SGNet: Folding Symmetrical Protein Complex with Deep Learning

Deep learning has made significant progress in protein structure prediction, advancing the development of computational biology. However, despite the high accuracy achieved in predicting single-chain structures, a significant number of large homo-oligomeric assemblies exhibit internal symmetry, posing a major challenge in structure determination. The performances of existing deep learning methods are limited since the symmetrical protein assembly usually has a long sequence, making structural computation infeasible. In addition, multiple identical subunits in symmetrical protein complex cause the issue of supervision ambiguity in label assignment, requiring a consistent structure modeling for the training. To tackle these problems, we propose a protein folding framework called SGNet to model protein-protein interactions in symmetrical assemblies. SGNet conducts feature extraction on a single subunit and generates the whole assembly using our proposed symmetry module, which largely mitigates computational problems caused by sequence length. Thanks to the elaborate design of modeling symmetry consistently, we can model all global symmetry types in quaternary protein structure prediction. Extensive experimental results on a benchmark of symmetrical protein complexes further demonstrate the effectiveness of our method.

Do Efficient Transformers Really Save Computation?

As transformer-based language models are trained on increasingly large datasets and with vast numbers of parameters, finding more efficient alternatives to the standard Transformer has become very valuable. While many efficient Transformers and Transformer alternatives have been proposed, none provide theoretical guarantees that they are a suitable replacement for the standard Transformer. This makes it challenging to identify when to use a specific model and what directions to prioritize for further investigation. In this paper, we aim to understand the capabilities and limitations of efficient Transformers, specifically the Sparse Transformer and the Linear Transformer. We focus on their reasoning capability as exhibited by Chain-of-Thought (CoT) prompts and follow previous works to model them as Dynamic Programming (DP) problems. Our results show that while these models are expressive enough to solve general DP tasks, contrary to expectations, they require a model size that scales with the problem size. Nonetheless, we identify a class of DP problems for which these models can be more efficient than the standard Transformer. We confirm our theoretical results through experiments on representative DP tasks, adding to the understanding of efficient Transformers' practical strengths and weaknesses.

Beyond Weisfeiler-Lehman: A Quantitative Framework for GNN Expressiveness

Designing expressive Graph Neural Networks (GNNs) is a fundamental topic in the graph learning community. So far, GNN expressiveness has been primarily assessed via the Weisfeiler-Lehman (WL) hierarchy. However, such an expressivity measure has notable limitations: it is inherently coarse, qualitative, and may not well reflect practical requirements (e.g., the ability to encode substructures). In this paper, we introduce a unified framework for quantitatively studying the expressiveness of GNN architectures, addressing all the above limitations. Specifically, we identify a fundamental expressivity measure termed homomorphism expressivity, which quantifies the ability of GNN models to count graphs under homomorphism. Homomorphism expressivity offers a complete and practical assessment tool: the completeness enables direct expressivity comparisons between GNN models, while the practicality allows for understanding concrete GNN abilities such as subgraph counting. By examining four classes of prominent GNNs as case studies, we derive simple, unified, and elegant descriptions of their homomorphism expressivity for both invariant and equivariant settings. Our results provide novel insights into a series of previous work, unify the landscape of different subareas in the community, and settle several open questions. Empirically, extensive experiments on both synthetic and real-world tasks verify our theory, showing that the practical performance of GNN models aligns well with the proposed metric.

Soaring from 4K to 400K: Extending LLM's Context with Activation Beacon

The utilization of long contexts poses a big challenge for large language models due to their limited context window length. Although the context window can be extended through fine-tuning, it will result in a considerable cost at both training and inference time, and exert an unfavorable impact to the LLM's original capabilities. In this work, we propose Activation Beacon, which condenses LLM's raw activations into more compact forms such that it can perceive a much longer context with a limited context window. Activation Beacon is introduced as a plug-and-play module for the LLM. It fully preserves the LLM's original capability on short contexts while extending the new capability on processing longer contexts. Besides, it works with short sliding windows to process the long context, which achieves a competitive memory and time efficiency in both training and inference. Activation Beacon is learned by the auto-regression task conditioned on a mixture of beacons with diversified condensing ratios. Thanks to such a treatment, it can be efficiently trained purely with short-sequence data in just 10K steps, which consumes less than 9 hours on a single 8xA800 GPU machine. The experimental studies show that Activation Beacon is able to extend Llama-2-7B's context length by $\times100$ times (from 4K to 400K), meanwhile achieving a superior result on both long-context generation and understanding tasks. Our model and code will be available at the BGE repository.

