Le Song

Xiaomin Fang, Fan Wang, Lihang Liu et al. · baidu

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.

Jing Gong, Minsheng Hao, Xingyi Cheng et al.

Advances in high-throughput sequencing technology have led to significant progress in measuring gene expressions at the single-cell level. The amount of publicly available single-cell RNA-seq (scRNA-seq) data is already surpassing 50M records for humans with each record measuring 20,000 genes. This highlights the need for unsupervised representation learning to fully ingest these data, yet classical transformer architectures are prohibitive to train on such data in terms of both computation and memory. To address this challenge, we propose a novel asymmetric encoder-decoder transformer for scRNA-seq data, called xTrimoGene$^α$ (or xTrimoGene for short), which leverages the sparse characteristic of the data to scale up the pre-training. This scalable design of xTrimoGene reduces FLOPs by one to two orders of magnitude compared to classical transformers while maintaining high accuracy, enabling us to train the largest transformer models over the largest scRNA-seq dataset today. Our experiments also show that the performance of xTrimoGene improves as we scale up the model sizes, and it also leads to SOTA performance over various downstream tasks, such as cell type annotation, perturb-seq effect prediction, and drug combination prediction. xTrimoGene model is now available for use as a service via the following link: https://api.biomap.com/xTrimoGene/apply.

Xingbo Du, Loka Li, Duzhen Zhang et al.

Memory systems have been designed to leverage past experiences in Large Language Model (LLM) agents. However, many deployed memory systems primarily optimize compression and storage, with comparatively less emphasis on explicit, closed-loop control of memory retrieval. From this observation, we build memory retrieval as an autonomous, accurate, and compatible agent system, named MemR$^3$, which has two core mechanisms: 1) a router that selects among retrieve, reflect, and answer actions to optimize answer quality; 2) a global evidence-gap tracker that explicitly renders the answering process transparent and tracks the evidence collection process. This design departs from the standard retrieve-then-answer pipeline by introducing a closed-loop control mechanism that enables autonomous decision-making. Empirical results on the LoCoMo benchmark demonstrate that MemR$^3$ surpasses strong baselines on LLM-as-a-Judge score, and particularly, it improves existing retrievers across four categories with an overall improvement on RAG (+7.29%) and Zep (+1.94%) using GPT-4.1-mini backend, offering a plug-and-play controller for existing memory stores.

Bo Chen, Xingyi Cheng, Pan Li et al.

Protein language models have shown remarkable success in learning biological information from protein sequences. However, most existing models are limited by either autoencoding or autoregressive pre-training objectives, which makes them struggle to handle protein understanding and generation tasks concurrently. We propose a unified protein language model, xTrimoPGLM, to address these two types of tasks simultaneously through an innovative pre-training framework. Our key technical contribution is an exploration of the compatibility and the potential for joint optimization of the two types of objectives, which has led to a strategy for training xTrimoPGLM at an unprecedented scale of 100 billion parameters and 1 trillion training tokens. Our extensive experiments reveal that 1) xTrimoPGLM significantly outperforms other advanced baselines in 18 protein understanding benchmarks across four categories. The model also facilitates an atomic-resolution view of protein structures, leading to an advanced 3D structural prediction model that surpasses existing language model-based tools. 2) xTrimoPGLM not only can generate de novo protein sequences following the principles of natural ones, but also can perform programmable generation after supervised fine-tuning (SFT) on curated sequences. These results highlight the substantial capability and versatility of xTrimoPGLM in understanding and generating protein sequences, contributing to the evolving landscape of foundation models in protein science.

Jian-Ya Ding, Chao Zhang, Lei Shen et al.

Mixed Integer Programming (MIP) is one of the most widely used modeling techniques for combinatorial optimization problems. In many applications, a similar MIP model is solved on a regular basis, maintaining remarkable similarities in model structures and solution appearances but differing in formulation coefficients. This offers the opportunity for machine learning methods to explore the correlations between model structures and the resulting solution values. To address this issue, we propose to represent an MIP instance using a tripartite graph, based on which a Graph Convolutional Network (GCN) is constructed to predict solution values for binary variables. The predicted solutions are used to generate a local branching type cut which can be either treated as a global (invalid) inequality in the formulation resulting in a heuristic approach to solve the MIP, or as a root branching rule resulting in an exact approach. Computational evaluations on 8 distinct types of MIP problems show that the proposed framework improves the primal solution finding performance significantly on a state-of-the-art open-source MIP solver.

Xingyi Cheng, Bo Chen, Pan Li et al.

