SUMMARY: Duplex-Indel is a novel Snakemake workflow for detecting somatic small insertions and deletions (Indels) from Tn5 transposase-based duplex sequencing data. Duplex-Indel enhances the accuracy of mutation calling at the single-molecule level by requiring consensus support from both DNA strands for each somatic Indel, minimizing confounding from technical artifacts. Duplex-Indel extends somatic mutation calling in Tn5 transposase-based duplex sequencing data to include Indels. We have demonstrated the accuracy and robustness of Duplex-Indel using cancer cell lines. AVAILABILITY AND IMPLEMENTATION: Source code and documentation are available under the MIT license on GitHub at https://github.com/ealee-lab/duplex-indel and archived on Zenodo at https://doi.org/10.5281/zenodo.19228799.

Abstract Motivation Large language models (LLMs) have demonstrated strong general reasoning abilities, but applying them to domain-specific tasks such as analysing single-cell RNA sequencing data remains a challenge. A central task in this domain is cell type annotation, which is critical for understanding cellular heterogeneity. Although recent foundation models attempt to automate this process, they typically annotate cells independently, without considering batch-level context or providing explanatory reasoning. To address this limitation, we introduce the CellPuzzles benchmark, which reformulates cell type annotation as a batch-level reasoning task. CellPuzzles spans diverse tissues, diseases, and donor conditions, and requires reasoning across the batch-level cellular context to ensure label uniqueness. Results We find that off-the-shelf LLMs struggle on this task, with the best baseline (OpenAI o1) achieving only 19.0% batch-level accuracy. To fill this gap, we propose Cell-o1, a 7B LLM trained via supervised fine-tuning on distilled reasoning traces, followed by reinforcement learning with batch-level rewards. Cell-o1 achieves state-of-the-art performance, outperforming OpenAI o1 by over 73% and generalizing well across contexts. Further analysis of training dynamics and reasoning behaviors provides insights into batch-level annotation performance and emergent expert-like reasoning. Availability and Implementation Code and data are available at https://github.com/ncbi-nlp/cell-o1.

Zihao Li, Lecheng Zheng, Bowen Jin, Dongqi Fu, Baoyu Jing, Yikun Ban, Jingrui He, Jiawei Han. Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2025.

The rapid development of Multimodal Large Language Models (MLLMs) has enabled the integration of multiple modalities, including texts and images, within the large language model (LLM) framework. However, texts and images are usually interconnected, forming a multimodal attributed graph (MMAG). It is underexplored how MLLMs can incorporate the relational information (i.e., graph structure) and semantic information (i.e., texts and images) on such graphs for multimodal comprehension and generation. In this paper, we propose GraphGPT-o, which supports omni-multimodal understanding and creation on MMAGs. We first comprehensively study linearization variants to transform semantic and structural information as input for MLLMs. Then, we propose a hierarchical aligner that enables deep graph encoding, bridging the gap between MMAGs and MLLMs. Finally, we explore the inference choices, adapting MLLM to interleaved text and image generation in graph scenarios. Extensive experiments on three datasets from different domains demonstrate the effectiveness of our proposed method. Datasets and codes will be publicly available at https://github.com/YiFang99/GraphGPT-o.

Retrieval-augmented generation (RAG) empowers large language models (LLMs) to utilize external knowledge sources. The increasing capacity of LLMs to process longer input sequences opens up avenues for providing more retrieved information, to potentially enhance the quality of generated outputs. From a long-context LLM perspective, it assumes that a larger retrieval set would contain more relevant information (higher recall), that might result in improved performance. However, our empirical findings demonstrate that for many long-context LLMs, the quality of generated output initially improves first, but then subsequently declines as the number of retrieved passages increases. This paper investigates this phenomenon, identifying the detrimental impact of retrieved "hard negatives" as a key contributor. To mitigate this and enhance the robustness of long-context LLM-based RAG, we propose both training-free and training-based approaches. We first showcase the effectiveness of retrieval reordering as a simple yet powerful training-free optimization. Furthermore, we explore training-based methods, specifically RAG-specific implicit LLM fine-tuning and RAG-oriented fine-tuning with intermediate reasoning, demonstrating their capacity for substantial performance gains. Finally, we conduct a systematic analysis of design choices for these training-based methods, including data distribution, retriever selection, and training context length.

