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Coarse-grained(CG) molecular dynamics simulations offer computational efficiency for exploring protein conformational ensembles and thermodynamic properties. Though coarse representations enable large-scale simulations across extended temporal and spatial ranges, the sacrifice of atomic-level details limits their utility in tasks such as ligand docking and protein-protein interaction prediction. Backmapping, the process of reconstructing all-atom structures from coarse-grained representations, is crucial for recovering these fine details. While recent machine learning methods have made strides in protein structure generation, challenges persist in reconstructing diverse atomistic conformations that maintain geometric accuracy and chemical validity. In this paper, we present Latent Diffusion Backmapping (LDB), a novel approach leveraging denoising diffusion within latent space to address these challenges. By combining discrete latent encoding with diffusion, LDB bypasses the need for equivariant and internal coordinate manipulation, significantly simplifying the training and sampling processes as well as facilitating better and wider exploration in configuration space. We evaluate LDB's state-of-the-art performance on three distinct protein datasets, demonstrating its ability to efficiently reconstruct structures with high structural accuracy and chemical validity. Moreover, LDB shows exceptional versatility in capturing diverse protein ensembles, highlighting its capability to explore intricate conformational spaces. Our results position LDB as a powerful and scalable approach for backmapping, effectively bridging the gap between CG simulations and atomic-level analyses in computational biology., Comment: Paper under review

Deep learning methods have been considered promising for accelerating molecular screening in drug discovery and material design. Due to the limited availability of labelled data, various self-supervised molecular pre-training methods have been presented. While many existing methods utilize common pre-training tasks in computer vision (CV) and natural language processing (NLP), they often overlook the fundamental physical principles governing molecules. In contrast, applying denoising in pre-training can be interpreted as an equivalent force learning, but the limited noise distribution introduces bias into the molecular distribution. To address this issue, we introduce a molecular pre-training framework called fractional denoising (Frad), which decouples noise design from the constraints imposed by force learning equivalence. In this way, the noise becomes customizable, allowing for incorporating chemical priors to significantly improve molecular distribution modeling. Experiments demonstrate that our framework consistently outperforms existing methods, establishing state-of-the-art results across force prediction, quantum chemical properties, and binding affinity tasks. The refined noise design enhances force accuracy and sampling coverage, which contribute to the creation of physically consistent molecular representations, ultimately leading to superior predictive performance.

Compressing lengthy context is a critical but technically challenging problem. In this paper, we propose a new method called UltraGist, which is distinguished for its high-quality compression of lengthy context due to the innovative design of the compression and learning algorithm. UltraGist brings forth the following important benefits. Firstly, it notably contributes to the flexibility of compression, as it can be effectively learned to support a broad range of context lengths and compression ratios. Secondly, it helps to produce fine-grained compression for the lengthy context, where each small segment of the context is progressively processed on top of a tailored cross-attention mechanism. Thirdly, it makes the training process sample-efficient and thus maximizes the use of training data. Finally, it facilitates the efficient running of compression for dynamic context, as the compression result can be progressively generated and hence incrementally updated. UltraGist is evaluated on a wide variety of tasks associated with lengthy context, such as document QA and summarization, few-shot learning, multi-session conversation, et al. Whilst the existing methods fail to handle these challenging scenarios, our approach is able to preserve a near-lossless compression performance throughout all the evaluations. Our data, model, and code have been released at \url{https://github.com/namespace-Pt/UltraGist}., Comment: Superceded by arXiv:2401.03462v3

We extend the context length of Llama-3-8B-Instruct from 8K to 80K via QLoRA fine-tuning. The entire training cycle is super efficient, which takes 8 hours on one 8xA800 (80G) GPU machine. The resulted model exhibits superior performances across a broad range of evaluation tasks, such as NIHS, topic retrieval, and long-context language understanding; meanwhile, it also well preserves the original capability over short contexts. The dramatic context extension is mainly attributed to merely 3.5K synthetic training samples generated by GPT-4 , which indicates the LLMs' inherent (yet largely underestimated) potential to extend its original context length. In fact, the context length could be extended far beyond 80K with more computation resources. Therefore, the team will publicly release the entire resources (including data, model, data generation pipeline, training code) so as to facilitate the future research from the community: \url{https://github.com/FlagOpen/FlagEmbedding}.

