BSM: Small but Powerful Biological Sequence Model for Genes and Proteins

Modeling biological sequences such as DNA, RNA, and proteins is crucial for understanding complex processes like gene regulation and protein synthesis. However, most current models either focus on a single type or treat multiple types of data separately, limiting their ability to capture cross-modal relationships. We propose that by learning the relationships between these modalities, the model can enhance its understanding of each type. To address this, we introduce BSM, a small but powerful mixed-modal biological sequence foundation model, trained on three types of data: RefSeq, Gene Related Sequences, and interleaved biological sequences from the web. These datasets capture the genetic flow, gene-protein relationships, and the natural co-occurrence of diverse biological data, respectively. By training on mixed-modal data, BSM significantly enhances learning efficiency and cross-modal representation, outperforming models trained solely on unimodal data. With only 110M parameters, BSM achieves performance comparable to much larger models across both single-modal and mixed-modal tasks, and uniquely demonstrates in-context learning capability for mixed-modal tasks, which is absent in existing models. Further scaling to 270M parameters demonstrates even greater performance gains, highlighting the potential of BSM as a significant advancement in multimodal biological sequence modeling.

CPL: Critical Planning Step Learning Boosts LLM Generalization in Reasoning Tasks

Post-training large language models (LLMs) to develop reasoning capabilities has proven effective across diverse domains, such as mathematical reasoning and code generation. However, existing methods primarily focus on improving task-specific reasoning but have not adequately addressed the model's generalization capabilities across a broader range of reasoning tasks. To tackle this challenge, we introduce Critical Planning Step Learning (CPL), which leverages Monte Carlo Tree Search (MCTS) to explore diverse planning steps in multi-step reasoning tasks. Based on long-term outcomes, CPL learns step-level planning preferences to improve the model's planning capabilities and, consequently, its general reasoning capabilities. Furthermore, while effective in many scenarios for aligning LLMs, existing preference learning approaches like Direct Preference Optimization (DPO) struggle with complex multi-step reasoning tasks due to their inability to capture fine-grained supervision at each step. We propose Step-level Advantage Preference Optimization (Step-APO), which integrates an advantage estimate for step-level preference pairs obtained via MCTS into the DPO. This enables the model to more effectively learn critical intermediate planning steps, thereby further improving its generalization in reasoning tasks. Experimental results demonstrate that our method, trained exclusively on GSM8K and MATH, not only significantly improves performance on GSM8K (+10.5%) and MATH (+6.5%), but also enhances out-of-domain reasoning benchmarks, such as ARC-C (+4.0%), BBH (+1.8%), MMLU-STEM (+2.2%), and MMLU (+0.9%).

NutePrune: Efficient Progressive Pruning with Numerous Teachers for Large Language Models

The considerable size of Large Language Models (LLMs) presents notable deployment challenges, particularly on resource-constrained hardware. Structured pruning, offers an effective means to compress LLMs, thereby reducing storage costs and enhancing inference speed for more efficient utilization. In this work, we study data-efficient and resource-efficient structure pruning methods to obtain smaller yet still powerful models. Knowledge Distillation is well-suited for pruning, as the intact model can serve as an excellent teacher for pruned students. However, it becomes challenging in the context of LLMs due to memory constraints. To address this, we propose an efficient progressive Numerous-teacher pruning method (NutePrune). NutePrune mitigates excessive memory costs by loading only one intact model and integrating it with various masks and LoRA modules, enabling it to seamlessly switch between teacher and student roles. This approach allows us to leverage numerous teachers with varying capacities to progressively guide the pruned model, enhancing overall performance. Extensive experiments across various tasks demonstrate the effectiveness of NutePrune. In LLaMA-7B zero-shot experiments, NutePrune retains 97.17% of the performance of the original model at 20% sparsity and 95.07% at 25% sparsity.