Large Language Models (LLMs) have revolutionized artificial intelligence with capabilities in reasoning, coding, and communication, driving innovation across industries. Their true potential depends on effective alignment to ensure correct, trustworthy and ethical behavior, addressing challenges like misinformation, hallucinations, bias and misuse. While existing Reinforcement Learning (RL)-based alignment methods are notoriously complex, direct optimization approaches offer a simpler alternative. In this work, we introduce a novel direct optimization approach for LLM alignment by drawing on established Information Retrieval (IR) principles. We present a systematic framework that bridges LLM alignment and IR methodologies, mapping LLM generation and reward models to IR’s retriever-reranker paradigm. Building on this foundation, we propose LLM Alignment as Retriever Preference Optimization (LarPO), a new alignment method that enhances overall alignment quality. Extensive experiments validate LarPO’s effectiveness with 38.9 % and 13.7 % averaged improvement on AlpacaEval2 and MixEval-Hard respectively. Our work opens new avenues for advancing LLM alignment by integrating IR foundations, offering a promising direction for future research.

Accurate weather forecasting is critical for science and society. However, existing methods have not achieved the combination of high accuracy, low uncertainty, and high computational efficiency simultaneously. On one hand, traditional numerical weather prediction (NWP) models are computationally intensive because of their complexity. On the other hand, most machine learning-based weather prediction (MLWP) approaches offer efficiency and accuracy but remain deterministic, lacking the ability to capture forecast uncertainty. To tackle these challenges, we propose a conditional diffusion model, CoDiCast, to generate global weather prediction, integrating accuracy and uncertainty quantification at a modest computational cost. The key idea behind the prediction task is to generate realistic weather scenarios at a future time point, conditioned on observations from the recent past. Due to the probabilistic nature of diffusion models, they can be properly applied to capture the uncertainty of weather predictions. Therefore, we accomplish uncertainty quantifications by repeatedly sampling from stochastic Gaussian noise for each initial weather state and running the denoising process multiple times. Experimental results demonstrate that CoDiCast outperforms several existing MLWP methods in accuracy, and is faster than NWP models in inference speed. Our model can generate 6-day global weather forecasts, at 6-hour steps and 5.625-degree latitude-longitude resolutions, for over 5 variables, in about 12 minutes on a commodity A100 GPU machine with 80GB memory. The source code is available at https://github.com/JimengShi/CoDiCast.

Recent advances in large language models (LLMs) have introduced latent reasoning as a promising alternative to autoregressive reasoning. By performing internal computation with hidden states from previous steps, latent reasoning benefit from more informative features rather than sampling a discrete chain-of-thought (CoT) path. Yet latent reasoning approaches are often incompatible with LLMs, as their continuous paradigm conflicts with the discrete nature of autoregressive generation. Moreover, these methods rely on CoT traces for training and thus fail to exploit the inherent reasoning patterns of LLMs. In this work, we explore latent reasoning by leveraging the intrinsic capabilities of LLMs via reinforcement learning (RL). To this end, we introduce hybrid reasoning policy optimization (HRPO), an RL-based hybrid latent reasoning approach that (1) integrates prior hidden states into sampled tokens with a learnable gating mechanism, and (2) initializes training with predominantly token embeddings while progressively incorporating more hidden features. This design maintains LLMs' generative capabilities and incentivizes hybrid reasoning using both discrete and continuous representations. In addition, the hybrid HRPO introduces stochasticity into latent reasoning via token sampling, thereby enabling RL-based optimization without requiring CoT trajectories. Extensive evaluations across diverse benchmarks show that HRPO outperforms prior methods in both knowledge- and reasoning-intensive tasks. Furthermore, HRPO-trained LLMs remain interpretable and exhibit intriguing behaviors like cross-lingual patterns and shorter completion lengths, highlighting the potential of our RL-based approach and offer insights for future work in latent reasoning.