Semi-Supervised Semantic Segmentation via Adaptive Equalization Learning

Due to the limited and even imbalanced data, semi-supervised semantic segmentation tends to have poor performance on some certain categories, e.g., tailed categories in Cityscapes dataset which exhibits a long-tailed label distribution. Existing approaches almost all neglect this problem, and treat categories equally. Some popular approaches such as consistency regularization or pseudo-labeling may even harm the learning of under-performing categories, that the predictions or pseudo labels of these categories could be too inaccurate to guide the learning on the unlabeled data. In this paper, we look into this problem, and propose a novel framework for semi-supervised semantic segmentation, named adaptive equalization learning (AEL). AEL adaptively balances the training of well and badly performed categories, with a confidence bank to dynamically track category-wise performance during training. The confidence bank is leveraged as an indicator to tilt training towards under-performing categories, instantiated in three strategies: 1) adaptive Copy-Paste and CutMix data augmentation approaches which give more chance for under-performing categories to be copied or cut; 2) an adaptive data sampling approach to encourage pixels from under-performing category to be sampled; 3) a simple yet effective re-weighting method to alleviate the training noise raised by pseudo-labeling. Experimentally, AEL outperforms the state-of-the-art methods by a large margin on the Cityscapes and Pascal VOC benchmarks under various data partition protocols. Code is available at https://github.com/hzhupku/SemiSeg-AEL

Decentralized Circle Formation Control for Fish-like Robots in the Real-world via Reinforcement Learning

In this paper, the circle formation control problem is addressed for a group of cooperative underactuated fish-like robots involving unknown nonlinear dynamics and disturbances. Based on the reinforcement learning and cognitive consistency theory, we propose a decentralized controller without the knowledge of the dynamics of the fish-like robots. The proposed controller can be transferred from simulation to reality. It is only trained in our established simulation environment, and the trained controller can be deployed to real robots without any manual tuning. Simulation results confirm that the proposed model-free robust formation control method is scalable with respect to the group size of the robots and outperforms other representative RL algorithms. Several experiments in the real world verify the effectiveness of our RL-based approach for circle formation control.

Discriminator Contrastive Divergence: Semi-Amortized Generative Modeling by Exploring Energy of the Discriminator

Generative Adversarial Networks (GANs) have shown great promise in modeling high dimensional data. The learning objective of GANs usually minimizes some measure discrepancy, \textit{e.g.}, $f$-divergence~($f$-GANs) or Integral Probability Metric~(Wasserstein GANs). With $f$-divergence as the objective function, the discriminator essentially estimates the density ratio, and the estimated ratio proves useful in further improving the sample quality of the generator. However, how to leverage the information contained in the discriminator of Wasserstein GANs (WGAN) is less explored. In this paper, we introduce the Discriminator Contrastive Divergence, which is well motivated by the property of WGAN's discriminator and the relationship between WGAN and energy-based model. Compared to standard GANs, where the generator is directly utilized to obtain new samples, our method proposes a semi-amortized generation procedure where the samples are produced with the generator's output as an initial state. Then several steps of Langevin dynamics are conducted using the gradient of the discriminator. We demonstrate the benefits of significant improved generation on both synthetic data and several real-world image generation benchmarks.

Suphx: Mastering Mahjong with Deep Reinforcement Learning

Artificial Intelligence (AI) has achieved great success in many domains, and game AI is widely regarded as its beachhead since the dawn of AI. In recent years, studies on game AI have gradually evolved from relatively simple environments (e.g., perfect-information games such as Go, chess, shogi or two-player imperfect-information games such as heads-up Texas hold'em) to more complex ones (e.g., multi-player imperfect-information games such as multi-player Texas hold'em and StartCraft II). Mahjong is a popular multi-player imperfect-information game worldwide but very challenging for AI research due to its complex playing/scoring rules and rich hidden information. We design an AI for Mahjong, named Suphx, based on deep reinforcement learning with some newly introduced techniques including global reward prediction, oracle guiding, and run-time policy adaptation. Suphx has demonstrated stronger performance than most top human players in terms of stable rank and is rated above 99.99% of all the officially ranked human players in the Tenhou platform. This is the first time that a computer program outperforms most top human players in Mahjong.

Beyond Exponentially Discounted Sum: Automatic Learning of Return Function

In reinforcement learning, Return, which is the weighted accumulated future rewards, and Value, which is the expected return, serve as the objective that guides the learning of the policy. In classic RL, return is defined as the exponentially discounted sum of future rewards. One key insight is that there could be many feasible ways to define the form of the return function (and thus the value), from which the same optimal policy can be derived, yet these different forms might render dramatically different speeds of learning this policy. In this paper, we research how to modify the form of the return function to enhance the learning towards the optimal policy. We propose to use a general mathematical form for return function, and employ meta-learning to learn the optimal return function in an end-to-end manner. We test our methods on a specially designed maze environment and several Atari games, and our experimental results clearly indicate the advantages of automatically learning optimal return functions in reinforcement learning.