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Add to EdgeMolCRAFT: Structure-Based Drug Design in Continuous Parameter Space
Apr 18, 2024
Generative models for structure-based drug design (SBDD) have shown promising results in recent years. Existing works mainly focus on how to generate molecules with higher binding affinity, ignoring the feasibility prerequisites for generated 3D poses and resulting in false positives. We conduct thorough studies on key factors of ill-conformational problems when applying autoregressive methods and diffusion to SBDD, including mode collapse and hybrid continuous-discrete space. In this paper, we introduce \ours, the first SBDD model that operates in the continuous parameter space, together with a novel noise reduced sampling strategy. Empirical results show that our model consistently achieves superior performance in binding affinity with more stable 3D structure, demonstrating our ability to accurately model interatomic interactions. To our best knowledge, MolCRAFT is the first to achieve reference-level Vina Scores (-6.59 kcal/mol), outperforming other strong baselines by a wide margin (-0.84 kcal/mol). Code is available at https://github.com/AlgoMole/MolCRAFT.
Unified Generative Modeling of 3D Molecules via Bayesian Flow Networks
Mar 17, 2024Advanced generative model (e.g., diffusion model) derived from simplified continuity assumptions of data distribution, though showing promising progress, has been difficult to apply directly to geometry generation applications due to the multi-modality and noise-sensitive nature of molecule geometry. This work introduces Geometric Bayesian Flow Networks (GeoBFN), which naturally fits molecule geometry by modeling diverse modalities in the differentiable parameter space of distributions. GeoBFN maintains the SE-(3) invariant density modeling property by incorporating equivariant inter-dependency modeling on parameters of distributions and unifying the probabilistic modeling of different modalities. Through optimized training and sampling techniques, we demonstrate that GeoBFN achieves state-of-the-art performance on multiple 3D molecule generation benchmarks in terms of generation quality (90.87% molecule stability in QM9 and 85.6% atom stability in GEOM-DRUG. GeoBFN can also conduct sampling with any number of steps to reach an optimal trade-off between efficiency and quality (e.g., 20-times speedup without sacrificing performance).
ClickPrompt: CTR Models are Strong Prompt Generators for Adapting Language Models to CTR Prediction
Oct 17, 2023
Click-through rate (CTR) prediction has become increasingly indispensable for various Internet applications. Traditional CTR models convert the multi-field categorical data into ID features via one-hot encoding, and extract the collaborative signals among features. Such a paradigm suffers from the problem of semantic information loss. Another line of research explores the potential of pretrained language models (PLMs) for CTR prediction by converting input data into textual sentences through hard prompt templates. Although semantic signals are preserved, they generally fail to capture the collaborative information (e.g., feature interactions, pure ID features), not to mention the unacceptable inference overhead brought by the huge model size. In this paper, we aim to model both the semantic knowledge and collaborative knowledge for accurate CTR estimation, and meanwhile address the inference inefficiency issue. To benefit from both worlds and close their gaps, we propose a novel model-agnostic framework (i.e., ClickPrompt), where we incorporate CTR models to generate interaction-aware soft prompts for PLMs. We design a prompt-augmented masked language modeling (PA-MLM) pretraining task, where PLM has to recover the masked tokens based on the language context, as well as the soft prompts generated by CTR model. The collaborative and semantic knowledge from ID and textual features would be explicitly aligned and interacted via the prompt interface. Then, we can either tune the CTR model with PLM for superior performance, or solely tune the CTR model without PLM for inference efficiency. Experiments on four real-world datasets validate the effectiveness of ClickPrompt compared with existing baselines.