Large Language Models (LLMs) excel at zero- and few-shot learning but are restricted by the length of context windows when processing long documents. Two strategies have emerged to overcome this limitation: (1) Long Context (LC) methods, which extend or compress transformer architectures to input more text; and (2) Retrieval-Augmented Generation (RAG), which integrates external knowledge sources via embedding- or index-based retrieval. This half-day tutorial offers a unified, beginner-friendly introduction to both approaches. We first review transformer fundamentals-positional encoding, attention complexity, and common LC techniques. Next, we explain the classic RAG pipeline and recent RAG strategies, alongside evaluation metrics and benchmarks. We also analyze recent empirical studies to highlight strengths, limitations, and trade-offs of LC vs. RAG in terms of scalability, computational cost, and retrieval effectiveness. We conclude with best practices for real-world deployments, emerging hybrid architectures, and open research directions, equipping IR researchers and practitioners with actionable guidelines for processing long documents in LLMs.

In specialized fields like the scientific domain, constructing large-scale human-annotated datasets poses a significant challenge due to the need for domain expertise. Recent methods have employed large language models to generate synthetic queries, which serve as proxies for actual user queries. However, they lack control over the content generated, often resulting in incomplete coverage of academic concepts in documents. We introduce Concept Coverage-based Query set Generation (CCQGen) framework, designed to generate a set of queries with comprehensive coverage of the document's concepts. A key distinction of CCQGen is that it adaptively adjusts the generation process based on the previously generated queries. We identify concepts not sufficiently covered by previous queries, and leverage them as conditions for subsequent query generation. This approach guides each new query to complement the previous ones, aiding in a thorough understanding of the document. Extensive experiments demonstrate that CCQGen significantly enhances query quality and retrieval performance.

With the rapid increase in paper submissions to academic conferences, the need for automated and accurate paper-reviewer matching is more critical than ever. Previous efforts in this area have considered various factors to assess the relevance of a reviewer's expertise to a paper, such as the semantic similarity, shared topics, and citation connections between the paper and the reviewer's previous works. However, most of these studies focus on only one factor, resulting in an incomplete evaluation of the paper-reviewer relevance. To address this issue, we propose a unified model for paper-reviewer matching that jointly considers semantic, topic, and citation factors. To be specific, during training, we instruction-tune a contextualized language model shared across all factors to capture their commonalities and characteristics; during inference, we chain the three factors to enable step-by-step, coarse-to-fine search for qualified reviewers given a submission. Experiments on four datasets (one of which is newly contributed by us) spanning various fields such as machine learning, computer vision, information retrieval, and data mining consistently demonstrate the effectiveness of our proposed Chain-of-Factors model in comparison with state-of-the-art paper-reviewer matching methods and scientific pre-trained language models.

In many scientific fields, large language models (LLMs) have revolutionized the way text and other modalities of data (e.g., molecules and proteins) are handled, achieving superior performance in various applications and augmenting the scientific discovery process.Nevertheless, previous surveys on scientific LLMs often concentrate on one or two fields or a single modality.In this paper, we aim to provide a more holistic view of the research landscape by unveiling cross-field and cross-modal connections between scientific LLMs regarding their architectures and pretraining techniques.To this end, we comprehensively survey over 260 scientific LLMs, discuss their commonalities and differences, as well as summarize pre-training datasets and evaluation tasks for each field and modality.Moreover, we investigate how LLMs have been deployed to benefit scientific discovery.Resources related to this survey are available at https://github.com/yuzhimanhua/ Awesome-Scientific-Language-Models.

