Protein-ligand binding representation learning from fine-grained interactions

The binding between proteins and ligands plays a crucial role in the realm of drug discovery. Previous deep learning approaches have shown promising results over traditional computationally intensive methods, but resulting in poor generalization due to limited supervised data. In this paper, we propose to learn protein-ligand binding representation in a self-supervised learning manner. Different from existing pre-training approaches which treat proteins and ligands individually, we emphasize to discern the intricate binding patterns from fine-grained interactions. Specifically, this self-supervised learning problem is formulated as a prediction of the conclusive binding complex structure given a pocket and ligand with a Transformer based interaction module, which naturally emulates the binding process. To ensure the representation of rich binding information, we introduce two pre-training tasks, i.e.~atomic pairwise distance map prediction and mask ligand reconstruction, which comprehensively model the fine-grained interactions from both structure and feature space. Extensive experiments have demonstrated the superiority of our method across various binding tasks, including protein-ligand affinity prediction, virtual screening and protein-ligand docking.

Preference Ranking Optimization for Human Alignment

Large language models (LLMs) often contain misleading content, emphasizing the need to align them with human values to ensure secur AI systems. Reinforcement learning from human feedback (RLHF) has been employed to achieve this alignment by combining a reward model, typically based on Bradley-Terry paired comparison, with an RL algorithm such as Proximal Policy Optimization (PPO) to optimize LLM responses. However, RLHF exhibits complexity, instability, and sensitivity to hyperparameters. In this paper, we propose Preference Ranking Optimization (PRO) as an alternative to PPO for directly aligning LLMs with the Bradley-Terry comparison. PRO extends the pairwise Bradley-Terry comparison to accommodate preference rankings of any length. By iteratively contrasting the likelihood of generating responses, PRO instructs the LLM to prioritize the best response while progressively ranking the remaining responses. In this manner, PRO effectively transforms human alignment into aligning the probability ranking of $n$ responses generated by LLM with the preference ranking of humans towards these responses. Experiments have shown that PRO outperforms existing alignment algorithms, achieving comparable results to ChatGPT and human responses through automatic-based, reward-based, GPT-4, and human evaluations. Furthermore, we demonstrate that longer, more diverse, and higher-quality preference ranking sequences can consistently enhance the performance of human alignment.

CPNet: Exploiting CLIP-based Attention Condenser and Probability Map Guidance for High-fidelity Talking Face Generation

Recently, talking face generation has drawn ever-increasing attention from the research community in computer vision due to its arduous challenges and widespread application scenarios, e.g. movie animation and virtual anchor. Although persevering efforts have been undertaken to enhance the fidelity and lip-sync quality of generated talking face videos, there is still large room for further improvements of synthesis quality and efficiency. Actually, these attempts somewhat ignore the explorations of fine-granularity feature extraction/integration and the consistency between probability distributions of landmarks, thereby recurring the issues of local details blurring and degraded fidelity. To mitigate these dilemmas, in this paper, a novel CLIP-based Attention and Probability Map Guided Network (CPNet) is delicately designed for inferring high-fidelity talking face videos. Specifically, considering the demands of fine-grained feature recalibration, a clip-based attention condenser is exploited to transfer knowledge with rich semantic priors from the prevailing CLIP model. Moreover, to guarantee the consistency in probability space and suppress the landmark ambiguity, we creatively propose the density map of facial landmark as auxiliary supervisory signal to guide the landmark distribution learning of generated frame. Extensive experiments on the widely-used benchmark dataset demonstrate the superiority of our CPNet against state of the arts in terms of image and lip-sync quality. In addition, a cohort of studies are also conducted to ablate the impacts of the individual pivotal components.

API-Bank: A Benchmark for Tool-Augmented LLMs

Recent research has shown that Large Language Models (LLMs) can utilize external tools to improve their contextual processing abilities, moving away from the pure language modeling paradigm and paving the way for Artificial General Intelligence. Despite this, there has been a lack of systematic evaluation to demonstrate the efficacy of LLMs using tools to respond to human instructions. This paper presents API-Bank, the first benchmark tailored for Tool-Augmented LLMs. API-Bank includes 53 commonly used API tools, a complete Tool-Augmented LLM workflow, and 264 annotated dialogues that encompass a total of 568 API calls. These resources have been designed to thoroughly evaluate LLMs' ability to plan step-by-step API calls, retrieve relevant APIs, and correctly execute API calls to meet human needs. The experimental results show that GPT-3.5 emerges the ability to use the tools relative to GPT3, while GPT-4 has stronger planning performance. Nevertheless, there remains considerable scope for further improvement when compared to human performance. Additionally, detailed error analysis and case studies demonstrate the feasibility of Tool-Augmented LLMs for daily use, as well as the primary challenges that future research needs to address.