We explore optimally training protein language models, an area of significant interest in biological research where guidance on best practices is limited. Most models are trained with extensive compute resources until performance gains plateau, focusing primarily on increasing model sizes rather than optimizing the efficient compute frontier that balances performance and compute budgets. Our investigation is grounded in a massive dataset consisting of 939 million protein sequences. We trained over 300 models ranging from 3.5 million to 10.7 billion parameters on 5 to 200 billion unique tokens, to investigate the relations between model sizes, training token numbers, and objectives. First, we observed the effect of diminishing returns for the Causal Language Model (CLM) and that of overfitting for the Masked Language Model~(MLM) when repeating the commonly used Uniref database. To address this, we included metagenomic protein sequences in the training set to increase the diversity and avoid the plateau or overfitting effects. Second, we obtained the scaling laws of CLM and MLM on Transformer, tailored to the specific characteristics of protein sequence data. Third, we observe a transfer scaling phenomenon from CLM to MLM, further demonstrating the effectiveness of transfer through scaling behaviors based on estimated Effectively Transferred Tokens. Finally, to validate our scaling laws, we compare the large-scale versions of ESM-2 and PROGEN2 on downstream tasks, encompassing evaluations of protein generation as well as structure- and function-related tasks, all within less or equivalent pre-training compute budgets.

Le Song, Eran Segal, Eric Xing

We present an approach of using AI to model and simulate biology and life. Why is it important? Because at the core of medicine, pharmacy, public health, longevity, agriculture and food security, environmental protection, and clean energy, it is biology at work. Biology in the physical world is too complex to manipulate and always expensive and risky to tamper with. In this perspective, we layout an engineering viable approach to address this challenge by constructing an AI-Driven Digital Organism (AIDO), a system of integrated multiscale foundation models, in a modular, connectable, and holistic fashion to reflect biological scales, connectedness, and complexities. An AIDO opens up a safe, affordable and high-throughput alternative platform for predicting, simulating and programming biology at all levels from molecules to cells to individuals. We envision that an AIDO is poised to trigger a new wave of better-guided wet-lab experimentation and better-informed first-principle reasoning, which can eventually help us better decode and improve life.

Junde Xu, Zijun Gao, Xinyi Zhou et al.

The inverse folding problem, aiming to design amino acid sequences that fold into desired three-dimensional structures, is pivotal for various biotechnological applications. Here, we introduce a novel approach leveraging Direct Preference Optimization (DPO) to fine-tune an inverse folding model using feedback from a protein folding model. Given a target protein structure, we begin by sampling candidate sequences from the inverse-folding model, then predict the three-dimensional structure of each sequence with the folding model to generate pairwise structural-preference labels. These labels are used to fine-tune the inverse-folding model under the DPO objective. Our results on the CATH 4.2 test set demonstrate that DPO fine-tuning not only improves sequence recovery of baseline models but also leads to a significant improvement in average TM-Score from 0.77 to 0.81, indicating enhanced structure similarity. Furthermore, iterative application of our DPO-based method on challenging protein structures yields substantial gains, with an average TM-Score increase of 79.5\% with regard to the baseline model. This work establishes a promising direction for enhancing protein sequence design ability from structure feedback by effectively utilizing preference optimization.

Bo Chen, Zhilei Bei, Xingyi Cheng et al.

Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families. The accuracy of protein structure predictions is often compromised for protein sequences that lack sufficient homologous information to construct high quality MSA. Although various methods have been proposed to generate virtual MSA under these conditions, they fall short in comprehensively capturing the intricate coevolutionary patterns within MSA or require guidance from external oracle models. Here we introduce MSAGPT, a novel approach to prompt protein structure predictions via MSA generative pretraining in the low MSA regime. MSAGPT employs a simple yet effective 2D evolutionary positional encoding scheme to model complex evolutionary patterns. Endowed by this, its flexible 1D MSA decoding framework facilitates zero or few shot learning. Moreover, we demonstrate that leveraging the feedback from AlphaFold2 can further enhance the model capacity via Rejective Fine tuning (RFT) and Reinforcement Learning from AF2 Feedback (RLAF). Extensive experiments confirm the efficacy of MSAGPT in generating faithful virtual MSA to enhance the structure prediction accuracy. The transfer learning capabilities also highlight its great potential for facilitating other protein tasks.

Xinshi Chen, Haoran Sun, Caleb Ellington et al.

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.

Yu-Ying Liu, Alexander Moreno, Maxwell A. Xu et al.

