Predicting how software is used, shared, and evolves across publications is essential to studying scientific progress. Existing methods for representing software usage in publications rely mainly on tabular or textual formats, which limit their structural expressiveness and consequently their ability to predict software usage. We address these gaps by representing software mentions and citations as a graph and formulating software usage prediction as a link prediction task. To support this study, we construct the first large-scale graph dataset of publication and software mentions, Graph-TempCZ, covering 1959-2022 with over six million mention relationships. Experiments using both traditional machine learning and Graph Neural Network (GNN) show that graph-based models substantially outperform feature-based baselines, achieving a 5.98% improvement in test accuracy. Temporal experiments further reveal that models trained on one year generalize effectively to nearby years but show gradual performance decay as the temporal gap increases. This work provides the first comprehensive foundation for analyzing software usage through a temporal graph representation.

Existing parameter-efficient fine-tuning (PEFT) methods primarily fall into two categories: addition-based and selective in-situ adaptation.The former, such as LoRA, introduce additional modules to adapt the model to downstream tasks, offering strong memory efficiency.However, their representational capacity is often limited, making them less suitable for fine-grained adaptation.In contrast, the latter directly finetunes a carefully chosen subset of the original model parameters, allowing for more precise and effective adaptation, but at the cost of significantly increased memory consumption.To reconcile this trade-off, we propose NeuroAda, a novel PEFT method that enables fine-grained model finetuning while maintaining high memory efficiency.Our approach first identifies important parameters (i.e., connections within the network) as in selective adaptation, and then introduces bypass connections for these selected parameters.During finetuning, only the bypass connections are updated, leaving the original model parameters frozen.Empirical results on 23+ tasks spanning both natural language generation and understanding demonstrate that NeuroAda achieves state-of-the-art performance with as little as ≤ 0.02% trainable parameters, while reducing CUDA memory usage by up to 60%.We release our code here: https://github.com/ FightingFighting/NeuroAda.git.

Gross primary productivity (GPP), the amount of carbon plants fixed by photosynthesis, is pivotal for understanding the global carbon cycle and ecosystem functioning. Process-based models built on the knowledge of ecological processes are susceptible to biases stemming from their assumptions and approximations. These limitations potentially result in considerable uncertainties in global GPP estimation, which may pose significant challenges to our net zero goals. This study presents UFLUX v2.0, a process-informed model that integrates state-of-the-art ecological knowledge and advanced machine learning (ML) technique to reduce uncertainties in GPP estimation by learning the biases between process-based models and eddy covariance (EC) measurements. In our findings, UFLUX v2.0 demonstrated a substantial improvement in model accuracy, achieving an$R {^{{2}}}$of 0.79 with a reduced RMSE of 1.60 g$\cdot $Cm−2d−1, compared to the process-based model’s$R {^{{2}}}$of 0.51 and RMSE of 3.09 g$\cdot $Cm−2d−1. Our global GPP distribution analysis indicates that while UFLUX v2.0 and the process-based model achieved similar global total GPP (137.47 and 132.23 PgC, respectively), they exhibited large differences in spatial distribution, particularly in latitudinal gradients. These differences are very likely due to systematic biases in the process-based model and differing sensitivities to climate and environmental conditions. This study offers improved adaptability for GPP modeling across diverse ecosystems and further enhances our understanding of global carbon cycles and its responses to environmental changes.

Knowledge graphs constantly evolve with new entities emerging, existing definitions being revised, and entity relationships changing. These changes lead to temporal degradation in entity linking models, characterized as a decline in model performance over time. To address this issue, we propose leveraging graph relationships to aggregate information from neighboring entities across different time periods. This approach enhances the ability to distinguish similar entities over time, thereby minimizing the impact of temporal degradation. We introduce CYCLE: Cross-Year Contrastive Learning for Entity-Linking. This model employs a novel graph contrastive learning method to tackle temporal performance degradation in entity linking tasks. Our contrastive learning method treats newly added graph relationships as positive samples and newly removed ones as negative samples. This approach helps our model effectively prevent temporal degradation, achieving a 13.90% performance improvement over the state-of-the-art from 2023 when the time gap is one year, and a 17.79% improvement as the gap expands to three years. Further analysis shows that CYCLE is particularly robust for low-degree entities, which are less resistant to temporal degradation due to their sparse connectivity, making them particularly suitable for our method. The code and data are made available at https://github.com/pengyu-zhang/CYCLE-Cross-Year-Contrastive-Learning-in-Entity-Linking

Knowledge graphs change over time, for example, when new entities are introduced or entity descriptions change. This impacts the performance of entity linking, a key task in many uses of knowledge graphs such as web search and recommendation. Specifically, entity linking models exhibit temporal degradation - their performance decreases the further a knowledge graph moves from its original state on which an entity linking model was trained. To tackle this challenge, we introduce TIGER: a Temporally Improved Graph Entity Linker. By incorporating structural information between entities into the model, we enhance the learned representation, making entities more distinguishable over time. The core idea is to integrate graph-based information into text-based information, from which both distinct and shared embeddings are based on an entity’s feature and structural relationships and their interaction. Experiments on three datasets show that our model can effectively prevent temporal degradation, demonstrating a 16.24% performance boost over the state-of-the-art in a temporal setting when the time gap is one year and an improvement to 20.93% as the gap expands to three years. The code and data are made available at https://github.com/pengyu-zhang/TIGER-Temporally-Improved-Graph-Entity-Linker.