MAP: A Model-agnostic Pretraining Framework for Click-through Rate Prediction
Aug 03, 2023
With the widespread application of personalized online services, click-through rate (CTR) prediction has received more and more attention and research. The most prominent features of CTR prediction are its multi-field categorical data format, and vast and daily-growing data volume. The large capacity of neural models helps digest such massive amounts of data under the supervised learning paradigm, yet they fail to utilize the substantial data to its full potential, since the 1-bit click signal is not sufficient to guide the model to learn capable representations of features and instances. The self-supervised learning paradigm provides a more promising pretrain-finetune solution to better exploit the large amount of user click logs, and learn more generalized and effective representations. However, self-supervised learning for CTR prediction is still an open question, since current works on this line are only preliminary and rudimentary. To this end, we propose a Model-agnostic pretraining (MAP) framework that applies feature corruption and recovery on multi-field categorical data, and more specifically, we derive two practical algorithms: masked feature prediction (MFP) and replaced feature detection (RFD). MFP digs into feature interactions within each instance through masking and predicting a small portion of input features, and introduces noise contrastive estimation (NCE) to handle large feature spaces. RFD further turns MFP into a binary classification mode through replacing and detecting changes in input features, making it even simpler and more effective for CTR pretraining. Our extensive experiments on two real-world large-scale datasets (i.e., Avazu, Criteo) demonstrate the advantages of these two methods on several strong backbones (e.g., DCNv2, DeepFM), and achieve new state-of-the-art performance in terms of both effectiveness and efficiency for CTR prediction.
Task-wise Split Gradient Boosting Trees for Multi-center Diabetes Prediction
Aug 16, 2021
Diabetes prediction is an important data science application in the social healthcare domain. There exist two main challenges in the diabetes prediction task: data heterogeneity since demographic and metabolic data are of different types, data insufficiency since the number of diabetes cases in a single medical center is usually limited. To tackle the above challenges, we employ gradient boosting decision trees (GBDT) to handle data heterogeneity and introduce multi-task learning (MTL) to solve data insufficiency. To this end, Task-wise Split Gradient Boosting Trees (TSGB) is proposed for the multi-center diabetes prediction task. Specifically, we firstly introduce task gain to evaluate each task separately during tree construction, with a theoretical analysis of GBDT's learning objective. Secondly, we reveal a problem when directly applying GBDT in MTL, i.e., the negative task gain problem. Finally, we propose a novel split method for GBDT in MTL based on the task gain statistics, named task-wise split, as an alternative to standard feature-wise split to overcome the mentioned negative task gain problem. Extensive experiments on a large-scale real-world diabetes dataset and a commonly used benchmark dataset demonstrate TSGB achieves superior performance against several state-of-the-art methods. Detailed case studies further support our analysis of negative task gain problems and provide insightful findings. The proposed TSGB method has been deployed as an online diabetes risk assessment software for early diagnosis.
A Simple but Tough-to-Beat Data Augmentation Approach for Natural Language Understanding and Generation
Oct 23, 2020
Adversarial training has been shown effective at endowing the learned representations with stronger generalization ability. However, it typically requires expensive computation to determine the direction of the injected perturbations. In this paper, we introduce a set of simple yet effective data augmentation strategies dubbed cutoff, where part of the information within an input sentence is erased to yield its restricted views (during the fine-tuning stage). Notably, this process relies merely on stochastic sampling and thus adds little computational overhead. A Jensen-Shannon Divergence consistency loss is further utilized to incorporate these augmented samples into the training objective in a principled manner. To verify the effectiveness of the proposed strategies, we apply cutoff to both natural language understanding and generation problems. On the GLUE benchmark, it is demonstrated that cutoff, in spite of its simplicity, performs on par or better than several competitive adversarial-based approaches. We further extend cutoff to machine translation and observe significant gains in BLEU scores (based upon the Transformer Base model). Moreover, cutoff consistently outperforms adversarial training and achieves state-of-the-art results on the IWSLT2014 German-English dataset.