The Continuous-Time Hidden Markov Model (CT-HMM) is an attractive approach to modeling disease progression due to its ability to describe noisy observations arriving irregularly in time. However, the lack of an efficient parameter learning algorithm for CT-HMM restricts its use to very small models or requires unrealistic constraints on the state transitions. In this paper, we present the first complete characterization of efficient EM-based learning methods for CT-HMM models, as well as the first solution to decoding the optimal state transition sequence and the corresponding state dwelling time. We show that EM-based learning consists of two challenges: the estimation of posterior state probabilities and the computation of end-state conditioned statistics. We solve the first challenge by reformulating the estimation problem as an equivalent discrete time-inhomogeneous hidden Markov model. The second challenge is addressed by adapting three distinct approaches from the continuous time Markov chain (CTMC) literature to the CT-HMM domain. Additionally, we further improve the efficiency of the most efficient method by a factor of the number of states. Then, for decoding, we incorporate a state-of-the-art method from the (CTMC) literature, and extend the end-state conditioned optimal state sequence decoding to the CT-HMM case with the computation of the expected state dwelling time. We demonstrate the use of CT-HMMs with more than 100 states to visualize and predict disease progression using a glaucoma dataset and an Alzheimer's disease dataset, and to decode and visualize the most probable state transition trajectory for individuals on the glaucoma dataset, which helps to identify progressing phenotypes in a comprehensive way. Finally, we apply the CT-HMM modeling and decoding strategy to investigate the progression of language acquisition and development.

Yuyu Zhang, Heng Chi, Binghong Chen et al.

A wide range of modern science and engineering applications are formulated as optimization problems with a system of partial differential equations (PDEs) as constraints. These PDE-constrained optimization problems are typically solved in a standard discretize-then-optimize approach. In many industry applications that require high-resolution solutions, the discretized constraints can easily have millions or even billions of variables, making it very slow for the standard iterative optimizer to solve the exact gradients. In this work, we propose a general framework to speed up PDE-constrained optimization using online neural synthetic gradients (ONSG) with a novel two-scale optimization scheme. We successfully apply our ONSG framework to computational morphogenesis, a representative and challenging class of PDE-constrained optimization problems. Extensive experiments have demonstrated that our method can significantly speed up computational morphogenesis (also known as topology optimization), and meanwhile maintain the quality of final solution compared to the standard optimizer. On a large-scale 3D optimal design problem with around 1,400,000 design variables, our method achieves up to 7.5x speedup while producing optimized designs with comparable objectives.

Qingru Zhang, David Wipf, Quan Gan et al.

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.

Binghong Chen, Chengtao Li, Hanjun Dai et al.

Retrosynthetic planning is a critical task in organic chemistry which identifies a series of reactions that can lead to the synthesis of a target product. The vast number of possible chemical transformations makes the size of the search space very big, and retrosynthetic planning is challenging even for experienced chemists. However, existing methods either require expensive return estimation by rollout with high variance, or optimize for search speed rather than the quality. In this paper, we propose Retro*, a neural-based A*-like algorithm that finds high-quality synthetic routes efficiently. It maintains the search as an AND-OR tree, and learns a neural search bias with off-policy data. Then guided by this neural network, it performs best-first search efficiently during new planning episodes. Experiments on benchmark USPTO datasets show that, our proposed method outperforms existing state-of-the-art with respect to both the success rate and solution quality, while being more efficient at the same time.

Xinshi Chen, Yu Li, Ramzan Umarov et al.

In this paper, we propose an end-to-end deep learning model, called E2Efold, for RNA secondary structure prediction which can effectively take into account the inherent constraints in the problem. The key idea of E2Efold is to directly predict the RNA base-pairing matrix, and use an unrolled algorithm for constrained programming as the template for deep architectures to enforce constraints. With comprehensive experiments on benchmark datasets, we demonstrate the superior performance of E2Efold: it predicts significantly better structures compared to previous SOTA (especially for pseudoknotted structures), while being as efficient as the fastest algorithms in terms of inference time.

Hanjun Dai, Chengtao Li, Connor W. Coley et al.

Retrosynthesis is one of the fundamental problems in organic chemistry. The task is to identify reactants that can be used to synthesize a specified product molecule. Recently, computer-aided retrosynthesis is finding renewed interest from both chemistry and computer science communities. Most existing approaches rely on template-based models that define subgraph matching rules, but whether or not a chemical reaction can proceed is not defined by hard decision rules. In this work, we propose a new approach to this task using the Conditional Graph Logic Network, a conditional graphical model built upon graph neural networks that learns when rules from reaction templates should be applied, implicitly considering whether the resulting reaction would be both chemically feasible and strategic. We also propose an efficient hierarchical sampling to alleviate the computation cost. While achieving a significant improvement of $8.1\%$ over current state-of-the-art methods on the benchmark dataset, our model also offers interpretations for the prediction.

Harsh Shrivastava, Xinshi Chen, Binghong Chen et al.