THC: Accelerating Distributed Deep Learning Using Tensor Homomorphic Compression

Deep neural networks (DNNs) are the de-facto standard for essential use cases, such as image classification, computer vision, and natural language processing. As DNNs and datasets get larger, they require distributed training on increasingly larger clusters. A main bottleneck is then the resulting communication overhead where workers exchange model updates (i.e., gradients) on a per-round basis. To address this bottleneck and accelerate training, a widely-deployed approach is compression. However, previous deployments often apply bi-directional compression schemes by simply using a uni-directional gradient compression scheme in each direction. This results in significant computational overheads at the parameter server and increased compression error, leading to longer training and lower accuracy. We introduce Tensor Homomorphic Compression (THC), a novel bi-directional compression framework that enables the direct aggregation of compressed values while optimizing the bandwidth to accuracy tradeoff, thus eliminating the aforementioned overheads. Moreover, THC is compatible with in-network aggregation (INA), which allows for further acceleration. Evaluation over a testbed shows that THC improves time-to-accuracy in comparison to alternatives by up to 1.32x with a software PS and up to 1.51x using INA. Finally, we demonstrate that THC is scalable and tolerant for acceptable packet-loss rates.

TrOCR: Transformer-based Optical Character Recognition with Pre-trained Models

Text recognition is a long-standing research problem for document digitalization. Existing approaches for text recognition are usually built based on CNN for image understanding and RNN for char-level text generation. In addition, another language model is usually needed to improve the overall accuracy as a post-processing step. In this paper, we propose an end-to-end text recognition approach with pre-trained image Transformer and text Transformer models, namely TrOCR, which leverages the Transformer architecture for both image understanding and wordpiece-level text generation. The TrOCR model is simple but effective, and can be pre-trained with large-scale synthetic data and fine-tuned with human-labeled datasets. Experiments show that the TrOCR model outperforms the current state-of-the-art models on both printed and handwritten text recognition tasks. The code and models will be publicly available at https://aka.ms/TrOCR.

Decentralized Global Connectivity Maintenance for Multi-Robot Navigation: A Reinforcement Learning Approach

The problem of multi-robot navigation of connectivity maintenance is challenging in multi-robot applications. This work investigates how to navigate a multi-robot team in unknown environments while maintaining connectivity. We propose a reinforcement learning (RL) approach to develop a decentralized policy, which is shared among multiple robots. Given range sensor measurements and the positions of other robots, the policy aims to generate control commands for navigation and preserve the global connectivity of the robot team. We incorporate connectivity concerns into the RL framework as constraints and introduce behavior cloning to reduce the exploration complexity of policy optimization. The policy is optimized with all transition data collected by multiple robots in random simulated scenarios. We validate the effectiveness of the proposed approach by comparing different combinations of connectivity constraints and behavior cloning. We also show that our policy can generalize to unseen scenarios in both simulation and holonomic robots experiments.

Adaptive Optimizers with Sparse Group Lasso for Neural Networks in CTR Prediction

We develop a novel framework that adds the regularizers of the sparse group lasso to a family of adaptive optimizers in deep learning, such as Momentum, Adagrad, Adam, AMSGrad, AdaHessian, and create a new class of optimizers, which are named Group Momentum, Group Adagrad, Group Adam, Group AMSGrad and Group AdaHessian, etc., accordingly. We establish theoretically proven convergence guarantees in the stochastic convex settings, based on primal-dual methods. We evaluate the regularized effect of our new optimizers on three large-scale real-world ad click datasets with state-of-the-art deep learning models. The experimental results reveal that compared with the original optimizers with the post-processing procedure which uses the magnitude pruning method, the performance of the models can be significantly improved on the same sparsity level. Furthermore, in comparison to the cases without magnitude pruning, our methods can achieve extremely high sparsity with significantly better or highly competitive performance.

DocBank: A Benchmark Dataset for Document Layout Analysis

Document layout analysis usually relies on computer vision models to understand documents while ignoring textual information that is vital to capture. Meanwhile, high quality labeled datasets with both visual and textual information are still insufficient. In this paper, we present \textbf{DocBank}, a benchmark dataset with fine-grained token-level annotations for document layout analysis. DocBank is constructed using a simple yet effective way with weak supervision from the \LaTeX{} documents available on the arXiv.com. With DocBank, models from different modalities can be compared fairly and multi-modal approaches will be further investigated and boost the performance of document layout analysis. We build several strong baselines and manually split train/dev/test sets for evaluation. Experiment results show that models trained on DocBank accurately recognize the layout information for a variety of documents. The DocBank dataset will be publicly available at \url{https://github.com/doc-analysis/DocBank}.