UniPTMs: The First Unified Multi-type PTM Site Prediction Model via Master-Slave Architecture-Based Multi-Stage Fusion Strategy and Hierarchical Contrastive Loss

As a core mechanism of epigenetic regulation in eukaryotes, protein post-translational modifications (PTMs) require precise prediction to decipher dynamic life activity networks. To address the limitations of existing deep learning models in cross-modal feature fusion, domain generalization, and architectural optimization, this study proposes UniPTMs: the first unified framework for multi-type PTM prediction. The framework innovatively establishes a "Master-Slave" dual-path collaborative architecture: The master path dynamically integrates high-dimensional representations of protein sequences, structures, and evolutionary information through a Bidirectional Gated Cross-Attention (BGCA) module, while the slave path optimizes feature discrepancies and recalibration between structural and traditional features using a Low-Dimensional Fusion Network (LDFN). Complemented by a Multi-scale Adaptive convolutional Pyramid (MACP) for capturing local feature patterns and a Bidirectional Hierarchical Gated Fusion Network (BHGFN) enabling multi-level feature integration across paths, the framework employs a Hierarchical Dynamic Weighting Fusion (HDWF) mechanism to intelligently aggregate multimodal features. Enhanced by a novel Hierarchical Contrastive loss function for feature consistency optimization, UniPTMs demonstrates significant performance improvements (3.2%-11.4% MCC and 4.2%-14.3% AP increases) over state-of-the-art models across five modification types and transcends the Single-Type Prediction Paradigm. To strike a balance between model complexity and performance, we have also developed a lightweight variant named UniPTMs-mini.

Vision Remember: Alleviating Visual Forgetting in Efficient MLLM with Vision Feature Resample

In this work, we study the Efficient Multimodal Large Language Model. Redundant vision tokens consume a significant amount of computational memory and resources. Therefore, many previous works compress them in the Vision Projector to reduce the number of vision tokens. However, simply compressing in the Vision Projector can lead to the loss of visual information, especially for tasks that rely on fine-grained spatial relationships, such as OCR and Chart \& Table Understanding. To address this problem, we propose Vision Remember, which is inserted between the LLM decoder layers to allow vision tokens to re-memorize vision features. Specifically, we retain multi-level vision features and resample them with the vision tokens that have interacted with the text token. During the resampling process, each vision token only attends to a local region in vision features, which is referred to as saliency-enhancing local attention. Saliency-enhancing local attention not only improves computational efficiency but also captures more fine-grained contextual information and spatial relationships within the region. Comprehensive experiments on multiple visual understanding benchmarks validate the effectiveness of our method when combined with various Efficient Vision Projectors, showing performance gains without sacrificing efficiency. Based on Vision Remember, LLaVA-VR with only 2B parameters is also superior to previous representative MLLMs such as Tokenpacker-HD-7B and DeepSeek-VL-7B.

Revisiting Self-attention for Cross-domain Sequential Recommendation

Sequential recommendation is a popular paradigm in modern recommender systems. In particular, one challenging problem in this space is cross-domain sequential recommendation (CDSR), which aims to predict future behaviors given user interactions across multiple domains. Existing CDSR frameworks are mostly built on the self-attention transformer and seek to improve by explicitly injecting additional domain-specific components (e.g. domain-aware module blocks). While these additional components help, we argue they overlook the core self-attention module already present in the transformer, a naturally powerful tool to learn correlations among behaviors. In this work, we aim to improve the CDSR performance for simple models from a novel perspective of enhancing the self-attention. Specifically, we introduce a Pareto-optimal self-attention and formulate the cross-domain learning as a multi-objective problem, where we optimize the recommendation task while dynamically minimizing the cross-domain attention scores. Our approach automates knowledge transfer in CDSR (dubbed as AutoCDSR) -- it not only mitigates negative transfer but also encourages complementary knowledge exchange among auxiliary domains. Based on the idea, we further introduce AutoCDSR+, a more performant variant with slight additional cost. Our proposal is easy to implement and works as a plug-and-play module that can be incorporated into existing transformer-based recommenders. Besides flexibility, it is practical to deploy because it brings little extra computational overheads without heavy hyper-parameter tuning. AutoCDSR on average improves Recall@10 for SASRec and Bert4Rec by 9.8% and 16.0% and NDCG@10 by 12.0% and 16.7%, respectively. Code is available at https://github.com/snap-research/AutoCDSR.