Recovering sparse conditional independence graphs from data is a fundamental problem in machine learning with wide applications. A popular formulation of the problem is an $\ell_1$ regularized maximum likelihood estimation. Many convex optimization algorithms have been designed to solve this formulation to recover the graph structure. Recently, there is a surge of interest to learn algorithms directly based on data, and in this case, learn to map empirical covariance to the sparse precision matrix. However, it is a challenging task in this case, since the symmetric positive definiteness (SPD) and sparsity of the matrix are not easy to enforce in learned algorithms, and a direct mapping from data to precision matrix may contain many parameters. We propose a deep learning architecture, GLAD, which uses an Alternating Minimization (AM) algorithm as our model inductive bias, and learns the model parameters via supervised learning. We show that GLAD learns a very compact and effective model for recovering sparse graphs from data.

Binghong Chen, Bo Dai, Qinjie Lin et al.

We propose a meta path planning algorithm named \emph{Neural Exploration-Exploitation Trees~(NEXT)} for learning from prior experience for solving new path planning problems in high dimensional continuous state and action spaces. Compared to more classical sampling-based methods like RRT, our approach achieves much better sample efficiency in high-dimensions and can benefit from prior experience of planning in similar environments. More specifically, NEXT exploits a novel neural architecture which can learn promising search directions from problem structures. The learned prior is then integrated into a UCB-type algorithm to achieve an online balance between \emph{exploration} and \emph{exploitation} when solving a new problem. We conduct thorough experiments to show that NEXT accomplishes new planning problems with more compact search trees and significantly outperforms state-of-the-art methods on several benchmarks.

Romain Lopez, Chenchen Li, Xiang Yan et al.

We address a practical problem ubiquitous in modern marketing campaigns, in which a central agent tries to learn a policy for allocating strategic financial incentives to customers and observes only bandit feedback. In contrast to traditional policy optimization frameworks, we take into account the additional reward structure and budget constraints common in this setting, and develop a new two-step method for solving this constrained counterfactual policy optimization problem. Our method first casts the reward estimation problem as a domain adaptation problem with supplementary structure, and then subsequently uses the estimators for optimizing the policy with constraints. We also establish theoretical error bounds for our estimation procedure and we empirically show that the approach leads to significant improvement on both synthetic and real datasets.

Xinshi Chen, Shuang Li, Hui Li et al.

There are great interests as well as many challenges in applying reinforcement learning (RL) to recommendation systems. In this setting, an online user is the environment; neither the reward function nor the environment dynamics are clearly defined, making the application of RL challenging. In this paper, we propose a novel model-based reinforcement learning framework for recommendation systems, where we develop a generative adversarial network to imitate user behavior dynamics and learn her reward function. Using this user model as the simulation environment, we develop a novel Cascading DQN algorithm to obtain a combinatorial recommendation policy which can handle a large number of candidate items efficiently. In our experiments with real data, we show this generative adversarial user model can better explain user behavior than alternatives, and the RL policy based on this model can lead to a better long-term reward for the user and higher click rate for the system.

Chenchen Li, Xiang Yan, Xiaotie Deng et al.

Uplift modeling aims to directly model the incremental impact of a treatment on an individual response. In this work, we address the problem from a new angle and reformulate it as a Markov Decision Process (MDP). We conducted extensive experiments on both a synthetic dataset and real-world scenarios, and showed that our method can achieve significant improvement over previous methods.

Shuang Li, Shuai Xiao, Shixiang Zhu et al.

Social goods, such as healthcare, smart city, and information networks, often produce ordered event data in continuous time. The generative processes of these event data can be very complex, requiring flexible models to capture their dynamics. Temporal point processes offer an elegant framework for modeling event data without discretizing the time. However, the existing maximum-likelihood-estimation (MLE) learning paradigm requires hand-crafting the intensity function beforehand and cannot directly monitor the goodness-of-fit of the estimated model in the process of training. To alleviate the risk of model-misspecification in MLE, we propose to generate samples from the generative model and monitor the quality of the samples in the process of training until the samples and the real data are indistinguishable. We take inspiration from reinforcement learning (RL) and treat the generation of each event as the action taken by a stochastic policy. We parameterize the policy as a flexible recurrent neural network and gradually improve the policy to mimic the observed event distribution. Since the reward function is unknown in this setting, we uncover an analytic and nonparametric form of the reward function using an inverse reinforcement learning formulation. This new RL framework allows us to derive an efficient policy gradient algorithm for learning flexible point process models, and we show that it performs well in both synthetic and real data.

Bo Dai, Hanjun Dai, Arthur Gretton et al.

