Hunyuan-Large: An Open-Source MoE Model with 52 Billion Activated Parameters by Tencent

In this paper, we introduce Hunyuan-Large, which is currently the largest open-source Transformer-based mixture of experts model, with a total of 389 billion parameters and 52 billion activation parameters, capable of handling up to 256K tokens. We conduct a thorough evaluation of Hunyuan-Large's superior performance across various benchmarks including language understanding and generation, logical reasoning, mathematical problem-solving, coding, long-context, and aggregated tasks, where it outperforms LLama3.1-70B and exhibits comparable performance when compared to the significantly larger LLama3.1-405B model. Key practice of Hunyuan-Large include large-scale synthetic data that is orders larger than in previous literature, a mixed expert routing strategy, a key-value cache compression technique, and an expert-specific learning rate strategy. Additionally, we also investigate the scaling laws and learning rate schedule of mixture of experts models, providing valuable insights and guidances for future model development and optimization. The code and checkpoints of Hunyuan-Large are released to facilitate future innovations and applications. Codes: https://github.com/Tencent/Hunyuan-Large Models: https://huggingface.co/tencent/Tencent-Hunyuan-Large

MeToken: Uniform Micro-environment Token Boosts Post-Translational Modification Prediction

Post-translational modifications (PTMs) profoundly expand the complexity and functionality of the proteome, regulating protein attributes and interactions that are crucial for biological processes. Accurately predicting PTM sites and their specific types is therefore essential for elucidating protein function and understanding disease mechanisms. Existing computational approaches predominantly focus on protein sequences to predict PTM sites, driven by the recognition of sequence-dependent motifs. However, these approaches often overlook protein structural contexts. In this work, we first compile a large-scale sequence-structure PTM dataset, which serves as the foundation for fair comparison. We introduce the MeToken model, which tokenizes the micro-environment of each amino acid, integrating both sequence and structural information into unified discrete tokens. This model not only captures the typical sequence motifs associated with PTMs but also leverages the spatial arrangements dictated by protein tertiary structures, thus providing a holistic view of the factors influencing PTM sites. Designed to address the long-tail distribution of PTM types, MeToken employs uniform sub-codebooks that ensure even the rarest PTMs are adequately represented and distinguished. We validate the effectiveness and generalizability of MeToken across multiple datasets, demonstrating its superior performance in accurately identifying PTM types. The results underscore the importance of incorporating structural data and highlight MeToken's potential in facilitating accurate and comprehensive PTM predictions, which could significantly impact proteomics research. The code and datasets are available at https://github.com/A4Bio/MeToken.

FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning

Molecular relational learning (MRL) is crucial for understanding the interaction behaviors between molecular pairs, a critical aspect of drug discovery and development. However, the large feasible model space of MRL poses significant challenges to benchmarking, and existing MRL frameworks face limitations in flexibility and scope. To address these challenges, avoid repetitive coding efforts, and ensure fair comparison of models, we introduce FlexMol, a comprehensive toolkit designed to facilitate the construction and evaluation of diverse model architectures across various datasets and performance metrics. FlexMol offers a robust suite of preset model components, including 16 drug encoders, 13 protein sequence encoders, 9 protein structure encoders, and 7 interaction layers. With its easy-to-use API and flexibility, FlexMol supports the dynamic construction of over 70, 000 distinct combinations of model architectures. Additionally, we provide detailed benchmark results and code examples to demonstrate FlexMol's effectiveness in simplifying and standardizing MRL model development and comparison.