CoDA: Contrast-enhanced and Diversity-promoting Data Augmentation for Natural Language Understanding
Oct 16, 2020
Data augmentation has been demonstrated as an effective strategy for improving model generalization and data efficiency. However, due to the discrete nature of natural language, designing label-preserving transformations for text data tends to be more challenging. In this paper, we propose a novel data augmentation framework dubbed CoDA, which synthesizes diverse and informative augmented examples by integrating multiple transformations organically. Moreover, a contrastive regularization objective is introduced to capture the global relationship among all the data samples. A momentum encoder along with a memory bank is further leveraged to better estimate the contrastive loss. To verify the effectiveness of the proposed framework, we apply CoDA to Transformer-based models on a wide range of natural language understanding tasks. On the GLUE benchmark, CoDA gives rise to an average improvement of 2.2% while applied to the RoBERTa-large model. More importantly, it consistently exhibits stronger results relative to several competitive data augmentation and adversarial training base-lines (including the low-resource settings). Extensive experiments show that the proposed contrastive objective can be flexibly combined with various data augmentation approaches to further boost their performance, highlighting the wide applicability of the CoDA framework.
Multi-document Summarization with Maximal Marginal Relevance-guided Reinforcement Learning
Sep 30, 2020
While neural sequence learning methods have made significant progress in single-document summarization (SDS), they produce unsatisfactory results on multi-document summarization (MDS). We observe two major challenges when adapting SDS advances to MDS: (1) MDS involves larger search space and yet more limited training data, setting obstacles for neural methods to learn adequate representations; (2) MDS needs to resolve higher information redundancy among the source documents, which SDS methods are less effective to handle. To close the gap, we present RL-MMR, Maximal Margin Relevance-guided Reinforcement Learning for MDS, which unifies advanced neural SDS methods and statistical measures used in classical MDS. RL-MMR casts MMR guidance on fewer promising candidates, which restrains the search space and thus leads to better representation learning. Additionally, the explicit redundancy measure in MMR helps the neural representation of the summary to better capture redundancy. Extensive experiments demonstrate that RL-MMR achieves state-of-the-art performance on benchmark MDS datasets. In particular, we show the benefits of incorporating MMR into end-to-end learning when adapting SDS to MDS in terms of both learning effectiveness and efficiency.
GIKT: A Graph-based Interaction Model for Knowledge Tracing
Sep 13, 2020
With the rapid development in online education, knowledge tracing (KT) has become a fundamental problem which traces students' knowledge status and predicts their performance on new questions. Questions are often numerous in online education systems, and are always associated with much fewer skills. However, the previous literature fails to involve question information together with high-order question-skill correlations, which is mostly limited by data sparsity and multi-skill problems. From the model perspective, previous models can hardly capture the long-term dependency of student exercise history, and cannot model the interactions between student-questions, and student-skills in a consistent way. In this paper, we propose a Graph-based Interaction model for Knowledge Tracing (GIKT) to tackle the above probems. More specifically, GIKT utilizes graph convolutional network (GCN) to substantially incorporate question-skill correlations via embedding propagation. Besides, considering that relevant questions are usually scattered throughout the exercise history, and that question and skill are just different instantiations of knowledge, GIKT generalizes the degree of students' master of the question to the interactions between the student's current state, the student's history related exercises, the target question, and related skills. Experiments on three datasets demonstrate that GIKT achieves the new state-of-the-art performance, with at least 1% absolute AUC improvement.
Dynamically Fused Graph Network for Multi-hop Reasoning
Jun 06, 2019
Text-based question answering (TBQA) has been studied extensively in recent years. Most existing approaches focus on finding the answer to a question within a single paragraph. However, many difficult questions require multiple supporting evidence from scattered text among two or more documents. In this paper, we propose Dynamically Fused Graph Network(DFGN), a novel method to answer those questions requiring multiple scattered evidence and reasoning over them. Inspired by human's step-by-step reasoning behavior, DFGN includes a dynamic fusion layer that starts from the entities mentioned in the given query, explores along the entity graph dynamically built from the text, and gradually finds relevant supporting entities from the given documents. We evaluate DFGN on HotpotQA, a public TBQA dataset requiring multi-hop reasoning. DFGN achieves competitive results on the public board. Furthermore, our analysis shows DFGN produces interpretable reasoning chains.