We investigate penalized maximum log-likelihood estimation for exponential family distributions whose natural parameter resides in a reproducing kernel Hilbert space. Key to our approach is a novel technique, doubly dual embedding, that avoids computation of the partition function. This technique also allows the development of a flexible sampling strategy that amortizes the cost of Monte-Carlo sampling in the inference stage. The resulting estimator can be easily generalized to kernel conditional exponential families. We establish a connection between kernel exponential family estimation and MMD-GANs, revealing a new perspective for understanding GANs. Compared to the score matching based estimators, the proposed method improves both memory and time efficiency while enjoying stronger statistical properties, such as fully capturing smoothness in its statistical convergence rate while the score matching estimator appears to saturate. Finally, we show that the proposed estimator empirically outperforms state-of-the-art

Shuai Xiao, Mehrdad Farajtabar, Xiaojing Ye et al.

Point processes are becoming very popular in modeling asynchronous sequential data due to their sound mathematical foundation and strength in modeling a variety of real-world phenomena. Currently, they are often characterized via intensity function which limits model's expressiveness due to unrealistic assumptions on its parametric form used in practice. Furthermore, they are learned via maximum likelihood approach which is prone to failure in multi-modal distributions of sequences. In this paper, we propose an intensity-free approach for point processes modeling that transforms nuisance processes to a target one. Furthermore, we train the model using a likelihood-free leveraging Wasserstein distance between point processes. Experiments on various synthetic and real-world data substantiate the superiority of the proposed point process model over conventional ones.

Shuai Xiao, Junchi Yan, Mehrdad Farajtabar et al.

A variety of real-world processes (over networks) produce sequences of data whose complex temporal dynamics need to be studied. More especially, the event timestamps can carry important information about the underlying network dynamics, which otherwise are not available from the time-series evenly sampled from continuous signals. Moreover, in most complex processes, event sequences and evenly-sampled times series data can interact with each other, which renders joint modeling of those two sources of data necessary. To tackle the above problems, in this paper, we utilize the rich framework of (temporal) point processes to model event data and timely update its intensity function by the synergic twin Recurrent Neural Networks (RNNs). In the proposed architecture, the intensity function is synergistically modulated by one RNN with asynchronous events as input and another RNN with time series as input. Furthermore, to enhance the interpretability of the model, the attention mechanism for the neural point process is introduced. The whole model with event type and timestamp prediction output layers can be trained end-to-end and allows a black-box treatment for modeling the intensity. We substantiate the superiority of our model in synthetic data and three real-world benchmark datasets.

Mehrdad Farajtabar, Jiachen Yang, Xiaojing Ye et al.

We propose the first multistage intervention framework that tackles fake news in social networks by combining reinforcement learning with a point process network activity model. The spread of fake news and mitigation events within the network is modeled by a multivariate Hawkes process with additional exogenous control terms. By choosing a feature representation of states, defining mitigation actions and constructing reward functions to measure the effectiveness of mitigation activities, we map the problem of fake news mitigation into the reinforcement learning framework. We develop a policy iteration method unique to the multivariate networked point process, with the goal of optimizing the actions for maximal total reward under budget constraints. Our method shows promising performance in real-time intervention experiments on a Twitter network to mitigate a surrogate fake news campaign, and outperforms alternatives on synthetic datasets.

Yichen Wang, Grady Williams, Evangelos Theodorou et al.

Temporal point processes have been widely applied to model event sequence data generated by online users. In this paper, we consider the problem of how to design the optimal control policy for point processes, such that the stochastic system driven by the point process is steered to a target state. In particular, we exploit the key insight to view the stochastic optimal control problem from the perspective of optimal measure and variational inference. We further propose a convex optimization framework and an efficient algorithm to update the policy adaptively to the current system state. Experiments on synthetic and real-world data show that our algorithm can steer the user activities much more accurately and efficiently than other stochastic control methods.

Bo Dai, Ruiqi Guo, Sanjiv Kumar et al.

Learning-based binary hashing has become a powerful paradigm for fast search and retrieval in massive databases. However, due to the requirement of discrete outputs for the hash functions, learning such functions is known to be very challenging. In addition, the objective functions adopted by existing hashing techniques are mostly chosen heuristically. In this paper, we propose a novel generative approach to learn hash functions through Minimum Description Length principle such that the learned hash codes maximally compress the dataset and can also be used to regenerate the inputs. We also develop an efficient learning algorithm based on the stochastic distributional gradient, which avoids the notorious difficulty caused by binary output constraints, to jointly optimize the parameters of the hash function and the associated generative model. Extensive experiments on a variety of large-scale datasets show that the proposed method achieves better retrieval results than the existing state-of-the-art methods.

