Curriculum Learning for Biological Sequence Prediction: The Case of De Novo Peptide Sequencing

Peptide sequencing-the process of identifying amino acid sequences from mass spectrometry data-is a fundamental task in proteomics. Non-Autoregressive Transformers (NATs) have proven highly effective for this task, outperforming traditional methods. Unlike autoregressive models, which generate tokens sequentially, NATs predict all positions simultaneously, leveraging bidirectional context through unmasked self-attention. However, existing NAT approaches often rely on Connectionist Temporal Classification (CTC) loss, which presents significant optimization challenges due to CTC's complexity and increases the risk of training failures. To address these issues, we propose an improved non-autoregressive peptide sequencing model that incorporates a structured protein sequence curriculum learning strategy. This approach adjusts protein's learning difficulty based on the model's estimated protein generational capabilities through a sampling process, progressively learning peptide generation from simple to complex sequences. Additionally, we introduce a self-refining inference-time module that iteratively enhances predictions using learned NAT token embeddings, improving sequence accuracy at a fine-grained level. Our curriculum learning strategy reduces NAT training failures frequency by more than 90% based on sampled training over various data distributions. Evaluations on nine benchmark species demonstrate that our approach outperforms all previous methods across multiple metrics and species.

Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing

De novo peptide sequencing is a critical task in proteomics. However, the performance of current deep learning-based methods is limited by the inherent complexity of mass spectrometry data and the heterogeneous distribution of noise signals, leading to data-specific biases. We present RankNovo, the first deep reranking framework that enhances de novo peptide sequencing by leveraging the complementary strengths of multiple sequencing models. RankNovo employs a list-wise reranking approach, modeling candidate peptides as multiple sequence alignments and utilizing axial attention to extract informative features across candidates. Additionally, we introduce two new metrics, PMD (Peptide Mass Deviation) and RMD (residual Mass Deviation), which offer delicate supervision by quantifying mass differences between peptides at both the sequence and residue levels. Extensive experiments demonstrate that RankNovo not only surpasses its base models used to generate training candidates for reranking pre-training, but also sets a new state-of-the-art benchmark. Moreover, RankNovo exhibits strong zero-shot generalization to unseen models whose generations were not exposed during training, highlighting its robustness and potential as a universal reranking framework for peptide sequencing. Our work presents a novel reranking strategy that fundamentally challenges existing single-model paradigms and advances the frontier of accurate de novo sequencing. Our source code is provided on GitHub.

A Novel WaveInst-based Network for Tree Trunk Structure Extraction and Pattern Analysis in Forest Inventory

The pattern analysis of tree structure holds significant scientific value for genetic breeding and forestry management. The current trunk and branch extraction technologies are mainly LiDAR-based or UAV-based. The former approaches obtain high-precision 3D data, but its equipment cost is high and the three-dimensional (3D) data processing is complex. The latter approaches efficiently capture canopy information, but they miss the 3-D structure of trees. In order to deal with the branch information extraction from the complex background interference and occlusion, this work proposes a novel WaveInst instance segmentation framework, involving a discrete wavelet transform, to enhance multi-scale edge information for accurately improving tree structure extraction. Experimental results of the proposed model show superior performance on SynthTree43k, CaneTree100, Urban Street and our PoplarDataset. Moreover, we present a new Phenotypic dataset PoplarDataset, which is dedicated to extract tree structure and pattern analysis from artificial forest. The proposed method achieves a mean average precision of 49.6 and 24.3 for the structure extraction of mature and juvenile trees, respectively, surpassing the existing state-of-the-art method by 9.9. Furthermore, by in tegrating the segmentation model within the regression model, we accurately achieve significant tree grown parameters, such as the location of trees, the diameter-at-breast-height of individual trees, and the plant height, from 2D images directly. This study provides a scientific and plenty of data for tree structure analysis in related to the phenotype research, offering a platform for the significant applications in precision forestry, ecological monitoring, and intelligent breeding.

