arXiv subjects

Le Song

Publications and source records attributed to Le Song.

At least 37 records · Page 2Linked to original sources

arXiv2023

Linker-Tuning: Optimizing Continuous Prompts for Heterodimeric Protein Prediction

Predicting the structure of interacting chains is crucial for understanding biological systems and developing new drugs. Large-scale pre-trained Protein Language Models (PLMs), such as ESM2, have shown impressive abilities in extracting biologically meaningful representations for protein structure prediction. In this paper, we show that ESMFold, which has been successful in computing accurate atomic structures for single-chain proteins, can be adapted to predict the heterodimer structures in a lightweight manner. We propose Linker-tuning, which learns a continuous prompt to connect the two chains in a dimer before running it as a single sequence in ESMFold. Experiment results show that our method successfully predicts 56.98% of interfaces on the i.i.d. heterodimer test set, with an absolute improvement of +12.79% over the ESMFold-Linker baseline. Furthermore, our model can generalize well to the out-of-distribution (OOD) test set HeteroTest2 and two antibody test sets Fab and Fv while being $9\times$ faster than AF-Multimer.

q-bio.BM↗

arXiv2023

Question Directed Graph Attention Network for Numerical Reasoning over Text

Numerical reasoning over texts, such as addition, subtraction, sorting and counting, is a challenging machine reading comprehension task, since it requires both natural language understanding and arithmetic computation. To address this challenge, we propose a heterogeneous graph representation for the context of the passage and question needed for such reasoning, and design a question directed graph attention network to drive multi-step numerical reasoning over this context graph. The code link is at: https://github.com/emnlp2020qdgat/QDGAT

cs.AI↗

arXiv2023

xTrimoABFold: De novo Antibody Structure Prediction without MSA

In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic understanding of its function. Therefore, antibody structure prediction from its sequence alone has always been a highly valuable problem for de novo antibody design. AlphaFold2, a breakthrough in the field of structural biology, provides a solution to predict protein structure based on protein sequences and computationally expensive coevolutionary multiple sequence alignments (MSAs). However, the computational efficiency and undesirable prediction accuracy of antibodies, especially on the complementarity-determining regions (CDRs) of antibodies limit their applications in the industrially high-throughput drug design. To learn an informative representation of antibodies, we employed a deep antibody language model (ALM) on curated sequences from the observed antibody space database via a transformer model. We also developed a novel model named xTrimoABFold to predict antibody structure from antibody sequence based on the pretrained ALM as well as efficient evoformers and structural modules. The model was trained end-to-end on the antibody structures in PDB by minimizing the ensemble loss of domain-specific focal loss on CDR and the frame-aligned point loss. xTrimoABFold outperforms AlphaFold2 and other protein language model based SOTAs, e.g., OmegaFold, HelixFold-Single, and IgFold with a large significant margin (30+\% improvement on RMSD) while performing 151 times faster than AlphaFold2. To the best of our knowledge, xTrimoABFold achieved state-of-the-art antibody structure prediction. Its improvement in both accuracy and efficiency makes it a valuable tool for de novo antibody design and could make further improvements in immuno-theory.

q-bio.QM↗

arXiv2023

HelixFold-Single: MSA-free Protein Structure Prediction by Using Protein Language Model as an Alternative

AI-based protein structure prediction pipelines, such as AlphaFold2, have achieved near-experimental accuracy. These advanced pipelines mainly rely on Multiple Sequence Alignments (MSAs) as inputs to learn the co-evolution information from the homologous sequences. Nonetheless, searching MSAs from protein databases is time-consuming, usually taking dozens of minutes. Consequently, we attempt to explore the limits of fast protein structure prediction by using only primary sequences of proteins. HelixFold-Single is proposed to combine a large-scale protein language model with the superior geometric learning capability of AlphaFold2. Our proposed method, HelixFold-Single, first pre-trains a large-scale protein language model (PLM) with thousands of millions of primary sequences utilizing the self-supervised learning paradigm, which will be used as an alternative to MSAs for learning the co-evolution information. Then, by combining the pre-trained PLM and the essential components of AlphaFold2, we obtain an end-to-end differentiable model to predict the 3D coordinates of atoms from only the primary sequence. HelixFold-Single is validated in datasets CASP14 and CAMEO, achieving competitive accuracy with the MSA-based methods on the targets with large homologous families. Furthermore, HelixFold-Single consumes much less time than the mainstream pipelines for protein structure prediction, demonstrating its potential in tasks requiring many predictions. The code of HelixFold-Single is available at https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/protein_folding/helixfold-single, and we also provide stable web services on https://paddlehelix.baidu.com/app/drug/protein-single/forecast.

