98 accepted papers
Previous approaches to persona simulation large language models (LLMs) have typically relied on learning basic biographical information, or using limited role-play dialogue datasets to capture a character’s responses. However, a holistic representation of an individual goes beyond surface-level fact…
Vector-Quantized Variational Autoencoders (VQVAEs) have enabled strong performance in generative modeling by mapping continuous data to learnable codes. In this work, we identify a surprising yet consistent phenomenon that we term \emph{dimensional collapse}: despite using high-dimensional embedding…
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 usi…
Graph Neural Networks (GNNs) often encounter significant performance degradation under distribution shifts between training and test data, hindering their applicability in real-world scenarios. Recent studies have proposed various methods to address the out-of-distribution (OOD) generalization chall…
Understanding the 3D structure of RNA is essential for deciphering its function and developing RNA-based therapeutics. Geometric Graph Neural Networks (GeoGNNs) that conform to the $\mathrm{E}(3)$-symmetry have advanced RNA structure evaluation, a crucial step toward RNA structure prediction. Howeve…
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…
Though some research efforts have been dedicated to constrained Bayesian optimization (BO), there remains a notable absence of a principled approach with a theoretical performance guarantee in the decoupled setting. Such a setting involves independent evaluations of the objective function and constr…
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 tha…
The structure of protein-protein complexes is critical for understanding binding dynamics, biological mechanisms, and intervention strategies. Rigid protein docking, a fundamental problem in this field, aims to predict the 3D structure of complexes from their unbound states without conformational ch…
Fully- and semi-supervised semantic segmentation of biomedical images have been advanced with the development of deep neural networks (DNNs). So far, however, DNN models are usually designed to support one of these two learning schemes, unified models that support both fully- and semi-supervised seg…
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…
We propose a principled method to learn a set of human-readable logic rules to explain temporal point processes. We assume that the generative mechanisms underlying the temporal point processes are governed by a set of first-order temporal logic rules, as a compact representation of domain knowledg…
Question Answering (QA) has been a long-standing research topic in AI and NLP fields, and a wealth of studies has been conducted to attempt to equip QA systems with human-level reasoning capability. To approximate the complicated human reasoning process, state-of-the-art QA systems commonly use pre-…
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 d…
Recovering sparse parameters from observational data is a fundamental problem in machine learning with wide applications. Many classic algorithms can solve this problem with theoretical guarantees, but their performances rely on choosing the correct hyperparameters. Besides, hand-designed algorithms…
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…
In this paper, we explore the problem of generating molecules using deep neural networks, which has recently gained much interest in chemistry. To this end, we propose a spanning tree-based graph generation (STGG) framework based on formulating molecular graph generation as a construction of a spann…
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 cont…
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…
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…
We study the problem of learning a named entity recognition (NER) tagger using noisy labels from multiple weak supervision sources. Though cheap to obtain, the labels from weak supervision sources are often incomplete, inaccurate, and contradictory, making it difficult to learn an accurate NER model…
The emergence of the Internet-of-Things (IoT) sheds light on applying the machine teaching (MT) algorithms for online personalized education on home devices. This direction becomes more promising during the COVID-19 pandemic when in-person education becomes infeasible. However, as one of the most in…
Optimizing molecules for desired properties is a fundamental yet challenging task in chemistry, material science, and drug discovery. This paper develops a novel algorithm for optimizing molecular properties via an Expectation-Maximization (EM) like explainable evolutionary process. The algorithm is…
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)…
The inductive bias of a neural network is largely determined by the architecture and the training algorithm. To achieve good generalization, how to effectively train a neural network is of great importance. We propose a novel orthogonal over-parameterized training (OPT) framework that can provably m…
Programs, consisting of semantic and structural information, play an important role in the communication between humans and agents. Towards learning general program executors to unify perception, reasoning, and decision making, we formulate program-guided tasks which require learning to execute a gi…
We consider the problem of searching an input maximizing a black-box objective function given a static dataset of input-output queries. A popular approach to solving this problem is maintaining a proxy model, e.g., a deep neural network (DNN), that approximates the true objective function. Here, the…