Relation extraction (RE) aims to identify semantic relationships between entities within text.Despite considerable advancements, existing models predominantly require extensive annotated training data, which is both costly and labor-intensive to collect.Moreover, these models often struggle to adapt to new or unseen relations.Few-shot learning, aiming to lessen annotation demands, typically provides incomplete and biased supervision for target relations, leading to degraded and unstable performance.To accurately and explicitly describe relation semantics while minimizing annotation demands, we explore the definition only zero-shot RE setting where only relation definitions expressed in natural language are used to train a RE model.We introduce REPAL, comprising three stages: (1) We leverage large language models (LLMs) to generate initial seed instances from relation definitions and an unlabeled corpus.(2) We fine-tune a bidirectional Small Language Model (SLM) with initial seeds to learn relations for the target domain.(3) We expand pattern coverage and mitigate bias from initial seeds by integrating feedback from the SLM's predictions on the unlabeled corpus and the synthesis history.To accomplish this, we leverage the multi-turn conversation ability of LLMs to generate new instances in follow-up dialogues, informed by both the feedback and synthesis history.Studies reveal that definition-oriented seed synthesis enhances pattern coverage whereas indiscriminately increasing seed quantity leads to performance saturation.Experiments on two datasets show REPAL significantly improved cost-effective zero-shot performance by large margins.

Developing a universal model that can effectively harness heterogeneous resources and respond to a wide range of personalized needs has been a longstanding community aspiration. Our daily choices, especially in domains like fashion and retail, are substantially shaped by multi-modal data, such as pictures and textual descriptions. These modalities not only offer intuitive guidance but also cater to personalized user preferences. However, the predominant personalization approaches mainly focus on ID or text-based recommendation problems, failing to comprehend the information spanning various tasks or modalities. In this paper, our goal is to establish a Unified paradigm for Multi-modal Personalization systems (UniMP), which effectively leverages multi-modal data while eliminating the complexities associated with task- and modality-specific customization. We argue that the advancements in foundational generative modeling have provided the flexibility and effectiveness necessary to achieve the objective. In light of this, we develop a generic and extensible personalization generative framework, that can handle a wide range of personalized needs including item recommendation, product search, preference prediction, explanation generation, and further user-guided image generation. Our methodology enhances the capabilities of foundational language models for personalized tasks by seamlessly ingesting interleaved cross-modal user history information, ensuring a more precise and customized experience for users. To train and evaluate the proposed multi-modal personalized tasks, we also introduce a novel and comprehensive benchmark covering a variety of user requirements. Our experiments on the real-world benchmark showcase the model's potential, outperforming competitive methods specialized for each task.

Semantic identifier (ID) is an important concept in information retrieval that aims to preserve the semantics of objects such as documents and items inside their IDs. Previous studies typically adopt a two-stage pipeline to learn semantic IDs by first procuring embeddings using off-the-shelf text encoders and then deriving IDs based on the embeddings. However, each step introduces potential information loss, and there is usually an inherent mismatch between the distribution of embeddings within the latent space produced by text encoders and the anticipated distribution required for semantic indexing. It is non-trivial to design a method that can learn the document’s semantic representations and its hierarchical structure simultaneously, given that semantic IDs are discrete and sequentially structured, and the semantic supervision is deficient. In this paper, we introduce LMIndexer, a self-supervised framework to learn semantic IDs with a generative language model. We tackle the challenge of sequential discrete ID by introducing a semantic indexer capable of generating neural sequential discrete representations with progressive training and contrastive learning. In response to the semantic supervision deficiency, we propose to train the model with a self-supervised document reconstruction objective. We show the high quality of the learned IDs and demonstrate their effectiveness on three tasks including recommendation, product search, and document retrieval on five datasets from various domains. Code is available at https://github.com/PeterGriffinJin/LMIndexer.