Nan Du, Yingyu Liang, Maria-Florina Balcan et al.

A typical viral marketing model identifies influential users in a social network to maximize a single product adoption assuming unlimited user attention, campaign budgets, and time. In reality, multiple products need campaigns, users have limited attention, convincing users incurs costs, and advertisers have limited budgets and expect the adoptions to be maximized soon. Facing these user, monetary, and timing constraints, we formulate the problem as a submodular maximization task in a continuous-time diffusion model under the intersection of a matroid and multiple knapsack constraints. We propose a randomized algorithm estimating the user influence in a network ($|\mathcal{V}|$ nodes, $|\mathcal{E}|$ edges) to an accuracy of $ε$ with $n=\mathcal{O}(1/ε^2)$ randomizations and $\tilde{\mathcal{O}}(n|\mathcal{E}|+n|\mathcal{V}|)$ computations. By exploiting the influence estimation algorithm as a subroutine, we develop an adaptive threshold greedy algorithm achieving an approximation factor $k_a/(2+2 k)$ of the optimal when $k_a$ out of the $k$ knapsack constraints are active. Extensive experiments on networks of millions of nodes demonstrate that the proposed algorithms achieve the state-of-the-art in terms of effectiveness and scalability.

Bo Xie, Yingyu Liang, Le Song

Neural networks are a powerful class of functions that can be trained with simple gradient descent to achieve state-of-the-art performance on a variety of applications. Despite their practical success, there is a paucity of results that provide theoretical guarantees on why they are so effective. Lying in the center of the problem is the difficulty of analyzing the non-convex loss function with potentially numerous local minima and saddle points. Can neural networks corresponding to the stationary points of the loss function learn the true target function? If yes, what are the key factors contributing to such nice optimization properties? In this paper, we answer these questions by analyzing one-hidden-layer neural networks with ReLU activation, and show that despite the non-convexity, neural networks with diverse units have no spurious local minima. We bypass the non-convexity issue by directly analyzing the first order optimality condition, and show that the loss can be made arbitrarily small if the minimum singular value of the "extended feature matrix" is large enough. We make novel use of techniques from kernel methods and geometric discrepancy, and identify a new relation linking the smallest singular value to the spectrum of a kernel function associated with the activation function and to the diversity of the units. Our results also suggest a novel regularization function to promote unit diversity for potentially better generalization.

Behzad Tabibian, Isabel Valera, Mehrdad Farajtabar et al.

Online knowledge repositories typically rely on their users or dedicated editors to evaluate the reliability of their content. These evaluations can be viewed as noisy measurements of both information reliability and information source trustworthiness. Can we leverage these noisy evaluations, often biased, to distill a robust, unbiased and interpretable measure of both notions? In this paper, we argue that the temporal traces left by these noisy evaluations give cues on the reliability of the information and the trustworthiness of the sources. Then, we propose a temporal point process modeling framework that links these temporal traces to robust, unbiased and interpretable notions of information reliability and source trustworthiness. Furthermore, we develop an efficient convex optimization procedure to learn the parameters of the model from historical traces. Experiments on real-world data gathered from Wikipedia and Stack Overflow show that our modeling framework accurately predicts evaluation events, provides an interpretable measure of information reliability and source trustworthiness, and yields interesting insights about real-world events.

Hanjun Dai, Yichen Wang, Rakshit Trivedi et al.

Recommender systems often use latent features to explain the behaviors of users and capture the properties of items. As users interact with different items over time, user and item features can influence each other, evolve and co-evolve over time. The compatibility of user and item's feature further influence the future interaction between users and items. Recently, point process based models have been proposed in the literature aiming to capture the temporally evolving nature of these latent features. However, these models often make strong parametric assumptions about the evolution process of the user and item latent features, which may not reflect the reality, and has limited power in expressing the complex and nonlinear dynamics underlying these processes. To address these limitations, we propose a novel deep coevolutionary network model (DeepCoevolve), for learning user and item features based on their interaction graph. DeepCoevolve use recurrent neural network (RNN) over evolving networks to define the intensity function in point processes, which allows the model to capture complex mutual influence between users and items, and the feature evolution over time. We also develop an efficient procedure for training the model parameters, and show that the learned models lead to significant improvements in recommendation and activity prediction compared to previous state-of-the-arts parametric models.

Bo Dai, Niao He, Yunpeng Pan et al.