GPA-RAM: Grasp-Pretraining Augmented Robotic Attention Mamba for Spatial Task Learning

Most existing robot manipulation methods prioritize task learning by enhancing perception through complex deep network architectures. However, they face challenges in real-time collision-free planning. Hence, Robotic Attention Mamba (RAM) is designed for refined planning. Specifically, by integrating Mamba and parallel single-view attention, RAM aligns multi-view vision and task-related language features, ensuring efficient fine-grained task planning with linear complexity and robust real-time performance. Nevertheless, it has the potential for further improvement in high-precision grasping and manipulation. Thus, Grasp-Pretraining Augmentation (GPA) is devised, with a grasp pose feature extractor pretrained utilizing object grasp poses directly inherited from whole-task demonstrations. Subsequently, the extracted grasp features are fused with the spatially aligned planning features from RAM through attention-based Pre-trained Location Fusion, preserving high-resolution grasping cues overshadowed by an overemphasis on global planning. To summarize, we propose Grasp-Pretraining Augmented Robotic Attention Mamba (GPA-RAM), dividing spatial task learning into RAM for planning skill learning and GPA for grasping skill learning. GPA-RAM demonstrates superior performance across three robot systems with distinct camera configurations in simulation and the real world. Compared with previous state-of-the-art methods, it improves the absolute success rate by 8.2% (from 79.3% to 87.5%) on the RLBench multi-task benchmark and 40\% (from 16% to 56%), 12% (from 86% to 98%) on the ALOHA bimanual manipulation tasks, while delivering notably faster inference. Furthermore, experimental results demonstrate that both RAM and GPA enhance task learning, with GPA proving robust to different architectures of pretrained grasp pose feature extractors. The website is: https://logssim.github.io/GPA\_RAM\_website/.

ChatAnyone: Stylized Real-time Portrait Video Generation with Hierarchical Motion Diffusion Model

Real-time interactive video-chat portraits have been increasingly recognized as the future trend, particularly due to the remarkable progress made in text and voice chat technologies. However, existing methods primarily focus on real-time generation of head movements, but struggle to produce synchronized body motions that match these head actions. Additionally, achieving fine-grained control over the speaking style and nuances of facial expressions remains a challenge. To address these limitations, we introduce a novel framework for stylized real-time portrait video generation, enabling expressive and flexible video chat that extends from talking head to upper-body interaction. Our approach consists of the following two stages. The first stage involves efficient hierarchical motion diffusion models, that take both explicit and implicit motion representations into account based on audio inputs, which can generate a diverse range of facial expressions with stylistic control and synchronization between head and body movements. The second stage aims to generate portrait video featuring upper-body movements, including hand gestures. We inject explicit hand control signals into the generator to produce more detailed hand movements, and further perform face refinement to enhance the overall realism and expressiveness of the portrait video. Additionally, our approach supports efficient and continuous generation of upper-body portrait video in maximum 512 * 768 resolution at up to 30fps on 4090 GPU, supporting interactive video-chat in real-time. Experimental results demonstrate the capability of our approach to produce portrait videos with rich expressiveness and natural upper-body movements.

Fin-R1: A Large Language Model for Financial Reasoning through Reinforcement Learning

Reasoning large language models are rapidly evolving across various domains. However, their capabilities in handling complex financial tasks still require in-depth exploration. In this paper, we introduce Fin-R1, a reasoning large language model specifically designed for the financial sector. Fin-R1 is built using a two-stage architecture, leveraging a financial reasoning dataset distilled and processed based on DeepSeek-R1. Through supervised fine-tuning (SFT) and reinforcement learning (RL) training, it demonstrates performance close to DeepSeek-R1 with a parameter size of 7 billion across a range of financial reasoning tasks. It achieves the state-of-the-art (SOTA) in the FinQA and ConvFinQA tasks between those LLMs in our evaluation, surpassing larger models in other tasks as well. Fin-R1 showcases strong reasoning and decision-making capabilities, providing solutions to various problems encountered in the financial domain. Our code is available at https://github.com/SUFE-AIFLM-Lab/Fin-R1.