q-bio.BM↗

arXiv2023

Drug Synergistic Combinations Predictions via Large-Scale Pre-Training and Graph Structure Learning

Drug combination therapy is a well-established strategy for disease treatment with better effectiveness and less safety degradation. However, identifying novel drug combinations through wet-lab experiments is resource intensive due to the vast combinatorial search space. Recently, computational approaches, specifically deep learning models have emerged as an efficient way to discover synergistic combinations. While previous methods reported fair performance, their models usually do not take advantage of multi-modal data and they are unable to handle new drugs or cell lines. In this study, we collected data from various datasets covering various drug-related aspects. Then, we take advantage of large-scale pre-training models to generate informative representations and features for drugs, proteins, and diseases. Based on that, a message-passing graph is built on top to propagate information together with graph structure learning flexibility. This is first introduced in the biological networks and enables us to generate pseudo-relations in the graph. Our framework achieves state-of-the-art results in comparison with other deep learning-based methods on synergistic prediction benchmark datasets. We are also capable of inferencing new drug combination data in a test on an independent set released by AstraZeneca, where 10% of improvement over previous methods is observed. In addition, we're robust against unseen drugs and surpass almost 15% AU ROC compared to the second-best model. We believe our framework contributes to both the future wet-lab discovery of novel drugs and the building of promising guidance for precise combination medicine.

cs.LG↗

arXiv2022

ReSel: N-ary Relation Extraction from Scientific Text and Tables by Learning to Retrieve and Select

We study the problem of extracting N-ary relation tuples from scientific articles. This task is challenging because the target knowledge tuples can reside in multiple parts and modalities of the document. Our proposed method ReSel decomposes this task into a two-stage procedure that first retrieves the most relevant paragraph/table and then selects the target entity from the retrieved component. For the high-level retrieval stage, ReSel designs a simple and effective feature set, which captures multi-level lexical and semantic similarities between the query and components. For the low-level selection stage, ReSel designs a cross-modal entity correlation graph along with a multi-view architecture, which models both semantic and document-structural relations between entities. Our experiments on three scientific information extraction datasets show that ReSel outperforms state-of-the-art baselines significantly.

cs.CL↗

arXiv2022

Uncovering the Structural Fairness in Graph Contrastive Learning

Recent studies show that graph convolutional network (GCN) often performs worse for low-degree nodes, exhibiting the so-called structural unfairness for graphs with long-tailed degree distributions prevalent in the real world. Graph contrastive learning (GCL), which marries the power of GCN and contrastive learning, has emerged as a promising self-supervised approach for learning node representations. How does GCL behave in terms of structural fairness? Surprisingly, we find that representations obtained by GCL methods are already fairer to degree bias than those learned by GCN. We theoretically show that this fairness stems from intra-community concentration and inter-community scatter properties of GCL, resulting in a much clear community structure to drive low-degree nodes away from the community boundary. Based on our theoretical analysis, we further devise a novel graph augmentation method, called GRAph contrastive learning for DEgree bias (GRADE), which applies different strategies to low- and high-degree nodes. Extensive experiments on various benchmarks and evaluation protocols validate the effectiveness of the proposed method.

cs.LG↗

arXiv2022

SciAnnotate: A Tool for Integrating Weak Labeling Sources for Sequence Labeling

Weak labeling is a popular weak supervision strategy for Named Entity Recognition (NER) tasks, with the goal of reducing the necessity for hand-crafted annotations. Although there are numerous remarkable annotation tools for NER labeling, the subject of integrating weak labeling sources is still unexplored. We introduce a web-based tool for text annotation called SciAnnotate, which stands for scientific annotation tool. Compared to frequently used text annotation tools, our annotation tool allows for the development of weak labels in addition to providing a manual annotation experience. Our tool provides users with multiple user-friendly interfaces for creating weak labels. SciAnnotate additionally allows users to incorporate their own language models and visualize the output of their model for evaluation. In this study, we take multi-source weak label denoising as an example, we utilized a Bertifying Conditional Hidden Markov Model to denoise the weak label generated by our tool. We also evaluate our annotation tool against the dataset provided by Mysore which contains 230 annotated materials synthesis procedures. The results shows that a 53.7% reduction in annotation time obtained AND a 1.6\% increase in recall using weak label denoising. Online demo is available at https://sciannotate.azurewebsites.net/(demo account can be found in README), but we don't host a model server with it, please check the README in supplementary material for model server usage.