Many machine learning tasks, such as learning with invariance and policy evaluation in reinforcement learning, can be characterized as problems of learning from conditional distributions. In such problems, each sample $x$ itself is associated with a conditional distribution $p(z|x)$ represented by samples $\{z_i\}_{i=1}^M$, and the goal is to learn a function $f$ that links these conditional distributions to target values $y$. These learning problems become very challenging when we only have limited samples or in the extreme case only one sample from each conditional distribution. Commonly used approaches either assume that $z$ is independent of $x$, or require an overwhelmingly large samples from each conditional distribution. To address these challenges, we propose a novel approach which employs a new min-max reformulation of the learning from conditional distribution problem. With such new reformulation, we only need to deal with the joint distribution $p(z,x)$. We also design an efficient learning algorithm, Embedding-SGD, and establish theoretical sample complexity for such problems. Finally, our numerical experiments on both synthetic and real-world datasets show that the proposed approach can significantly improve over the existing algorithms.

Mohammad Reza Karimi, Erfan Tavakoli, Mehrdad Farajtabar et al.

Many users in online social networks are constantly trying to gain attention from their followers by broadcasting posts to them. These broadcasters are likely to gain greater attention if their posts can remain visible for a longer period of time among their followers' most recent feeds. Then when to post? In this paper, we study the problem of smart broadcasting using the framework of temporal point processes, where we model users feeds and posts as discrete events occurring in continuous time. Based on such continuous-time model, then choosing a broadcasting strategy for a user becomes a problem of designing the conditional intensity of her posting events. We derive a novel formula which links this conditional intensity with the visibility of the user in her followers' feeds. Furthermore, by exploiting this formula, we develop an efficient convex optimization framework for the when-to-post problem. Our method can find broadcasting strategies that reach a desired visibility level with provable guarantees. We experimented with data gathered from Twitter, and show that our framework can consistently make broadcasters' post more visible than alternatives.

Mehrdad Farajtabar, Safoora Yousefi, Long Q. Tran et al.

The overwhelming amount and rate of information update in online social media is making it increasingly difficult for users to allocate their attention to their topics of interest, thus there is a strong need for prioritizing news feeds. The attractiveness of a post to a user depends on many complex contextual and temporal features of the post. For instance, the contents of the post, the responsiveness of a third user, and the age of the post may all have impact. So far, these static and dynamic features has not been incorporated in a unified framework to tackle the post prioritization problem. In this paper, we propose a novel approach for prioritizing posts based on a feature modulated multi-dimensional point process. Our model is able to simultaneously capture textual and sentiment features, and temporal features such as self-excitation, mutual-excitation and bursty nature of social interaction. As an evaluation, we also curated a real-world conversational benchmark dataset crawled from Facebook. In our experiments, we demonstrate that our algorithm is able to achieve the-state-of-the-art performance in terms of analyzing, predicting, and prioritizing events. In terms of interpretability of our method, we observe that features indicating individual user profile and linguistic characteristics of the events work best for prediction and prioritization of new events.

Mehrdad Farajtabar, Yichen Wang, Manuel Gomez Rodriguez et al.

Information diffusion in online social networks is affected by the underlying network topology, but it also has the power to change it. Online users are constantly creating new links when exposed to new information sources, and in turn these links are alternating the way information spreads. However, these two highly intertwined stochastic processes, information diffusion and network evolution, have been predominantly studied separately, ignoring their co-evolutionary dynamics. We propose a temporal point process model, COEVOLVE, for such joint dynamics, allowing the intensity of one process to be modulated by that of the other. This model allows us to efficiently simulate interleaved diffusion and network events, and generate traces obeying common diffusion and network patterns observed in real-world networks. Furthermore, we also develop a convex optimization framework to learn the parameters of the model from historical diffusion and network evolution traces. We experimented with both synthetic data and data gathered from Twitter, and show that our model provides a good fit to the data as well as more accurate predictions than alternatives.

Shuang Li, Yao Xie, Hanjun Dai et al.

Detecting the emergence of an abrupt change-point is a classic problem in statistics and machine learning. Kernel-based nonparametric statistics have been used for this task which enjoy fewer assumptions on the distributions than the parametric approach and can handle high-dimensional data. In this paper we focus on the scenario when the amount of background data is large, and propose two related computationally efficient kernel-based statistics for change-point detection, which are inspired by the recently developed $B$-statistics. A novel theoretical result of the paper is the characterization of the tail probability of these statistics using the change-of-measure technique, which focuses on characterizing the tail of the detection statistics rather than obtaining its asymptotic distribution under the null distribution. Such approximations are crucial to control the false alarm rate, which corresponds to the significance level in offline change-point detection and the average-run-length in online change-point detection. Our approximations are shown to be highly accurate. Thus, they provide a convenient way to find detection thresholds for both offline and online cases without the need to resort to the more expensive simulations or bootstrapping. We show that our methods perform well on both synthetic data and real data.