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.

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., Comment: 20 pages, ICML 2024 Camera Ready Version

Long context compression is a critical research problem due to its significance in reducing the high computational and memory costs associated with LLMs. In this paper, we propose Activation Beacon, a plug-in module for transformer-based LLMs that targets effective, efficient, and flexible compression of long contexts. To achieve this, our method introduces the following technical designs. 1) We directly compress the activations (i.e. keys and values at every layer), rather than leveraging soft prompts to relay information (which constitute a major bottleneck to encapsulate the complex information within long contexts). 2) We tailor the compression workflow, where each fine-grained input unit is progressively compressed, enabling high-quality compression and efficient computation during both training and inference. 3) We train the model through compression-based auto-regression, making full use of plain texts and instructional data to optimize the model's compression performance. 4) During training, we randomly sample a compression ratio at each step, teaching the model to support a wide range of compression configurations. Extensive evaluations are conducted on various long-context tasks whose lengths (e.g., 128K) may far exceed the maximum training length (20K), such as document understanding, few-shot learning, and Needle-in-a-Haystack. Whilst existing methods struggle to handle these challenging tasks, Activation Beacon maintains a comparable performance to the uncompressed baseline across various scenarios, achieving a 2x acceleration in inference time and an 8x reduction of memory costs for KV cache. Our data, model, and code have been released at \url{https://github.com/FlagOpen/FlagEmbedding/}., Comment: Newer version of Activation Beacon

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, Comment: Accepted by NeurIPS 2021 (spotlight). Code is available at https://github.com/hzhupku/SemiSeg-AEL

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., Comment: to be published in ICRA2021

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., Comment: 17 pages, 9 figures, pre-submmited to cvpr2019

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.

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.

A fundamental issue in reinforcement learning algorithms is the balance between exploration of the environment and exploitation of information already obtained by the agent. Especially, exploration has played a critical role for both efficiency and efficacy of the learning process. However, Existing works for exploration involve task-agnostic design, that is performing well in one environment, but be ill-suited to another. To the purpose of learning an effective and efficient exploration policy in an automated manner. We formalized a feasible metric for measuring the utility of exploration based on counterfactual ideology. Based on that, We proposed an end-to-end algorithm to learn exploration policy by meta-learning. We demonstrate that our method achieves good results compared to previous works in the high-dimensional control tasks in MuJoCo simulator.

Decision tree (and its extensions such as Gradient Boosting Decision Trees and Random Forest) is a widely used machine learning algorithm, due to its practical effectiveness and model interpretability. With the emergence of big data, there is an increasing need to parallelize the training process of decision tree. However, most existing attempts along this line suffer from high communication costs. In this paper, we propose a new algorithm, called \emph{Parallel Voting Decision Tree (PV-Tree)}, to tackle this challenge. After partitioning the training data onto a number of (e.g., $M$) machines, this algorithm performs both local voting and global voting in each iteration. For local voting, the top-$k$ attributes are selected from each machine according to its local data. Then, globally top-$2k$ attributes are determined by a majority voting among these local candidates. Finally, the full-grained histograms of the globally top-$2k$ attributes are collected from local machines in order to identify the best (most informative) attribute and its split point. PV-Tree can achieve a very low communication cost (independent of the total number of attributes) and thus can scale out very well. Furthermore, theoretical analysis shows that this algorithm can learn a near optimal decision tree, since it can find the best attribute with a large probability. Our experiments on real-world datasets show that PV-Tree significantly outperforms the existing parallel decision tree algorithms in the trade-off between accuracy and efficiency.