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Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this challenge, with sampling-based and regression-based methods emerging as two prominent approaches. However, these methods have notable limitations. Sampling-based methods often suffer from low efficiency due to the need for generating multiple candidate structures for selection. On the other hand, regression-based methods offer fast predictions but may experience decreased accuracy. Additionally, the variation in protein sizes often requires external modules for selecting suitable binding pockets, further impacting efficiency. In this work, we propose $\mathbf{FABind}$, an end-to-end model that combines pocket prediction and docking to achieve accurate and fast protein-ligand binding. $\mathbf{FABind}$ incorporates a unique ligand-informed pocket prediction module, which is also leveraged for docking pose estimation. The model further enhances the docking process by incrementally integrating the predicted pocket to optimize protein-ligand binding, reducing discrepancies between training and inference. Through extensive experiments on benchmark datasets, our proposed $\mathbf{FABind}$ demonstrates strong advantages in terms of effectiveness and efficiency compared to existing methods. Our code is available at //github.com/QizhiPei/FABind

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FAST:Conference on File and Storage Technologies。 Explanation:文件和(he)存(cun)儲技術會議。 Publisher:USENIX。 SIT:

The ability of Large Language Models (LLMs) to critique and refine their reasoning is crucial for their application in evaluation, feedback provision, and self-improvement. This paper introduces CriticBench, a comprehensive benchmark designed to assess LLMs' abilities to critique and rectify their reasoning across a variety of tasks. CriticBench encompasses five reasoning domains: mathematical, commonsense, symbolic, coding, and algorithmic. It compiles 15 datasets and incorporates responses from three LLM families. Utilizing CriticBench, we evaluate and dissect the performance of 17 LLMs in generation, critique, and correction reasoning, i.e., GQC reasoning. Our findings reveal: (1) a linear relationship in GQC capabilities, with critique-focused training markedly enhancing performance; (2) a task-dependent variation in correction effectiveness, with logic-oriented tasks being more amenable to correction; (3) GQC knowledge inconsistencies that decrease as model size increases; and (4) an intriguing inter-model critiquing dynamic, where stronger models are better at critiquing weaker ones, while weaker models can surprisingly surpass stronger ones in their self-critique. We hope these insights into the nuanced critique-correct reasoning of LLMs will foster further research in LLM critique and self-improvement.

Though reasoning abilities are considered language-agnostic, existing LLMs exhibit inconsistent reasoning abilities across different languages, e.g., reasoning in the dominant language like English is superior to other languages due to the imbalance of multilingual training data. To enhance reasoning abilities in non-dominant languages, we propose a Multilingual-Alignment-as-Preference Optimization framework (MAPO), aiming to align the reasoning processes in other languages with the dominant language. Specifically, we harness an off-the-shelf translation model for the consistency between answers in non-dominant and dominant languages, which we adopt as the preference for optimization, e.g., Direct Preference Optimization (DPO) or Proximal Policy Optimization (PPO). Experiments show that MAPO stably achieves significant improvements in the multilingual reasoning of various models on all three benchmarks (MSVAMP +16.2%, MGSM +6.1%, and MNumGLUESub +13.3%), with improved reasoning consistency across languages.

Transfer entropy (TE) is a measurement in information theory that reveals the directional flow of information between processes, providing valuable insights for a wide range of real-world applications. This work proposes Transfer Entropy Estimation via Transformers (TREET), a novel transformer-based approach for estimating the TE for stationary processes. The proposed approach employs Donsker-Vardhan (DV) representation to TE and leverages the attention mechanism for the task of neural estimation. We propose a detailed theoretical and empirical study of the TREET, comparing it to existing methods. To increase its applicability, we design an estimated TE optimization scheme that is motivated by the functional representation lemma. Afterwards, we take advantage of the joint optimization scheme to optimize the capacity of communication channels with memory, which is a canonical optimization problem in information theory, and show the memory capabilities of our estimator. Finally, we apply TREET to real-world feature analysis. Our work, applied with state-of-the-art deep learning methods, opens a new door for communication problems which are yet to be solved.

Accurate prediction of protein-ligand binding structures, a task known as molecular docking is crucial for drug design but remains challenging. While deep learning has shown promise, existing methods often depend on holo-protein structures (docked, and not accessible in realistic tasks) or neglect pocket sidechain conformations, leading to limited practical utility and unrealistic conformation predictions. To fill these gaps, we introduce an under-explored task, named flexible docking to predict poses of ligand and pocket sidechains simultaneously and introduce Re-Dock, a novel diffusion bridge generative model extended to geometric manifolds. Specifically, we propose energy-to-geometry mapping inspired by the Newton-Euler equation to co-model the binding energy and conformations for reflecting the energy-constrained docking generative process. Comprehensive experiments on designed benchmark datasets including apo-dock and cross-dock demonstrate our model's superior effectiveness and efficiency over current methods.

