We carefully select datasets from the Protein Data Bank (PDB) and AlphaFold database to encompass a broad spectrum of peptide sequences and structures. The experimental data highlights PepHarmony's exceptional capability in capturing the intricate relationship between peptide sequences and structures compared with the baseline and fine-tuned models. The robustness of our model is confirmed through extensive ablation studies, which emphasize the crucial roles of contrastive loss and strategic data sorting in enhancing predictive performance. The proposed PepHarmony framework serves as a notable contribution to peptide representations, and offers valuable insights for future applications in peptide drug discovery and peptide engineering. We have made all the source code utilized in this study publicly accessible via GitHub at https://github.com/zhangruochi/PepHarmony or http://www.healthinformaticslab.org/supp/.