Deep learning and symbolic reasoning are complementary techniques for an intelligent system. However, principled combinations of these techniques have limited scalability, rendering them ill-suited for real-world applications. We propose Scallop, a system that builds upon probabilistic deductive dat…
Service robots should be able to operate autonomously in dynamic and daily changing environments over an extended period of time. While Simultaneous Localization And Mapping (SLAM) is one of the most fundamental problems for robotic autonomy, most existing SLAM works are evaluated with data sequence…
Several sampling algorithms with variance reduction have been proposed for accelerating the training of Graph Convolution Networks (GCNs). However, due to the intractable computation of optimal sampling distribution, these sampling algorithms are suboptimal for GCNs and are not applicable to more g…
Counterfactual regret minimization (CFR) is a fundamental and effective technique for solving Imperfect Information Games (IIG). However, the original CFR algorithm only works for discrete states and action spaces, and the resulting strategy is maintained as a tabular representation. Such tabular re…
Markov Logic Networks (MLNs), which elegantly combine logic rules and probabilistic graphical models, can be used to address many knowledge graph problems. However, inference in MLN is computationally intensive, making the industrial-scale application of MLN very difficult. In recent years, graph ne…
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 formula…
We present a learning-based approach to detect and fix a broad range of bugs in Javascript programs. We frame the problem in terms of learning a sequence of graph transformations: given a buggy program modeled by a graph structure, our model makes a sequence of predictions including the position of…
The capability of making interpretable and self-explanatory decisions is essential for developing responsible machine learning systems. In this work, we study the learning to explain the problem in the scope of inductive logic programming (ILP). We propose Neural Logic Inductive Learning (NLIL), an…
There is a recent surge of interest in designing deep architectures based on the update steps in traditional algorithms, or learning neural networks to improve and replace traditional algorithms. While traditional algorithms have certain stopping criteria for outputting results at different iteratio…
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 approa…
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 algorit…
Inspired by the Thomson problem in physics where the distribution of multiple propelling electrons on a unit sphere can be modeled via minimizing some potential energy, hyperspherical energy minimization has demonstrated its potential in regularizing neural networks and improving their generalizatio…
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…
We propose a modeling framework for event data and aim to answer questions such as \emph{when} and \emph{why} the next event would happen. Our proposed model excels in small data regime with the ability to incorporate domain knowledge in terms of logic rules. We model the dynamics of the event start…
Macroscopic data aggregated from microscopic events are pervasive in machine learning, such as country-level COVID-19 infection statistics based on city-level data. Yet, many existing approaches for predicting macroscopic behavior only use aggregated data, leaving a large amount of fine-grained micr…
Recently, there is a surge of interest in combining deep learning models with reasoning in order to handle more sophisticated learning tasks. In many cases, a reasoning task can be solved by an iterative algorithm. This algorithm is often unrolled, truncated, and used as a specialized layer in the d…
We present an efficient algorithm for maximum likelihood estimation (MLE) of exponential family models, with a general parametrization of the energy function that includes neural networks. We exploit the primal-dual view of the MLE with a kinetics augmented model to obtain an estimate associated wi…
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…
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 al…
Instancewise feature scoring is a method for model interpretation, which yields, for each test instance, a vector of importance scores associated with features. Methods based on the Shapley score have been proposed as a fair way of computing feature attributions, but incur an exponential complexity…
We study a general formulation of program synthesis called syntax-guided synthesis(SyGuS) that concerns synthesizing a program that follows a given grammar and satisfies a given logical specification. Both the logical specification and the grammar have complex structures and can vary from task to ta…
Neural Architecture Search (NAS) has been quite successful in constructing state-of-the-art models on a variety of tasks. Unfortunately, the computational cost can make it difficult to scale. In this paper, we make the first attempt to study Meta Architecture Search which aims at learning a task-agn…
Inner product-based convolution has been the founding stone of convolutional neural networks (CNNs), enabling end-to-end learning of visual representation. By generalizing inner product with a bilinear matrix, we propose the neural similarity which serves as a learnable parametric similarity measure…
We present a particle flow realization of Bayes’ rule, where an ODE-based neural operator is used to transport particles from a prior to its posterior after a new observation. We prove that such an ODE operator exists. Its neural parameterization can be trained in a meta-learning framework, allowing…