In this paper, we approach an overlooked yet critical task Graph2Image: generating images from multimodal attributed graphs (MMAGs). This task poses significant challenges due to the explosion in graph size, dependencies among graph entities, and the need for controllability in graph conditions. To address these challenges, we propose a graph context-conditioned diffusion model called InstructG2I. InstructG2I first exploits the graph structure and multimodal information to conduct informative neighbor sampling by combining personalized page rank and re-ranking based on vision-language features. Then, a graph QFormer encoder adaptively encodes the graph nodes into an auxiliary set of graph prompts to guide the denoising process of diffusion. Finally, we propose graph classifier-free guidance, enabling controllable generation by varying the strength of graph guidance and multiple connected edges to a node. Extensive experiments conducted on three datasets from different domains demonstrate the effectiveness and controllability of our approach. The code is available at https://github.com/PeterGriffinJin/InstructG2I.

Geospatial topological relation extraction (GeoTopoRE) aims to extract topological relations between named geospatial entities (i.e., geo-entities) in text. It is a domain-specific relation extraction (RE) task essential in geospatial knowledge graph construction and spatial reasoning. Unlike general-purpose RE, which primarily depends on semantic and syntactic cues, GeoTopoRE requires integrating geometric knowledge about geo-entities. This is essential for accurately capturing or inferring the complex geospatial relationships among entities. GeoTopoRE is not studied systematically and lacks dedicated datasets for evaluation, posing significant challenges to developing and assessing effective models. This study presents two major contributions: (i) the introduction of a high-quality, human-labeled dataset WikiTopo for the GeoTopoRE task, and (ii) a novel framework GeoWISE designed to adapt existing RE models to the GeoTopoRE task, With Integrated Semantic and External geospatial domain knowledge. We leverage coarse-to-fine-grained natural language inference (NLI) to align externally sourced knowledge with the semantic text context, enhanced by geospatial expertise. This integrated knowledge is then conveyed to language models as geospatial cues, enabling a nuanced understanding of topological relations. Empirical results demonstrate the efficacy of our framework in few-shot settings, showing significant and consistent improvements in the GeoTopoRE task for diverse state-of-the-art RE models.

Graphs and texts are two key modalities in data mining. In many cases, the data presents a mixture of the two modalities and the information is often complementary: in e-commerce data, the product-user graph and product descriptions capture different aspects of product features; in scientific literature, the citation graph, author metadata, and the paper content all contribute to modeling the paper impact.

Document retrieval has greatly benefited from the advancements of large-scale pre-trained language models (PLMs). However, their effectiveness is often limited in theme-specific applications for specialized areas or industries, due to unique terminologies, incomplete contexts of user queries, and specialized search intents. To capture the theme-specific information and improve retrieval, we propose to use a corpus topical taxonomy, which outlines the latent topic structure of the corpus while reflecting user-interested aspects. We introduce ToTER (Topical Taxonomy Enhanced Retrieval) framework, which identifies the central topics of queries and documents with the guidance of the taxonomy, and exploits their topical relatedness to supplement missing contexts. As a plug-and-play framework, ToTER can be flexibly employed to enhance various PLM-based retrievers. Through extensive quantitative, ablative, and exploratory experiments on two real-world datasets, we ascertain the benefits of using topical taxonomy for retrieval in theme-specific applications and demonstrate the effectiveness of ToTER.

Recent research has shown that transformer networks can be used as differentiable search indexes by representing each document as a sequence of document ID tokens. These generative retrieval models cast the retrieval problem to a document ID generation problem for each query. Despite their elegant design, existing generative retrieval models only perform well on artificially-constructed and small-scale collections. This paper represents an important milestone in generative retrieval research by showing that generative retrieval models can be trained to perform effectively on large-scale standard retrieval benchmarks. In more detail, we propose RIPOR- an optimization framework for generative retrieval that is designed based on two often-overlooked fundamental design considerations. First, RIPOR introduces a novel prefix-oriented ranking optimization algorithm for accurate estimation of relevance score during sequential document ID generation. Second, RIPOR constructs document IDs based on the relevance associations between queries and documents. Evaluation on MSMARCO and TREC Deep Learning Track reveals that RIPOR surpasses state-of-the-art generative retrieval models by a large margin (e.g., 30.5% MRR improvements on MS MARCO Dev Set).