Evolutionary training-free guidance in diffusion model for 3D multi-objective molecular generation

Discovering novel 3D molecular structures that simultaneously satisfy multiple property targets remains a central challenge in materials and drug design. Although recent diffusion-based models can generate 3D conformations, they require expensive retraining for each new property or property-combination and lack flexibility in enforcing structural constraints. We introduce EGD (Evolutionary Guidance in Diffusion), a training-free framework that embeds evolutionary operators directly into the diffusion sampling process. By performing crossover on noise-perturbed samples and then denoising them with a pretrained Unconditional diffusion model, EGD seamlessly blends structural fragments and steers generation toward user-specified objectives without any additional model updates. On both single- and multi-target 3D conditional generation tasks-and on multi-objective optimization of quantum properties EGD outperforms state-of-the-art conditional diffusion methods in accuracy and runs up to five times faster per generation. In the single-objective optimization of protein ligands, EGD enables customized ligand generation. Moreover, EGD can embed arbitrary 3D fragments into the generated molecules while optimizing multiple conflicting properties in one unified process. This combination of efficiency, flexibility, and controllable structure makes EGD a powerful tool for rapid, guided exploration of chemical space.

Learning Universal User Representations Leveraging Cross-domain User Intent at Snapchat

The development of powerful user representations is a key factor in the success of recommender systems (RecSys). Online platforms employ a range of RecSys techniques to personalize user experience across diverse in-app surfaces. User representations are often learned individually through user's historical interactions within each surface and user representations across different surfaces can be shared post-hoc as auxiliary features or additional retrieval sources. While effective, such schemes cannot directly encode collaborative filtering signals across different surfaces, hindering its capacity to discover complex relationships between user behaviors and preferences across the whole platform. To bridge this gap at Snapchat, we seek to conduct universal user modeling (UUM) across different in-app surfaces, learning general-purpose user representations which encode behaviors across surfaces. Instead of replacing domain-specific representations, UUM representations capture cross-domain trends, enriching existing representations with complementary information. This work discusses our efforts in developing initial UUM versions, practical challenges, technical choices and modeling and research directions with promising offline performance. Following successful A/B testing, UUM representations have been launched in production, powering multiple use cases and demonstrating their value. UUM embedding has been incorporated into (i) Long-form Video embedding-based retrieval, leading to 2.78% increase in Long-form Video Open Rate, (ii) Long-form Video L2 ranking, with 19.2% increase in Long-form Video View Time sum, (iii) Lens L2 ranking, leading to 1.76% increase in Lens play time, and (iv) Notification L2 ranking, with 0.87% increase in Notification Open Rate.

Trans-Zero: Self-Play Incentivizes Large Language Models for Multilingual Translation Without Parallel Data

The rise of Large Language Models (LLMs) has reshaped machine translation (MT), but multilingual MT still relies heavily on parallel data for supervised fine-tuning (SFT), facing challenges like data scarcity for low-resource languages and catastrophic forgetting. To address these issues, we propose TRANS-ZERO, a self-play framework that leverages only monolingual data and the intrinsic multilingual knowledge of LLM. TRANS-ZERO combines Genetic Monte-Carlo Tree Search (G-MCTS) with preference optimization, achieving strong translation performance that rivals supervised methods. Experiments demonstrate that this approach not only matches the performance of models trained on large-scale parallel data but also excels in non-English translation directions. Further analysis reveals that G-MCTS itself significantly enhances translation quality by exploring semantically consistent candidates through iterative translations, providing a robust foundation for the framework's succuss.