The growth of social media, characterized by its multimodal nature, has led to the emergence of diverse phenomena and challenges, which calls for an effective approach to uniformly solve automated tasks. The powerful Large Vision Language Models make it possible to handle a variety of tasks simultaneously, but even with carefully designed prompting methods, the general domain models often fall short in aligning with the unique speaking style and context of social media tasks. In this paper, we introduce a Large Vision Language Model for Social Media Processing (SoMeLVLM), which is a cognitive framework equipped with five key capabilities including knowledge & comprehension, application, analysis, evaluation, and creation. SoMeLVLM is designed to understand and generate realistic social media behavior. We have developed a 654k multimodal social media instruction-tuning dataset to support our cognitive framework and fine-tune our model. Our experiments demonstrate that SoMeLVLM achieves state-of-the-art performance in multiple social media tasks. Further analysis shows its significant advantages over baselines in terms of cognitive abilities.

Localizing the bronchoscope in real time is essential for ensuring intervention quality. However, most existing methods struggle to balance between speed and generalization. To address these challenges, we present BronchoTrack, an innovative real-time framework for accurate branch-level localization, encompassing lumen detection, tracking, and airway association.To achieve real-time performance, we employ a benchmark lightweight detector for efficient lumen detection. We are the first to introduce multi-object tracking to bronchoscopic localization, mitigating temporal confusion in lumen identification caused by rapid bronchoscope movement and complex airway structures. To ensure generalization across patient cases, we propose a training-free detection-airway association method based on a semantic airway graph that encodes the hierarchy of bronchial tree structures.Experiments on nine patient datasets demonstrate BronchoTrack's localization accuracy of 85.64 \%, while accessing up to the 4th generation of airways.Furthermore, we tested BronchoTrack in an in-vivo animal study using a porcine model, where it successfully localized the bronchoscope into the 8th generation airway.Experimental evaluation underscores BronchoTrack's real-time performance in both satisfying accuracy and generalization, demonstrating its potential for clinical applications.

Causal Machine Learning (CausalML) is an umbrella term for machine learning methods that formalize the data-generation process as a structural causal model (SCM). This allows one to reason about the effects of changes to this process (i.e., interventions) and what would have happened in hindsight (i.e., counterfactuals). We categorize work in \causalml into five groups according to the problems they tackle: (1) causal supervised learning, (2) causal generative modeling, (3) causal explanations, (4) causal fairness, (5) causal reinforcement learning. For each category, we systematically compare its methods and point out open problems. Further, we review modality-specific applications in computer vision, natural language processing, and graph representation learning. Finally, we provide an overview of causal benchmarks and a critical discussion of the state of this nascent field, including recommendations for future work.

The study of network robustness is a critical tool in the characterization and sense making of complex interconnected systems such as infrastructure, communication and social networks. While significant research has been conducted in all of these areas, gaps in the surveying literature still exist. Answers to key questions are currently scattered across multiple scientific fields and numerous papers. In this survey, we distill key findings across numerous domains and provide researchers crucial access to important information by--(1) summarizing and comparing recent and classical graph robustness measures; (2) exploring which robustness measures are most applicable to different categories of networks (e.g., social, infrastructure; (3) reviewing common network attack strategies, and summarizing which attacks are most effective across different network topologies; and (4) extensive discussion on selecting defense techniques to mitigate attacks across a variety of networks. This survey guides researchers and practitioners in navigating the expansive field of network robustness, while summarizing answers to key questions. We conclude by highlighting current research directions and open problems.

With the capability of modeling bidirectional contexts, denoising autoencoding based pretraining like BERT achieves better performance than pretraining approaches based on autoregressive language modeling. However, relying on corrupting the input with masks, BERT neglects dependency between the masked positions and suffers from a pretrain-finetune discrepancy. In light of these pros and cons, we propose XLNet, a generalized autoregressive pretraining method that (1) enables learning bidirectional contexts by maximizing the expected likelihood over all permutations of the factorization order and (2) overcomes the limitations of BERT thanks to its autoregressive formulation. Furthermore, XLNet integrates ideas from Transformer-XL, the state-of-the-art autoregressive model, into pretraining. Empirically, XLNet outperforms BERT on 20 tasks, often by a large margin, and achieves state-of-the-art results on 18 tasks including question answering, natural language inference, sentiment analysis, and document ranking.

Recurrent neural nets (RNN) and convolutional neural nets (CNN) are widely used on NLP tasks to capture the long-term and local dependencies, respectively. Attention mechanisms have recently attracted enormous interest due to their highly parallelizable computation, significantly less training time, and flexibility in modeling dependencies. We propose a novel attention mechanism in which the attention between elements from input sequence(s) is directional and multi-dimensional (i.e., feature-wise). A light-weight neural net, "Directional Self-Attention Network (DiSAN)", is then proposed to learn sentence embedding, based solely on the proposed attention without any RNN/CNN structure. DiSAN is only composed of a directional self-attention with temporal order encoded, followed by a multi-dimensional attention that compresses the sequence into a vector representation. Despite its simple form, DiSAN outperforms complicated RNN models on both prediction quality and time efficiency. It achieves the best test accuracy among all sentence encoding methods and improves the most recent best result by 1.02% on the Stanford Natural Language Inference (SNLI) dataset, and shows state-of-the-art test accuracy on the Stanford Sentiment Treebank (SST), Multi-Genre natural language inference (MultiNLI), Sentences Involving Compositional Knowledge (SICK), Customer Review, MPQA, TREC question-type classification and Subjectivity (SUBJ) datasets.

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