Generative AI in Education: From Foundational Insights to the Socratic Playground for Learning

This paper explores the synergy between human cognition and Large Language Models (LLMs), highlighting how generative AI can drive personalized learning at scale. We discuss parallels between LLMs and human cognition, emphasizing both the promise and new perspectives on integrating AI systems into education. After examining challenges in aligning technology with pedagogy, we review AutoTutor-one of the earliest Intelligent Tutoring Systems (ITS)-and detail its successes, limitations, and unfulfilled aspirations. We then introduce the Socratic Playground, a next-generation ITS that uses advanced transformer-based models to overcome AutoTutor's constraints and provide personalized, adaptive tutoring. To illustrate its evolving capabilities, we present a JSON-based tutoring prompt that systematically guides learner reflection while tracking misconceptions. Throughout, we underscore the importance of placing pedagogy at the forefront, ensuring that technology's power is harnessed to enhance teaching and learning rather than overshadow it.

MaskGaussian: Adaptive 3D Gaussian Representation from Probabilistic Masks

While 3D Gaussian Splatting (3DGS) has demonstrated remarkable performance in novel view synthesis and real-time rendering, the high memory consumption due to the use of millions of Gaussians limits its practicality. To mitigate this issue, improvements have been made by pruning unnecessary Gaussians, either through a hand-crafted criterion or by using learned masks. However, these methods deterministically remove Gaussians based on a snapshot of the pruning moment, leading to sub-optimized reconstruction performance from a long-term perspective. To address this issue, we introduce MaskGaussian, which models Gaussians as probabilistic entities rather than permanently removing them, and utilize them according to their probability of existence. To achieve this, we propose a masked-rasterization technique that enables unused yet probabilistically existing Gaussians to receive gradients, allowing for dynamic assessment of their contribution to the evolving scene and adjustment of their probability of existence. Hence, the importance of Gaussians iteratively changes and the pruned Gaussians are selected diversely. Extensive experiments demonstrate the superiority of the proposed method in achieving better rendering quality with fewer Gaussians than previous pruning methods, pruning over 60% of Gaussians on average with only a 0.02 PSNR decline. Our code can be found at: https://github.com/kaikai23/MaskGaussian

Adaptive Traffic Element-Based Streetlight Control Using Neighbor Discovery Algorithm Based on IoT Events

Intelligent streetlight systems divide the streetlight network into multiple sectors, activating only the streetlights in the corresponding sectors when traffic elements pass by, rather than all streetlights, effectively reducing energy waste. This strategy requires streetlights to understand their neighbor relationships to illuminate only the streetlights in their respective sectors. However, manually configuring the neighbor relationships for a large number of streetlights in complex large-scale road streetlight networks is cumbersome and prone to errors. Due to the crisscrossing nature of roads, it is also difficult to determine the neighbor relationships using GPS or communication positioning. In response to these issues, this article proposes a systematic approach to model the streetlight network as a social network and construct a neighbor relationship probabilistic graph using IoT event records of streetlights detecting traffic elements. Based on this, a multi-objective genetic algorithm based probabilistic graph clustering method is designed to discover the neighbor relationships of streetlights. Considering the characteristic that pedestrians and vehicles usually move at a constant speed on a section of a road, speed consistency is introduced as an optimization objective, which, together with traditional similarity measures, forms a multi-objective function, enhancing the accuracy of neighbor relationship discovery. Extensive experiments on simulation datasets were conducted, comparing the proposed algorithm with other probabilistic graph clustering algorithms. The results demonstrate that the proposed algorithm can more accurately identify the neighbor relationships of streetlights compared to other algorithms, effectively achieving adaptive streetlight control for traffic elements.

On the Performance Analysis of Momentum Method: A Frequency Domain Perspective

Momentum-based optimizers are widely adopted for training neural networks. However, the optimal selection of momentum coefficients remains elusive. This uncertainty impedes a clear understanding of the role of momentum in stochastic gradient methods. In this paper, we present a frequency domain analysis framework that interprets the momentum method as a time-variant filter for gradients, where adjustments to momentum coefficients modify the filter characteristics. Our experiments support this perspective and provide a deeper understanding of the mechanism involved. Moreover, our analysis reveals the following significant findings: high-frequency gradient components are undesired in the late stages of training; preserving the original gradient in the early stages, and gradually amplifying low-frequency gradient components during training both enhance generalization performance. Based on these insights, we propose Frequency Stochastic Gradient Descent with Momentum (FSGDM), a heuristic optimizer that dynamically adjusts the momentum filtering characteristic with an empirically effective dynamic magnitude response. Experimental results demonstrate the superiority of FSGDM over conventional momentum optimizers.