Large language models (LLMs), such as GPT4 and LLaMA, are creating significant advancements in natural language processing, due to their strong text encoding/decoding ability and newly found emergent capability (e.g., reasoning). While LLMs are mainly designed to process pure texts, there are many real-world scenarios where text data is associated with rich structure information in the form of graphs (e.g., academic networks, and e-commerce networks) or scenarios where graph data is paired with rich textual information (e.g., molecules with descriptions). Besides, although LLMs have shown their pure text-based reasoning ability, it is underexplored whether such ability can be generalized to graphs (i.e., graph-based reasoning). In this paper, we provide a systematic review of scenarios and techniques related to large language models on graphs. We first summarize potential scenarios of adopting LLMs on graphs into three categories, namely pure graphs, text-attributed graphs, and text-paired graphs. We then discuss detailed techniques for utilizing LLMs on graphs, including LLM as Predictor, LLM as Encoder, and LLM as Aligner, and compare the advantages and disadvantages of different schools of models. Furthermore, we discuss the real-world applications of such methods and summarize open-source codes and benchmark datasets. Finally, we conclude with potential future research directions in this fast-growing field.

A real-world text corpus sometimes comprises not only text documents, but also semantic links between them (e.g., academic papers in a bibliographic network are linked by citations and co-authorships).Text documents and semantic connections form a text-rich network, which empowers a wide range of downstream tasks such as classification and retrieval.However, pretraining methods for such structures are still lacking, making it difficult to build one generic model that can be adapted to various tasks on text-rich networks.Current pretraining objectives, such as masked language modeling, purely model texts and do not take interdocument structure information into consideration.To this end, we propose our PretrAining on TexT-Rich NetwOrk framework PATTON.PATTON 1 includes two pretraining strategies: network-contextualized masked language modeling and masked node prediction, to capture the inherent dependency between textual attributes and network structure.We conduct experiments on four downstream tasks in five datasets from both academic and e-commerce domains, where PATTON outperforms baselines significantly and consistently.

Today a tremendous amount of geospatial knowledge is hidden in massive volumes of text data. To facilitate flexible and powerful geospatial analysis and applications, we introduce a new architecture: geospatial knowledge hypercube, a multi-scale, multidimensional knowledge structure that integrates information from geospatial dimensions, thematic themes and diverse application semantics, extracted and computed from spatial-related text data. To construct such a knowledge hypercube, weakly supervised language models are leveraged for automatic, dynamic and incremental extraction of heterogeneous geospatial data, thematic themes, latent connections and relationships, and application semantics, through combining a variety of information from unstructured text, structured tables, and maps. The hypercube lays a foundation for many knowledge discovery and in-depth spatial analysis, and other advanced applications. We have deployed a prototype web application of proposed geospatial knowledge hypercube for public access at: https://hcwebapp.cigi.illinois.edu/.

Representation learning on networks aims to derive a meaningful vector representation for each node, thereby facilitating downstream tasks such as link prediction, node classification, and node clustering. In heterogeneous text-rich networks, this task is more challenging due to (1) presence or absence of text: Some nodes are associated with rich textual information, while others are not; (2) diversity of types: Nodes and edges of multiple types form a heterogeneous network structure. As pretrained language models (PLMs) have demonstrated their effectiveness in obtaining widely generalizable text representations, a substantial amount of effort has been made to incorporate PLMs into representation learning on text-rich networks. However, few of them can jointly consider heterogeneous structure (network) information as well as rich textual semantic information of each node effectively. In this paper, we propose Heterformer, a Heterogeneous Network-Empowered Transformer that performs contextualized text encoding and heterogeneous structure encoding in a unified model. Specifically, we inject heterogeneous structure information into each Transformer layer when encoding node texts. Meanwhile, Heterformer is capable of characterizing node/edge type heterogeneity and encoding nodes with or without texts. We conduct comprehensive experiments on three tasks (i.e., link prediction, node classification, and node clustering) on three large-scale datasets from different domains, where Heterformer outperforms competitive baselines significantly and consistently. The code can be found at https://github.com/PeterGriffinJin/Heterformer.