cs.CL↗

arXiv2022

Graph Condensation via Receptive Field Distribution Matching

Graph neural networks (GNNs) enable the analysis of graphs using deep learning, with promising results in capturing structured information in graphs. This paper focuses on creating a small graph to represent the original graph, so that GNNs trained on the size-reduced graph can make accurate predictions. We view the original graph as a distribution of receptive fields and aim to synthesize a small graph whose receptive fields share a similar distribution. Thus, we propose Graph Condesation via Receptive Field Distribution Matching (GCDM), which is accomplished by optimizing the synthetic graph through the use of a distribution matching loss quantified by maximum mean discrepancy (MMD). Additionally, we demonstrate that the synthetic graph generated by GCDM is highly generalizable to a variety of models in evaluation phase and that the condensing speed is significantly improved using this framework.

cs.LG↗

arXiv2022

Sparse Conditional Hidden Markov Model for Weakly Supervised Named Entity Recognition

Weakly supervised named entity recognition methods train label models to aggregate the token annotations of multiple noisy labeling functions (LFs) without seeing any manually annotated labels. To work well, the label model needs to contextually identify and emphasize well-performed LFs while down-weighting the under-performers. However, evaluating the LFs is challenging due to the lack of ground truths. To address this issue, we propose the sparse conditional hidden Markov model (Sparse-CHMM). Instead of predicting the entire emission matrix as other HMM-based methods, Sparse-CHMM focuses on estimating its diagonal elements, which are considered as the reliability scores of the LFs. The sparse scores are then expanded to the full-fledged emission matrix with pre-defined expansion functions. We also augment the emission with weighted XOR scores, which track the probabilities of an LF observing incorrect entities. Sparse-CHMM is optimized through unsupervised learning with a three-stage training pipeline that reduces the training difficulty and prevents the model from falling into local optima. Compared with the baselines in the Wrench benchmark, Sparse-CHMM achieves a 3.01 average F1 score improvement on five comprehensive datasets. Experiments show that each component of Sparse-CHMM is effective, and the estimated LF reliabilities strongly correlate with true LF F1 scores.

cs.CL↗

arXiv2022

PRBoost: Prompt-Based Rule Discovery and Boosting for Interactive Weakly-Supervised Learning

Weakly-supervised learning (WSL) has shown promising results in addressing label scarcity on many NLP tasks, but manually designing a comprehensive, high-quality labeling rule set is tedious and difficult. We study interactive weakly-supervised learning -- the problem of iteratively and automatically discovering novel labeling rules from data to improve the WSL model. Our proposed model, named PRBoost, achieves this goal via iterative prompt-based rule discovery and model boosting. It uses boosting to identify large-error instances and then discovers candidate rules from them by prompting pre-trained LMs with rule templates. The candidate rules are judged by human experts, and the accepted rules are used to generate complementary weak labels and strengthen the current model. Experiments on four tasks show PRBoost outperforms state-of-the-art WSL baselines up to 7.1% and bridges the gaps with fully supervised models. Our Implementation is available at \url{https://github.com/rz-zhang/PRBoost}.

cs.CL↗

arXiv2022

Learning Temporal Rules from Noisy Timeseries Data

Events across a timeline are a common data representation, seen in different temporal modalities. Individual atomic events can occur in a certain temporal ordering to compose higher level composite events. Examples of a composite event are a patient's medical symptom or a baseball player hitting a home run, caused distinct temporal orderings of patient vitals and player movements respectively. Such salient composite events are provided as labels in temporal datasets and most works optimize models to predict these composite event labels directly. We focus on uncovering the underlying atomic events and their relations that lead to the composite events within a noisy temporal data setting. We propose Neural Temporal Logic Programming (Neural TLP) which first learns implicit temporal relations between atomic events and then lifts logic rules for composite events, given only the composite events labels for supervision. This is done through efficiently searching through the combinatorial space of all temporal logic rules in an end-to-end differentiable manner. We evaluate our method on video and healthcare datasets where it outperforms the baseline methods for rule discovery.

cs.LG↗

arXiv2022

Variational Policy Propagation for Multi-agent Reinforcement Learning

We propose a \emph{collaborative} multi-agent reinforcement learning algorithm named variational policy propagation (VPP) to learn a \emph{joint} policy through the interactions over agents. We prove that the joint policy is a Markov Random Field under some mild conditions, which in turn reduces the policy space effectively. We integrate the variational inference as special differentiable layers in policy such that the actions can be efficiently sampled from the Markov Random Field and the overall policy is differentiable. We evaluate our algorithm on several large scale challenging tasks and demonstrate that it outperforms previous state-of-the-arts.