HisTrackMap: Global Vectorized High-Definition Map Construction via History Map Tracking

As an essential component of autonomous driving systems, high-definition (HD) maps provide rich and precise environmental information for auto-driving scenarios; however, existing methods, which primarily rely on query-based detection frameworks to directly model map elements or implicitly propagate queries over time, often struggle to maintain consistent temporal perception outcomes. These inconsistencies pose significant challenges to the stability and reliability of real-world autonomous driving and map data collection systems. To address this limitation, we propose a novel end-to-end tracking framework for global map construction by temporally tracking map elements' historical trajectories. Firstly, instance-level historical rasterization map representation is designed to explicitly store previous perception results, which can control and maintain different global instances' history information in a fine-grained way. Secondly, we introduce a Map-Trajectory Prior Fusion module within this tracking framework, leveraging historical priors for tracked instances to improve temporal smoothness and continuity. Thirdly, we propose a global perspective metric to evaluate the quality of temporal geometry construction in HD maps, filling the gap in current metrics for assessing global geometric perception results. Substantial experiments on the nuScenes and Argoverse2 datasets demonstrate that the proposed method outperforms state-of-the-art (SOTA) methods in both single-frame and temporal metrics. our project page: $\href{https://yj772881654.github.io/HisTrackMap/}{https://yj772881654.github.io/HisTrackMap.}$

Multi-LLM Collaborative Search for Complex Problem Solving

Large language models (LLMs) often struggle with complex reasoning tasks due to their limitations in addressing the vast reasoning space and inherent ambiguities of natural language. We propose the Mixture-of-Search-Agents (MoSA) paradigm, a novel approach leveraging the collective expertise of multiple LLMs to enhance search-based reasoning. MoSA integrates diverse reasoning pathways by combining independent exploration with iterative refinement among LLMs, mitigating the limitations of single-model approaches. Using Monte Carlo Tree Search (MCTS) as a backbone, MoSA enables multiple agents to propose and aggregate reasoning steps, resulting in improved accuracy. Our comprehensive evaluation across four reasoning benchmarks demonstrates MoSA's consistent performance improvements over single-agent and other multi-agent baselines, particularly in complex mathematical and commonsense reasoning tasks.

From Drafts to Answers: Unlocking LLM Potential via Aggregation Fine-Tuning

Scaling data and model size has been proven effective for boosting the performance of large language models. In addition to training-time scaling, recent studies have revealed that increasing test-time computational resources can further improve performance. In this work, we introduce Aggregation Fine-Tuning (AFT), a supervised finetuning paradigm where the model learns to synthesize multiple draft responses, referred to as proposals, into a single, refined answer, termed aggregation. At inference time, a propose-and-aggregate strategy further boosts performance by iteratively generating proposals and aggregating them. Empirical evaluations on benchmark datasets show that AFT-trained models substantially outperform standard SFT. Notably, an AFT model, fine-tuned from Llama3.1-8B-Base with only 64k data, achieves a 41.3% LC win rate on AlpacaEval 2, surpassing significantly larger LLMs such as Llama3.1-405B-Instruct and GPT4. By combining sequential refinement and parallel sampling, the propose-and-aggregate framework scales inference-time computation in a flexible manner. Overall, These findings position AFT as a promising approach to unlocking additional capabilities of LLMs without resorting to increasing data volume or model size.

Revisiting MLLMs: An In-Depth Analysis of Image Classification Abilities

With the rapid advancement of Multimodal Large Language Models (MLLMs), a variety of benchmarks have been introduced to evaluate their capabilities. While most evaluations have focused on complex tasks such as scientific comprehension and visual reasoning, little attention has been given to assessing their fundamental image classification abilities. In this paper, we address this gap by thoroughly revisiting the MLLMs with an in-depth analysis of image classification. Specifically, building on established datasets, we examine a broad spectrum of scenarios, from general classification tasks (e.g., ImageNet, ObjectNet) to more fine-grained categories such as bird and food classification. Our findings reveal that the most recent MLLMs can match or even outperform CLIP-style vision-language models on several datasets, challenging the previous assumption that MLLMs are bad at image classification \cite{VLMClassifier}. To understand the factors driving this improvement, we conduct an in-depth analysis of the network architecture, data selection, and training recipe used in public MLLMs. Our results attribute this success to advancements in language models and the diversity of training data sources. Based on these observations, we further analyze and attribute the potential reasons to conceptual knowledge transfer and enhanced exposure of target concepts, respectively. We hope our findings will offer valuable insights for future research on MLLMs and their evaluation in image classification tasks.