Instead of relying on human-annotated training samples to build a classifier, weakly supervised scientific paper classification aims to classify papers only using category descriptions (e.g., category names, category-indicative keywords). Existing studies on weakly supervised paper classification are less concerned with two challenges: (1) Papers should be classified into not only coarse-grained research topics but also fine-grained themes, and potentially into multiple themes, given a large and fine-grained label space; and (2) full text should be utilized to complement the paper title and abstract for classification. Moreover, instead of viewing the entire paper as a long linear sequence, one should exploit the structural information such as citation links across papers and the hierarchy of sections and paragraphs in each paper. To tackle these challenges, in this study, we propose FUTEX, a framework that uses the cross-paper network structure and the in-paper hierarchy structure to classify full-text scientific papers under weak supervision. A network-aware contrastive fine-tuning module and a hierarchy-aware aggregation module are designed to leverage the two types of structural signals, respectively. Experiments on two benchmark datasets demonstrate that FUTEX significantly outperforms competitive baselines and is on par with fully supervised classifiers that use 1,000 to 60,000 ground-truth training samples.

Due to the exponential growth of scientific publications on the Web, there is a pressing need to tag each paper with fine-grained topics so that researchers can track their interested fields of study rather than drowning in the whole literature. Scientific literature tagging is beyond a pure multi-label text classification task because papers on the Web are prevalently accompanied by metadata information such as venues, authors, and references, which may serve as additional signals to infer relevant tags. Although there have been studies making use of metadata in academic paper classification, their focus is often restricted to one or two scientific fields (e.g., computer science and biomedicine) and to one specific model. In this work, we systematically study the effect of metadata on scientific literature tagging across 19 fields. We select three representative multi-label classifiers (i.e., a bag-of-words model, a sequence-based model, and a pre-trained language model) and explore their performance change in scientific literature tagging when metadata are fed to the classifiers as additional features. We observe some ubiquitous patterns of metadata’s effects across all fields (e.g., venues are consistently beneficial to paper tagging in almost all cases), as well as some unique patterns in fields other than computer science and biomedicine, which are not explored in previous studies.

Traditional recommendation models that usually utilize only one type of user-item interaction are faced with serious data sparsity or cold start issues. Multi-behavior recommendation taking use of multiple types of user-item interactions, such as clicks and favorites, can serve as an effective solution. Early efforts towards multi-behavior recommendation fail to capture behaviors' different influence strength on target behavior. They also ignore behaviors' semantics which is implied in multi-behavior data. Both of these two limitations make the data not fully exploited for improving the recommendation performance on the target behavior.

How muscles are used is a key to understanding the internal driving of fish swimming. However, the underlying mechanisms of some features of the muscle activation patterns and their differential appearance in different species are still obscure. In this study, we explain the muscle activation patterns by using 3D computational fluid dynamics models coupled to the motion of fish with prescribed deformation and examining the torque and power required along the fish body with two primary swimming modes. We find that the torque required by the hydrodynamic forces and body inertia exhibits a wave pattern that travels faster than the curvature wave in both anguilliform and carangiform swimmers, which can explain the traveling wave speeds of the muscle activations. Notably, intermittent negative power (i.e., power delivered by the fluid to the body) on the posterior part, along with a timely transfer of torque and energy by tendons, explains the decrease in the duration of muscle activation towards the tail. The torque contribution from the body elasticity further clarifies the wave speed increase or the reverse of the wave direction of the muscle activation on the posterior part of a carangiform swimmer. For anguilliform swimmers, the absence of the aforementioned changes in the muscle activation on the posterior part is consistent with our torque prediction and the absence of long tendons from experimental observations. These results provide novel insights into the functions of muscles and tendons as an integral part of the internal driving system, especially from an energy perspective, and they highlight the differences in the internal driving systems between the two primary swimming modes.