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 existi…
We consider the networked multi-agent reinforcement learning (MARL) problem in a fully decentralized setting, where agents learn to coordinate to achieve joint success. This problem is widely encountered in many areas including traffic control, distributed control, and smart grids. We assume each…
Recently, there is a surge of interest in using point processes to model continuous-time user activities. This framework has resulted in novel models and improved performance in diverse applications. However, most previous works focus on the ”open loop” setting where learned models are used for pred…
Deep learning on graph structures has shown exciting results in various applications. However, few attentions have been paid to the robustness of such models, in contrast to numerous research work for image or text adversarial attack and defense. In this paper, we focus on the adversarial attacks th…
This paper proposes a new actor-critic-style algorithm called Dual Actor-Critic or Dual-AC. It is derived in a principled way from the Lagrangian dual form of the Bellman optimality equation, which can be viewed as a two-player game between the actor and a critic-like function, which is named as du…
Variational inference plays a vital role in learning graphical models, especially on large-scale datasets. Much of its success depends on a proper choice of auxiliary distribution class for posterior approximation. However, how to pursue an auxiliary distribution class that achieves both good approx…
Inner product-based convolution has been a central component of convolutional neural networks (CNNs) and the key to learning visual representations. Inspired by the observation that CNN-learned features are naturally decoupled with the norm of features corresponding to the intra-class variation and…
Large-scale datasets possessing clean label annotations are crucial for training Convolutional Neural Networks (CNNs). However, labeling large-scale data can be very costly and error-prone, and even high-quality datasets are likely to contain noisy (incorrect) labels. Existing works usually employ a…
A fundamental problem in program verification concerns inferring loop invariants. The problem is undecidable and even practical instances are challenging. Inspired by how human experts construct loop invariants, we propose a reasoning framework Code2Inv that constructs the solution by multi-step dec…
Many graph analytics problems can be solved via iterative algorithms where the solutions are often characterized by a set of steady-state conditions. Different algorithms respect to different set of fixed point constraints, so instead of using these traditional algorithms, can we learn an algorithm…
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…
We introduce instancewise feature selection as a methodology for model interpretation. Our method is based on learning a function to extract a subset of features that are most informative for each given example. This feature selector is trained to maximize the mutual information between selected fea…
Neural networks are a powerful class of nonlinear functions that can be trained end-to-end on various applications. While the over-parametrization nature in many neural networks renders the ability to fit complex functions and the strong representation power to handle challenging tasks, it also lead…
Kernel methods are powerful tools for modeling nonlinear data. However, the amount of computation and memory required for kernel methods becomes the bottleneck when dealing with large-scale problems. In this paper, we propose Nested Nystrom Method (NNM) which achieves a delicate balance between the…
When function approximation is used, solving the Bellman optimality equation with stability guarantees has remained a major open problem in reinforcement learning for decades. The fundamental difficulty is that the Bellman operator may become an expansion in general, resulting in oscillating and eve…
Graph convolutional networks (GCNs) are powerful deep neural networks for graph-structured data. However, GCN computes the representation of a node recursively from its neighbors, making the receptive field size grow exponentially with the number of layers. Previous attempts on reducing the receptiv…
Deep generative models have been enjoying success in modeling continuous data. However it remains challenging to capture the representations for discrete structures with formal grammars and semantics, e.g., computer programs and molecular structures. How to generate both syntactically and semantical…
In this paper, we make an important step towards the black-box machine teaching by considering the cross-space machine teaching, where the teacher and the learner use different feature representations and the teacher can not fully observe the learner’s model. In such scenario, we study how the teach…
Convolution as inner product has been the founding basis of convolutional neural networks (CNNs) and the key to end-to-end visual representation learning. Benefiting from deeper architectures, recent CNNs have demonstrated increasingly strong representation abilities. Despite such improvement, the i…
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. L…
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 addition…
In this paper, we consider the problem of machine teaching, the inverse problem of machine learning. Different from traditional machine teaching which views the learners as batch algorithms, we study a new paradigm where the learner uses an iterative algorithm and a teacher can feed examples sequent…
