As the application of large language models (LLMs) has broadened into the realm of biological predictions, leveraging their capacity for self-supervised learning to create feature representations of amino acid sequences, these models have set a new benchmark in tackling downstream challenges, such as subcellular localization. However, previous studies have primarily focused on either the structural design of models or differing strategies for fine-tuning, largely overlooking investigations into the nature of the features derived from LLMs. In this research, we propose different ESM2 representation extraction strategies, considering both the character type and position within the ESM2 input sequence. Using model dimensionality reduction, predictive analysis and interpretability techniques, we have illuminated potential associations between diverse feature types and specific subcellular localizations. Particularly, the prediction of Mitochondrion and Golgi apparatus prefer segments feature closer to the N-terminal, and phosphorylation site-based features could mirror phosphorylation properties. We also evaluate the prediction performance and interpretability robustness of Random Forest and Deep Neural Networks with varied feature inputs. This work offers novel insights into maximizing LLMs' utility, understanding their mechanisms, and extracting biological domain knowledge. Furthermore, we have made the code, feature extraction API, and all relevant materials available at https://github.com/yujuan-zhang/feature-representation-for-LLMs.

Remote sensing image scene classification aims to automatically assign semantic labels for remote sensing images. Recently, to overcome the distribution discrepancy of training data and test data, domain adaptation has been applied to remote sensing image scene classification. Most domain adaptation approaches usually explore transferability under the assumption that the source domain and target domain have common classes. However, in real applications, new categories may appear in the target domain. Besides, only considering the transferability will degrade the classification performance due to the strong interclass similarity of remote sensing images. In this article, we present an open set domain adaptation algorithm via exploring transferability and discriminability (OSDA-ETD) for remote sensing image scene classification. To be specific, we propose the transferability technology, which aims at the high interdomain variations and high intraclass diversity of remote sensing images. The purpose of transferability is to reduce the global distribution difference of domains and the local distribution discrepancy of the same classes in different domains. For high interclass similarity in remote sensing images, we adopt the discriminability strategy. The discriminability intends to enlarge the distribution discrepancy of different classes in different domains. To further promote the effectiveness of scene classification, we integrate the transferability and the discriminability into a framework. Moreover, we prove that the algorithm has a unique optimizer.

Sparse hyperspectral unmixing has attracted increasing investigations during the past decade. Recent research has indicated that library pruning algorithms can significantly improve the unmixing accuracies by reducing the mutual coherence of the spectral library. Inspired by the good performance of library pruning, in this article we propose a new hyperspectral unmixing algorithm which integrates the idea of library pruning and sparse representation. An obvious challenge for pruning algorithms is that the real endmembers must be preserved after pruning. Unfortunately, recent proposed pruning algorithms, such as multiple signal classification are actually prepruning strategies, which cannot guarantee that the endmembers exactly exist in the selected spectral subset when the image noise is strong. To overcome this difficulty, we develop a simultaneous optimization approach which involves the pruning operation into the optimization process. Compared with existing prepruning-based unmixing methods, the proposed algorithm can gradually compress the search space of sparse representation, which may relieve the loss of spectral information caused by the rapid compression of the library. Instead of simply designing a regularizer, in this article we utilize a multiobjective-based framework where reconstruction error, sparsity error, and the pruning projection function are considered as three parallel objectives, so as to avoid the manually settings of regularization parameters. Moreover, we have provided theoretical analysis and proof for the reasonability of our pruning objective. Experiments on synthetic hyperspectral data may indicate the superiority of the proposed method under high-noise conditions.