Parameter-efficient is not sufficient: Exploring Parameter, Memory, and Time Efficient Adapter Tuning for Dense Predictions

Pre-training & fine-tuning is a prevalent paradigm in computer vision (CV). Recently, parameter-efficient transfer learning (PETL) methods have shown promising performance in transferring knowledge from pre-trained models with only a few trainable parameters. Despite their success, the existing PETL methods in CV can be computationally expensive and require large amounts of memory and time cost during training, which limits low-resource users from conducting research and applications on large models. In this work, we propose Parameter, Memory, and Time Efficient Visual Adapter ($\mathrm{E^3VA}$) tuning to address this issue. We provide a gradient backpropagation highway for low-rank adapters which removes large gradient computations for the frozen pre-trained parameters, resulting in substantial savings of training memory and training time. Furthermore, we optimise the $\mathrm{E^3VA}$ structure for dense predictions tasks to promote model performance. Extensive experiments on COCO, ADE20K, and Pascal VOC benchmarks show that $\mathrm{E^3VA}$ can save up to 62.2% training memory and 26.2% training time on average, while achieving comparable performance to full fine-tuning and better performance than most PETL methods. Note that we can even train the Swin-Large-based Cascade Mask RCNN on GTX 1080Ti GPUs with less than 1.5% trainable parameters.

Time-aware Graph Structure Learning via Sequence Prediction on Temporal Graphs

Temporal Graph Learning, which aims to model the time-evolving nature of graphs, has gained increasing attention and achieved remarkable performance recently. However, in reality, graph structures are often incomplete and noisy, which hinders temporal graph networks (TGNs) from learning informative representations. Graph contrastive learning uses data augmentation to generate plausible variations of existing data and learn robust representations. However, rule-based augmentation approaches may be suboptimal as they lack learnability and fail to leverage rich information from downstream tasks. To address these issues, we propose a Time-aware Graph Structure Learning (TGSL) approach via sequence prediction on temporal graphs, which learns better graph structures for downstream tasks through adding potential temporal edges. In particular, it predicts time-aware context embedding based on previously observed interactions and uses the Gumble-Top-K to select the closest candidate edges to this context embedding. Additionally, several candidate sampling strategies are proposed to ensure both efficiency and diversity. Furthermore, we jointly learn the graph structure and TGNs in an end-to-end manner and perform inference on the refined graph. Extensive experiments on temporal link prediction benchmarks demonstrate that TGSL yields significant gains for the popular TGNs such as TGAT and GraphMixer, and it outperforms other contrastive learning methods on temporal graphs. We will release the code in the future.

AdapterGNN: Efficient Delta Tuning Improves Generalization Ability in Graph Neural Networks

Fine-tuning pre-trained models has recently yielded remarkable performance gains in graph neural networks (GNNs). In addition to pre-training techniques, inspired by the latest work in the natural language fields, more recent work has shifted towards applying effective fine-tuning approaches, such as parameter-efficient tuning (delta tuning). However, given the substantial differences between GNNs and transformer-based models, applying such approaches directly to GNNs proved to be less effective. In this paper, we present a comprehensive comparison of delta tuning techniques for GNNs and propose a novel delta tuning method specifically designed for GNNs, called AdapterGNN. AdapterGNN preserves the knowledge of the large pre-trained model and leverages highly expressive adapters for GNNs, which can adapt to downstream tasks effectively with only a few parameters, while also improving the model's generalization ability on the downstream tasks. Extensive experiments show that AdapterGNN achieves higher evaluation performance (outperforming full fine-tuning by 1.4% and 5.5% in the chemistry and biology domains respectively, with only 5% of its parameters tuned) and lower generalization gaps compared to full fine-tuning. Moreover, we empirically show that a larger GNN model can have a worse generalization ability, which differs from the trend observed in large language models. We have also provided a theoretical justification for delta tuning can improve the generalization ability of GNNs by applying generalization bounds.

Adaptive Transfer Learning on Graph Neural Networks

Graph neural networks (GNNs) is widely used to learn a powerful representation of graph-structured data. Recent work demonstrates that transferring knowledge from self-supervised tasks to downstream tasks could further improve graph representation. However, there is an inherent gap between self-supervised tasks and downstream tasks in terms of optimization objective and training data. Conventional pre-training methods may be not effective enough on knowledge transfer since they do not make any adaptation for downstream tasks. To solve such problems, we propose a new transfer learning paradigm on GNNs which could effectively leverage self-supervised tasks as auxiliary tasks to help the target task. Our methods would adaptively select and combine different auxiliary tasks with the target task in the fine-tuning stage. We design an adaptive auxiliary loss weighting model to learn the weights of auxiliary tasks by quantifying the consistency between auxiliary tasks and the target task. In addition, we learn the weighting model through meta-learning. Our methods can be applied to various transfer learning approaches, it performs well not only in multi-task learning but also in pre-training and fine-tuning. Comprehensive experiments on multiple downstream tasks demonstrate that the proposed methods can effectively combine auxiliary tasks with the target task and significantly improve the performance compared to state-of-the-art methods.