Deep neural networks, particularly Transformers, have been widely adopted for predicting the functional properties of proteins. In this work, we focus on exploring whether Protein Transformers can capture biological intelligence among protein sequences. To achieve our goal, we first introduce a protein function dataset, namely Protein-FN, providing over 9000 protein data with meaningful labels. Second, we devise a new Transformer architecture, namely Sequence Protein Transformers (SPT), for computationally efficient protein function predictions. Third, we develop a novel Explainable Artificial Intelligence (XAI) technique called Sequence Score, which can efficiently interpret the decision-making processes of protein models, thereby overcoming the difficulty of deciphering biological intelligence bided in Protein Transformers. Remarkably, even our smallest SPT-Tiny model, which contains only 5.4M parameters, demonstrates impressive predictive accuracy, achieving 94.3% on the Antibiotic Resistance (AR) dataset and 99.6% on the Protein-FN dataset, all accomplished by training from scratch. Besides, our Sequence Score technique helps reveal that our SPT models can discover several meaningful patterns underlying the sequence structures of protein data, with these patterns aligning closely with the domain knowledge in the biology community. We have officially released our Protein-FN dataset on Hugging Face Datasets https://huggingface.co/datasets/Protein-FN/Protein-FN. Our code is available at https://github.com/fudong03/BioIntelligence.

The age and mass of red giants are essential for understanding the structure and evolution of the Milky Way. Traditional isochrone methods for these estimations are inherently limited due to overlapping isochrones in the Hertzsprung-Russell diagram, while asteroseismology, though more precise, requires high-precision, long-term observations. In response to these challenges, we developed a novel framework, Spectral Transformer (SPT), to predict the age and mass of red giants aligned with asteroseismology from their spectra. A key component of SPT, the Multi-head Hadamard Self-Attention mechanism, designed specifically for spectra, can capture complex relationships across different wavelength. Further, we introduced a Mahalanobis distance-based loss function to address scale imbalance and interaction mode loss, and incorporated Monte Carlo dropout for quantitative analysis of prediction uncertainty. Trained and tested on 3,880 red giant spectra from LAMOST, the SPT achieved remarkable age and mass estimations with average percentage errors of 17.64% and 6.61%, respectively, and provided uncertainties for each corresponding prediction. The results significantly outperform those of traditional machine learning algorithms and demonstrate a high level of consistency with asteroseismology methods and isochrone fitting techniques. In the future, our work will leverage datasets from the Chinese Space Station Telescope and the Large Synoptic Survey Telescope to enhance the precision of the model and broaden its applicability in the field of astronomy and astrophysics.

We consider the problem of spatial path planning. In contrast to the classical solutions which optimize a new plan from scratch and assume access to the full map with ground truth obstacle locations, we learn a planner from the data in a differentiable manner that allows us to leverage statistical regularities from past data. We propose Spatial Planning Transformers (SPT), which given an obstacle map learns to generate actions by planning over long-range spatial dependencies, unlike prior data-driven planners that propagate information locally via convolutional structure in an iterative manner. In the setting where the ground truth map is not known to the agent, we leverage pre-trained SPTs in an end-to-end framework that has the structure of mapper and planner built into it which allows seamless generalization to out-of-distribution maps and goals. SPTs outperform prior state-of-the-art differentiable planners across all the setups for both manipulation and navigation tasks, leading to an absolute improvement of 7-19%.