The availability of large scale event data with time stamps has given rise to dynamically evolving knowledge graphs that contain temporal information for each edge. Reasoning over time in such dynamic knowledge graphs is not yet well understood. To this end, we present Know-Evolve, a novel deep evol…
The design of good heuristics or approximation algorithms for NP-hard combinatorial optimization problems often requires significant specialized knowledge and trial-and-error. Can we automate this challenging, tedious process, and learn the algorithms instead? In many real-world applications, it is…
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 sam…
User behaviors in social networks are microscopic with fine grained temporal information. Predicting a macroscopic quantity based on users’ collective behaviors is an important problem. However, existing works are mainly problem-specific models for the microscopic behaviors and typically design appr…
The stunning empirical successes of neural networks currently lack rigorous theoretical explanation. What form would such an explanation take, in the face of existing complexity-theoretic lower bounds? A first step might be to show that data generated by neural networks with a single hidden layer, s…
Point processes are powerful tools to model user activities and have a plethora of applications in social sciences. Predicting user activities based on point processes is a central problem. However, existing works are mostly problem specific, use heuristics, or simplify the stochastic nature of poin…
Segmentation and labeling of high dimensional time series data has wide applications in behavior understanding and medical diagnosis. Due to the difficulty in obtaining the label information for high dimensional data, realizing this objective in an unsupervised way is highly desirable. Hidden Semi-M…
This paper addresses deep face recognition (FR) problem under open-set protocol, where ideal face features are expected to have smaller maximal intra-class distance than minimal inter-class distance under a suitably chosen metric space. However, few existing algorithms can effectively achieve this c…
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 existi…
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.…
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 unrealis…
Matching users to the right items at the right time is a fundamental task in recommendation systems. As users interact with different items over time, users' and items' feature may evolve and co-evolve over time. Traditional models based on static latent features or discretizing time into epochs can…
Kernel classifiers and regressors designed for structured data, such as sequences, trees and graphs, have significantly advanced a number of interdisciplinary areas such as computational biology and drug design. Typically, kernels are designed beforehand for a data type which either exploit statisti…
Hawkes processes are powerful tools for modeling the mutual-excitation phenomena commonly observed in event data from a variety of domains, such as social networks, quantitative finance and healthcare records. The intensity function of a Hawkes process is typically assumed to be linear in the sum of…
We consider control problems for multi-stage campaigning over social networks. The dynamic programming framework is employed to balance the high present reward and large penalty on low future outcome in the presence of extensive uncertainties. In particular, we establish theoretical foundations of o…
Bayesian methods are appealing in their flexibility in modeling complex data and ability in capturing uncertainty in parameters. However, when Bayes’ rule does not result in tractable closed-form, most approximate inference algorithms lack either scalability or rigorous guarantees. To tackle this ch…
Recently, significant progress has been made developing kernel mean expressions for Bayesian inference. An important success in this domain is the nonparametric kernel Bayes’ filter (nKB-filter), which can be used for sequential inference in state space models. We expand upon this work by introducin…
Kernel methods have great promise for learning rich statistical representations of large modern datasets. However, compared to neural networks, kernel methods have been perceived as lacking in scalability and flexibility. We introduce a family of fast, flexible, general purpose, and lightly parametr…
When a piece of malicious information becomes rampant in an information diffusion network, can we identify the source node that originally introduced the piece into the network and infer the time when it initiated this? Being able to do so is critical for curtailing the spread of malicious informati…
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…
The fully connected layers of a deep convolutional neural network typically contain over 90% of the network parameters, and consume the majority of the memory required to store the network. Reducing the number of parameters while preserving predictive performance is critically important for deployin…
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…
Detecting the emergence of an abrupt change-point is a classic problem in statistics and machine learning. Kernel-based nonparametric statistics have been proposed for this task which make fewer assumptions on the distributions than traditional parametric approach. However, none of the existing kern…
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 t…
By making personalized suggestions, a recommender system is playing a crucial role in improving the engagement of users in modern web-services. However, most recommendation algorithms do not explicitly take into account the temporal behavior and the recurrent activities of users. Two central but les…