Density Functional Theory (DFT) is a pivotal method within quantum chemistry and materials science, with its core involving the construction and solution of the Kohn-Sham Hamiltonian. Despite its importance, the application of DFT is frequently limited by the substantial computational resources required to construct the Kohn-Sham Hamiltonian. In response to these limitations, current research has employed deep-learning models to efficiently predict molecular and solid Hamiltonians, with roto-translational symmetries encoded in their neural networks. However, the scalability of prior models may be problematic when applied to large molecules, resulting in non-physical predictions of ground-state properties. In this study, we generate a substantially larger training set (PubChemQH) than used previously and use it to create a scalable model for DFT calculations with physical accuracy. For our model, we introduce a loss function derived from physical principles, which we call Wavefunction Alignment Loss (WALoss). WALoss involves performing a basis change on the predicted Hamiltonian to align it with the observed one; thus, the resulting differences can serve as a surrogate for orbital energy differences, allowing models to make better predictions for molecular orbitals and total energies than previously possible. WALoss also substantially accelerates self-consistent-field (SCF) DFT calculations. Here, we show it achieves a reduction in total energy prediction error by a factor of 1347 and an SCF calculation speed-up by a factor of 18%. These substantial improvements set new benchmarks for achieving accurate and applicable predictions in larger molecular systems.

Camouflaged Object Detection (COD), the task of identifying objects concealed within their environments, has seen rapid growth due to its wide range of practical applications. A key step toward developing trustworthy COD systems is the estimation and effective utilization of uncertainty. In this work, we propose a human-machine collaboration framework for classifying the presence of camouflaged objects, leveraging the complementary strengths of computer vision (CV) models and noninvasive brain-computer interfaces (BCIs). Our approach introduces a multiview backbone to estimate uncertainty in CV model predictions, utilizes this uncertainty during training to improve efficiency, and defers low-confidence cases to human evaluation via RSVP-based BCIs during testing for more reliable decision-making. We evaluated the framework in the CAMO dataset, achieving state-of-the-art results with an average improvement of 4.56\% in balanced accuracy (BA) and 3.66\% in the F1 score compared to existing methods. For the best-performing participants, the improvements reached 7.6\% in BA and 6.66\% in the F1 score. Analysis of the training process revealed a strong correlation between our confidence measures and precision, while an ablation study confirmed the effectiveness of the proposed training policy and the human-machine collaboration strategy. In general, this work reduces human cognitive load, improves system reliability, and provides a strong foundation for advancements in real-world COD applications and human-computer interaction. Our code and data are available at: https://github.com/ziyuey/Uncertainty-aware-human-machine-collaboration-in-camouflaged-object-identification.

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

Hamiltonian matrix prediction is pivotal in computational chemistry, serving as the foundation for determining a wide range of molecular properties. While SE(3) equivariant graph neural networks have achieved remarkable success in this domain, their substantial computational cost-driven by high-order tensor product (TP) operations-restricts their scalability to large molecular systems with extensive basis sets. To address this challenge, we introduce SPHNet, an efficient and scalable equivariant network that incorporates adaptive sparsity into Hamiltonian prediction. SPHNet employs two innovative sparse gates to selectively constrain non-critical interaction combinations, significantly reducing tensor product computations while maintaining accuracy. To optimize the sparse representation, we develop a Three-phase Sparsity Scheduler, ensuring stable convergence and achieving high performance at sparsity rates of up to 70 percent. Extensive evaluations on QH9 and PubchemQH datasets demonstrate that SPHNet achieves state-of-the-art accuracy while providing up to a 7x speedup over existing models. Beyond Hamiltonian prediction, the proposed sparsification techniques also hold significant potential for improving the efficiency and scalability of other SE(3) equivariant networks, further broadening their applicability and impact.

Equivariant Graph Neural Networks (EGNNs) have demonstrated significant success in modeling microscale systems, including those in chemistry, biology and materials science. However, EGNNs face substantial computational challenges due to the high cost of constructing edge features via spherical tensor products, making them impractical for large-scale systems. To address this limitation, we introduce E2Former, an equivariant and efficient transformer architecture that incorporates the Wigner $6j$ convolution (Wigner $6j$ Conv). By shifting the computational burden from edges to nodes, the Wigner $6j$ Conv reduces the complexity from $O(|\mathcal{E}|)$ to $ O(| \mathcal{V}|)$ while preserving both the model's expressive power and rotational equivariance. We show that this approach achieves a 7x-30x speedup compared to conventional $\mathrm{SO}(3)$ convolutions. Furthermore, our empirical results demonstrate that the derived E2Former mitigates the computational challenges of existing approaches without compromising the ability to capture detailed geometric information. This development could suggest a promising direction for scalable and efficient molecular modeling.

Targeting the notorious cumulative drift errors in NeRF SLAM, we propose a Semantic-guided Loop Closure with Shared Latent Code, dubbed SLC$^2$-SLAM. Especially, we argue that latent codes stored in many NeRF SLAM systems are not fully exploited, as they are only used for better reconstruction. In this paper, we propose a simple yet effective way to detect potential loops using the same latent codes as local features. To further improve the loop detection performance, we use the semantic information, which are also decoded from the same latent codes to guide the aggregation of local features. Finally, with the potential loops detected, we close them with a graph optimization followed by bundle adjustment to refine both the estimated poses and the reconstructed scene. To evaluate the performance of our SLC$^2$-SLAM, we conduct extensive experiments on Replica and ScanNet datasets. Our proposed semantic-guided loop closure significantly outperforms the pre-trained NetVLAD and ORB combined with Bag-of-Words, which are used in all the other NeRF SLAM with loop closure. As a result, our SLC$^2$-SLAM also demonstrated better tracking and reconstruction performance, especially in larger scenes with more loops, like ScanNet.