Rethinking Medical Anomaly Detection in Brain MRI: An Image Quality Assessment Perspective

Reconstruction-based methods, particularly those leveraging autoencoders, have been widely adopted to perform anomaly detection in brain MRI. While most existing works try to improve detection accuracy by proposing new model structures or algorithms, we tackle the problem through image quality assessment, an underexplored perspective in the field. We propose a fusion quality loss function that combines Structural Similarity Index Measure loss with l1 loss, offering a more comprehensive evaluation of reconstruction quality. Additionally, we introduce a data pre-processing strategy that enhances the average intensity ratio (AIR) between normal and abnormal regions, further improving the distinction of anomalies. By fusing the aforementioned two methods, we devise the image quality assessment (IQA) approach. The proposed IQA approach achieves significant improvements (>10%) in terms of Dice coefficient (DICE) and Area Under the Precision-Recall Curve (AUPRC) on the BraTS21 (T2, FLAIR) and MSULB datasets when compared with state-of-the-art methods. These results highlight the importance of invoking the comprehensive image quality assessment in medical anomaly detection and provide a new perspective for future research in this field.

NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Many deep learning methods have been developed for \emph{de novo} peptide sequencing task, i.e., predicting the peptide sequence for the observed mass spectrum. However, two key challenges seriously hinder the further advancement of this important task. Firstly, since there is no consensus for the evaluation datasets, the empirical results in different research papers are often not comparable, leading to unfair comparison. Secondly, the current methods are usually limited to amino acid-level or peptide-level precision and recall metrics. In this work, we present the first unified benchmark NovoBench for \emph{de novo} peptide sequencing, which comprises diverse mass spectrum data, integrated models, and comprehensive evaluation metrics. Recent impressive methods, including DeepNovo, PointNovo, Casanovo, InstaNovo, AdaNovo and $\pi$-HelixNovo are integrated into our framework. In addition to amino acid-level and peptide-level precision and recall, we evaluate the models' performance in terms of identifying post-tranlational modifications (PTMs), efficiency and robustness to peptide length, noise peaks and missing fragment ratio, which are important influencing factors while seldom be considered. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development. The benchmark will be open-sourced to facilitate future research and application.

Enabling On-Device Learning via Experience Replay with Efficient Dataset Condensation

Upon deployment to edge devices, it is often desirable for a model to further learn from streaming data to improve accuracy. However, extracting representative features from such data is challenging because it is typically unlabeled, non-independent and identically distributed (non-i.i.d), and is seen only once. To mitigate this issue, a common strategy is to maintain a small data buffer on the edge device to hold the most representative data for further learning. As most data is either never stored or quickly discarded, identifying the most representative data to avoid significant information loss becomes critical. In this paper, we propose an on-device framework that addresses this issue by condensing incoming data into more informative samples. Specifically, to effectively handle unlabeled incoming data, we propose a pseudo-labeling technique designed for unlabeled on-device learning environments. Additionally, we develop a dataset condensation technique that only requires little computation resources. To counteract the effects of noisy labels during the condensation process, we further utilize a contrastive learning objective to improve the purity of class data within the buffer. Our empirical results indicate substantial improvements over existing methods, particularly when buffer capacity is severely restricted. For instance, with a buffer capacity of just one sample per class, our method achieves an accuracy that outperforms the best existing baseline by 58.4% on the CIFAR-10 dataset.

Towards Energy-Aware Federated Learning via MARL: A Dual-Selection Approach for Model and Client

Although Federated Learning (FL) is promising in knowledge sharing for heterogeneous Artificial Intelligence of Thing (AIoT) devices, their training performance and energy efficacy are severely restricted in practical battery-driven scenarios due to the ``wooden barrel effect'' caused by the mismatch between homogeneous model paradigms and heterogeneous device capability. As a result, due to various kinds of differences among devices, it is hard for existing FL methods to conduct training effectively in energy-constrained scenarios, such as the battery constraints of devices. To tackle the above issues, we propose an energy-aware FL framework named DR-FL, which considers the energy constraints in both clients and heterogeneous deep learning models to enable energy-efficient FL. Unlike Vanilla FL, DR-FL adopts our proposed Muti-Agents Reinforcement Learning (MARL)-based dual-selection method, which allows participated devices to make contributions to the global model effectively and adaptively based on their computing capabilities and energy capacities in a MARL-based manner. Experiments on various well-known datasets show that DR-FL can not only maximise knowledge sharing among heterogeneous models under the energy constraint of large-scale AIoT systems but also improve the model performance of each involved heterogeneous device.