Bo Xie, Yingyu Liang, Le Song

Nonlinear component analysis such as kernel Principle Component Analysis (KPCA) and kernel Canonical Correlation Analysis (KCCA) are widely used in machine learning, statistics and data analysis, but they can not scale up to big datasets. Recent attempts have employed random feature approximations to convert the problem to the primal form for linear computational complexity. However, to obtain high quality solutions, the number of random features should be the same order of magnitude as the number of data points, making such approach not directly applicable to the regime with millions of data points. We propose a simple, computationally efficient, and memory friendly algorithm based on the "doubly stochastic gradients" to scale up a range of kernel nonlinear component analysis, such as kernel PCA, CCA and SVD. Despite the \emph{non-convex} nature of these problems, our method enjoys theoretical guarantees that it converges at the rate $\tilde{O}(1/t)$ to the global optimum, even for the top $k$ eigen subspace. Unlike many alternatives, our algorithm does not require explicit orthogonalization, which is infeasible on big datasets. We demonstrate the effectiveness and scalability of our algorithm on large scale synthetic and real world datasets.

Hadi Daneshmand, Manuel Gomez-Rodriguez, Le Song et al.

Information spreads across social and technological networks, but often the network structures are hidden from us and we only observe the traces left by the diffusion processes, called cascades. Can we recover the hidden network structures from these observed cascades? What kind of cascades and how many cascades do we need? Are there some network structures which are more difficult than others to recover? Can we design efficient inference algorithms with provable guarantees? Despite the increasing availability of cascade data and methods for inferring networks from these data, a thorough theoretical understanding of the above questions remains largely unexplored in the literature. In this paper, we investigate the network structure inference problem for a general family of continuous-time diffusion models using an $l_1$-regularized likelihood maximization framework. We show that, as long as the cascade sampling process satisfies a natural incoherence condition, our framework can recover the correct network structure with high probability if we observe $O(d^3 \log N)$ cascades, where $d$ is the maximum number of parents of a node and $N$ is the total number of nodes. Moreover, we develop a simple and efficient soft-thresholding inference algorithm, which we use to illustrate the consequences of our theoretical results, and show that our framework outperforms other alternatives in practice.

Nan Du, Yingyu Liang, Maria Florina Balcan et al.

The typical algorithmic problem in viral marketing aims to identify a set of influential users in a social network, who, when convinced to adopt a product, shall influence other users in the network and trigger a large cascade of adoptions. However, the host (the owner of an online social platform) often faces more constraints than a single product, endless user attentions, unlimited budget and unbounded time; in reality, multiple products need to be advertised, each user can tolerate only a small number of recommendations, influencing user has a cost and advertisers have only limited budgets, and the adoptions need to be maximized within a short time window. Given theses myriads of user, monetary, and timing constraints, it is extremely challenging for the host to design principled and efficient viral market algorithms with provable guarantees. In this paper, we provide a novel solution by formulating the problem as a submodular maximization in a continuous-time diffusion model under an intersection of a matroid and multiple knapsack constraints. We also propose an adaptive threshold greedy algorithm which can be faster than the traditional greedy algorithm with lazy evaluation, and scalable to networks with million of nodes. Furthermore, our mathematical formulation allows us to prove that the algorithm can achieve an approximation factor of $k_a/(2+2 k)$ when $k_a$ out of the $k$ knapsack constraints are active, which also improves over previous guarantees from combinatorial optimization literature. In the case when influencing each user has uniform cost, the approximation becomes even better to a factor of $1/3$. Extensive synthetic and real world experiments demonstrate that our budgeted influence maximization algorithm achieves the-state-of-the-art in terms of both effectiveness and scalability, often beating the next best by significant margins.

Nan Du, Le Song, Manuel Gomez Rodriguez et al.

If a piece of information is released from a media site, can it spread, in 1 month, to a million web pages? This influence estimation problem is very challenging since both the time-sensitive nature of the problem and the issue of scalability need to be addressed simultaneously. In this paper, we propose a randomized algorithm for influence estimation in continuous-time diffusion networks. Our algorithm can estimate the influence of every node in a network with |V| nodes and |E| edges to an accuracy of $\varepsilon$ using $n=O(1/\varepsilon^2)$ randomizations and up to logarithmic factors O(n|E|+n|V|) computations. When used as a subroutine in a greedy influence maximization algorithm, our proposed method is guaranteed to find a set of nodes with an influence of at least (1-1/e)OPT-2$\varepsilon$, where OPT is the optimal value. Experiments on both synthetic and real-world data show that the proposed method can easily scale up to networks of millions of nodes while significantly improves over previous state-of-the-arts in terms of the accuracy of the estimated influence and the quality of the selected nodes in maximizing the influence.