Constructing compact and informative 3D scene representations is essential for effective embodied exploration and reasoning, especially in complex environments over extended periods. Existing representations, such as object-centric 3D scene graphs, oversimplify spatial relationships by modeling scenes as isolated objects with restrictive textual relationships, making it difficult to address queries requiring nuanced spatial understanding. Moreover, these representations lack natural mechanisms for active exploration and memory management, hindering their application to lifelong autonomy. In this work, we propose 3D-Mem, a novel 3D scene memory framework for embodied agents. 3D-Mem employs informative multi-view images, termed Memory Snapshots, to represent the scene and capture rich visual information of explored regions. It further integrates frontier-based exploration by introducing Frontier Snapshots-glimpses of unexplored areas-enabling agents to make informed decisions by considering both known and potential new information. To support lifelong memory in active exploration settings, we present an incremental construction pipeline for 3D-Mem, as well as a memory retrieval technique for memory management. Experimental results on three benchmarks demonstrate that 3D-Mem significantly enhances agents' exploration and reasoning capabilities in 3D environments, highlighting its potential for advancing applications in embodied AI.

We introduce UniMuMo, a unified multimodal model capable of taking arbitrary text, music, and motion data as input conditions to generate outputs across all three modalities. To address the lack of time-synchronized data, we align unpaired music and motion data based on rhythmic patterns to leverage existing large-scale music-only and motion-only datasets. By converting music, motion, and text into token-based representation, our model bridges these modalities through a unified encoder-decoder transformer architecture. To support multiple generation tasks within a single framework, we introduce several architectural improvements. We propose encoding motion with a music codebook, mapping motion into the same feature space as music. We introduce a music-motion parallel generation scheme that unifies all music and motion generation tasks into a single transformer decoder architecture with a single training task of music-motion joint generation. Moreover, the model is designed by fine-tuning existing pre-trained single-modality models, significantly reducing computational demands. Extensive experiments demonstrate that UniMuMo achieves competitive results on all unidirectional generation benchmarks across music, motion, and text modalities. Quantitative results are available in the \href{https://hanyangclarence.github.io/unimumo_demo/}{project page}.

To enhance the robustness of the Light Gradient Boosting Machine (LightGBM) algorithm for image classification, a topological data analysis (TDA)-based robustness optimization algorithm for LightGBM, TDA-LightGBM, is proposed to address the interference of noise on image classification. Initially, the method partitions the feature engineering process into two streams: pixel feature stream and topological feature stream for feature extraction respectively. Subsequently, these pixel and topological features are amalgamated into a comprehensive feature vector, serving as the input for LightGBM in image classification tasks. This fusion of features not only encompasses traditional feature engineering methodologies but also harnesses topological structure information to more accurately encapsulate the intrinsic features of the image. The objective is to surmount challenges related to unstable feature extraction and diminished classification accuracy induced by data noise in conventional image processing. Experimental findings substantiate that TDA-LightGBM achieves a 3% accuracy improvement over LightGBM on the SOCOFing dataset across five classification tasks under noisy conditions. In noise-free scenarios, TDA-LightGBM exhibits a 0.5% accuracy enhancement over LightGBM on two classification tasks, achieving a remarkable accuracy of 99.8%. Furthermore, the method elevates the classification accuracy of the Ultrasound Breast Images for Breast Cancer dataset and the Masked CASIA WebFace dataset by 6% and 15%, respectively, surpassing LightGBM in the presence of noise. These empirical results underscore the efficacy of the TDA-LightGBM approach in fortifying the robustness of LightGBM by integrating topological features, thereby augmenting the performance of image classification tasks amidst data perturbations.

Large language models (LLM) have demonstrated remarkable capabilities in various biomedical natural language processing (NLP) tasks, leveraging the demonstration within the input context to adapt to new tasks. However, LLM is sensitive to the selection of demonstrations. To address the hallucination issue inherent in LLM, retrieval-augmented LLM (RAL) offers a solution by retrieving pertinent information from an established database. Nonetheless, existing research work lacks rigorous evaluation of the impact of retrieval-augmented large language models on different biomedical NLP tasks. This deficiency makes it challenging to ascertain the capabilities of RAL within the biomedical domain. Moreover, the outputs from RAL are affected by retrieving the unlabeled, counterfactual, or diverse knowledge that is not well studied in the biomedical domain. However, such knowledge is common in the real world. Finally, exploring the self-awareness ability is also crucial for the RAL system. So, in this paper, we systematically investigate the impact of RALs on 5 different biomedical tasks (triple extraction, link prediction, classification, question answering, and natural language inference). We analyze the performance of RALs in four fundamental abilities, including unlabeled robustness, counterfactual robustness, diverse robustness, and negative awareness. To this end, we proposed an evaluation framework to assess the RALs' performance on different biomedical NLP tasks and establish four different testbeds based on the aforementioned fundamental abilities. Then, we evaluate 3 representative LLMs with 3 different retrievers on 5 tasks over 9 datasets.