AdaNovo: Adaptive \emph{De Novo} Peptide Sequencing with Conditional Mutual Information

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological samples. Despite the development of various deep learning methods for identifying amino acid sequences (peptides) responsible for observed spectra, challenges persist in \emph{de novo} peptide sequencing. Firstly, prior methods struggle to identify amino acids with post-translational modifications (PTMs) due to their lower frequency in training data compared to canonical amino acids, further resulting in decreased peptide-level identification precision. Secondly, diverse types of noise and missing peaks in mass spectra reduce the reliability of training data (peptide-spectrum matches, PSMs). To address these challenges, we propose AdaNovo, a novel framework that calculates conditional mutual information (CMI) between the spectrum and each amino acid/peptide, using CMI for adaptive model training. Extensive experiments demonstrate AdaNovo's state-of-the-art performance on a 9-species benchmark, where the peptides in the training set are almost completely disjoint from the peptides of the test sets. Moreover, AdaNovo excels in identifying amino acids with PTMs and exhibits robustness against data noise. The supplementary materials contain the official code.

A Graph is Worth $K$ Words: Euclideanizing Graph using Pure Transformer

Can we model non-Euclidean graphs as pure language or even Euclidean vectors while retaining their inherent information? The non-Euclidean property have posed a long term challenge in graph modeling. Despite recent GNN and Graphformer efforts encoding graphs as Euclidean vectors, recovering original graph from the vectors remains a challenge. We introduce GraphsGPT, featuring a Graph2Seq encoder that transforms non-Euclidean graphs into learnable graph words in a Euclidean space, along with a GraphGPT decoder that reconstructs the original graph from graph words to ensure information equivalence. We pretrain GraphsGPT on 100M molecules and yield some interesting findings: (1) Pretrained Graph2Seq excels in graph representation learning, achieving state-of-the-art results on 8/9 graph classification and regression tasks. (2) Pretrained GraphGPT serves as a strong graph generator, demonstrated by its ability to perform both unconditional and conditional graph generation. (3) Graph2Seq+GraphGPT enables effective graph mixup in the Euclidean space, overcoming previously known non-Euclidean challenge. (4) Our proposed novel edge-centric GPT pretraining task is effective in graph fields, underscoring its success in both representation and generation.

Online Differentiable Clustering for Intent Learning in Recommendation

Mining users' intents plays a crucial role in sequential recommendation. The recent approach, ICLRec, was introduced to extract underlying users' intents using contrastive learning and clustering. While it has shown effectiveness, the existing method suffers from complex and cumbersome alternating optimization, leading to two main issues. Firstly, the separation of representation learning and clustering optimization within a generalized expectation maximization (EM) framework often results in sub-optimal performance. Secondly, performing clustering on the entire dataset hampers scalability for large-scale industry data. To address these challenges, we propose a novel intent learning method called \underline{ODCRec}, which integrates representation learning into an \underline{O}nline \underline{D}ifferentiable \underline{C}lustering framework for \underline{Rec}ommendation. Specifically, we encode users' behavior sequences and initialize the cluster centers as differentiable network parameters. Additionally, we design a clustering loss that guides the networks to differentiate between different cluster centers and pull similar samples towards their respective cluster centers. This allows simultaneous optimization of recommendation and clustering using mini-batch data. Moreover, we leverage the learned cluster centers as self-supervision signals for representation learning, resulting in further enhancement of recommendation performance. Extensive experiments conducted on open benchmarks and industry data validate the superiority, effectiveness, and efficiency of our proposed ODCRec method. Code is available at: https://github.com/yueliu1999/ELCRec.