cs.LG↗

arXiv2021

Efficient Dynamic Graph Representation Learning at Scale

Dynamic graphs with ordered sequences of events between nodes are prevalent in real-world industrial applications such as e-commerce and social platforms. However, representation learning for dynamic graphs has posed great computational challenges due to the time and structure dependency and irregular nature of the data, preventing such models from being deployed to real-world applications. To tackle this challenge, we propose an efficient algorithm, Efficient Dynamic Graph lEarning (EDGE), which selectively expresses certain temporal dependency via training loss to improve the parallelism in computations. We show that EDGE can scale to dynamic graphs with millions of nodes and hundreds of millions of temporal events and achieve new state-of-the-art (SOTA) performance.

cs.LG↗

arXiv2021

Molecular Attributes Transfer from Non-Parallel Data

Optimizing chemical molecules for desired properties lies at the core of drug development. Despite initial successes made by deep generative models and reinforcement learning methods, these methods were mostly limited by the requirement of predefined attribute functions or parallel data with manually pre-compiled pairs of original and optimized molecules. In this paper, for the first time, we formulate molecular optimization as a style transfer problem and present a novel generative model that could automatically learn internal differences between two groups of non-parallel data through adversarial training strategies. Our model further enables both preservation of molecular contents and optimization of molecular properties through combining auxiliary guided-variational autoencoders and generative flow techniques. Experiments on two molecular optimization tasks, toxicity modification and synthesizability improvement, demonstrate that our model significantly outperforms several state-of-the-art methods.

cs.LG↗

arXiv2021

A General Framework for Lifelong Localization and Mapping in Changing Environment

The environment of most real-world scenarios such as malls and supermarkets changes at all times. A pre-built map that does not account for these changes becomes out-of-date easily. Therefore, it is necessary to have an up-to-date model of the environment to facilitate long-term operation of a robot. To this end, this paper presents a general lifelong simultaneous localization and mapping (SLAM) framework. Our framework uses a multiple session map representation, and exploits an efficient map updating strategy that includes map building, pose graph refinement and sparsification. To mitigate the unbounded increase of memory usage, we propose a map-trimming method based on the Chow-Liu maximum-mutual-information spanning tree. The proposed SLAM framework has been comprehensively validated by over a month of robot deployment in real supermarket environment. Furthermore, we release the dataset collected from the indoor and outdoor changing environment with the hope to accelerate lifelong SLAM research in the community. Our dataset is available at https://github.com/sanduan168/lifelong-SLAM-dataset.

cs.RO↗

arXiv2021

A Biased Graph Neural Network Sampler with Near-Optimal Regret

Graph neural networks (GNN) have recently emerged as a vehicle for applying deep network architectures to graph and relational data. However, given the increasing size of industrial datasets, in many practical situations the message passing computations required for sharing information across GNN layers are no longer scalable. Although various sampling methods have been introduced to approximate full-graph training within a tractable budget, there remain unresolved complications such as high variances and limited theoretical guarantees. To address these issues, we build upon existing work and treat GNN neighbor sampling as a multi-armed bandit problem but with a newly-designed reward function that introduces some degree of bias designed to reduce variance and avoid unstable, possibly-unbounded pay outs. And unlike prior bandit-GNN use cases, the resulting policy leads to near-optimal regret while accounting for the GNN training dynamics introduced by SGD. From a practical standpoint, this translates into lower variance estimates and competitive or superior test accuracy across several benchmarks.

cs.LG↗

arXiv2021

Multi-task Learning of Order-Consistent Causal Graphs

We consider the problem of discovering $K$ related Gaussian directed acyclic graphs (DAGs), where the involved graph structures share a consistent causal order and sparse unions of supports. Under the multi-task learning setting, we propose a $l_1/l_2$-regularized maximum likelihood estimator (MLE) for learning $K$ linear structural equation models. We theoretically show that the joint estimator, by leveraging data across related tasks, can achieve a better sample complexity for recovering the causal order (or topological order) than separate estimations. Moreover, the joint estimator is able to recover non-identifiable DAGs, by estimating them together with some identifiable DAGs. Lastly, our analysis also shows the consistency of union support recovery of the structures. To allow practical implementation, we design a continuous optimization problem whose optimizer is the same as the joint estimator and can be approximated efficiently by an iterative algorithm. We validate the theoretical analysis and the effectiveness of the joint estimator in experiments.

cs.LG↗