60 accepted papers
Recent advances in diffusion models show promise for Structure-Based Drug Design (SBDD), which aims to generate 3D ligand molecules that bind tightly to specific protein targets. This involves jointly optimizing the ligand's 3D conformation and its binding position within the protein pocket. However…
Rejoining fragment images of precious artifacts is a meaningful task because complete artifacts could provide valuable clues for the research of human civilization. However, existing rejoining methods face several challenges including time-consuming manual annotation, insufficient rejoining accuracy
Molecular docking is a key task in computational biology that has attracted increasing interest from the machine learning community. While existing methods have achieved success, they generally treat each protein-ligand pair in isolation. Inspired by the biochemical observation that ligands binding…
Peptides, short chains of amino acids, interact with target proteins, making them a unique class of protein-based therapeutics for treating human diseases. Recently, deep generative models have shown great promise in peptide generation. However, several challenges remain in designing effective pepti…
With the popularity of federated learning, federated domain generalization (FedDG) has attracted more and more attentions. Existing works of federated learning indicate that the generalization performance of the global model can be improved when the global model is obtained by aggregating local mode…
In the field of class-agnostic counting (CAC), counting only objects of interest that are similar to exemplars in multi-class scenarios has been a challenging task. To address this challenge, recent research has proposed the extract-and-match paradigm based on the vision transformer (ViT) architectu…
We introduce Statistical Flow Matching (SFM), a novel and mathematically rigorous flow-matching framework on the manifold of parameterized probability measures inspired by the results from information geometry. We demonstrate the effectiveness of our method on the discrete generation problem by inst…
Predicting the effects of protein mutations is crucial for analyzing protein functions and understanding genetic diseases. However, existing models struggle to effectively extract mutation-related local structure motifs from protein databases, which hinders their predictive accuracy and robustness.…
Despite the striking success of general protein folding models such as AlphaFold2 (AF2), the accurate computational modeling of antibody-antigen complexes remains a challenging task. In this paper, we first analyze AF2's primary loss function, known as the Frame Aligned Point Error (FAPE), and raise…
Peptides, short chains of amino acid residues, play a vital role in numerous biological processes by interacting with other target molecules, offering substantial potential in drug discovery. In this work, we present *PepFlow*, the first multi-modal deep generative model grounded in the flow-matchin…
Robotic object packing has broad practical applications in the logistics and automation industry, often formulated by researchers as the online 3D Bin Packing Problem (3D-BPP). However, existing DRL-based methods primarily focus on enhancing performance in limited packing environments while neglecti
Diffusion models have revolutionized text-to-image generation with its exceptional quality and creativity. However, its multi-step sampling process is known to be slow, often requiring tens of inference steps to obtain satisfactory results. Previous attempts to improve its sampling speed and reduce…
Discovering new drug molecules is a pivotal yet challenging process due to the near-infinitely large chemical space and notorious demands on time and resources. Numerous generative models have recently been introduced to accelerate the drug discovery process, but their progression to experimental va…
Rich data and powerful machine learning models allow us to design drugs for a specific protein target <em>in silico</em>. Recently, the inclusion of 3D structures during targeted drug design shows superior performance to other target-free models as the atomic interaction in the 3D space is explicitl…
Designing 3D ligands within a target binding site is a fundamental task in drug discovery. Existing structured-based drug design methods treat all ligand atoms equally, which ignores different roles of atoms in the ligand for drug design and can be less efficient for exploring the large drug-like mo…
We propose a general architecture that combines the coefficient learning scheme with a residual operator layer for learning mappings between continuous functions in the 3D Euclidean space. Our proposed model is guaranteed to achieve SE(3)-equivariance by design. From the graph spectrum view, our met…
Targeted protein degradation techniques, such as PROteolysis TArgeting Chimeras (PROTACs), have emerged as powerful tools for selectively removing disease-causing proteins. One challenging problem in this field is designing a linker to connect different molecular fragments to form a stable drug-cand…
Recently, Transformer-based methods have achieved surprising performance in the field of long-term series forecasting, but the attention mechanism for computing global correlations entails high complexity. And they do not allow for targeted modeling of local features as CNN structures do. To solve t…
Protein-protein interactions are crucial to many biological processes, and predicting the effect of amino acid mutations on binding is important for protein engineering. While data-driven approaches using deep learning have shown promise, the scarcity of annotated experimental data remains a major c…
Antibodies are immune system proteins that protect the host by binding to specific antigens such as viruses and bacteria. The binding between antibodies and antigens is mainly determined by the complementarity-determining regions (CDR) of the antibodies. In this work, we develop a deep generative mo…
Learning new task-specific skills from a few trials is a fundamental challenge for artificial intelligence. Meta reinforcement learning (meta-RL) tackles this problem by learning transferable policies that support few-shot adaptation to unseen tasks. Despite recent advances in meta-RL, most existing…
This paper studies an important problem in computational chemistry: predicting a molecule's spatial atom arrangements, or a molecular conformation. We propose a neural energy minimization formulation that casts the prediction problem into an unrolled optimization process, where a neural network is p…
Equivariance has been a long-standing concern in various fields ranging from computer vision to physical modeling. Most previous methods struggle with generality, simplicity, and expressiveness --- some are designed ad hoc for specific data types, some are too complex to be accessible, and some sacr…
Meta-reinforcement learning (meta-RL) algorithms allow for agents to learn new behaviors from small amounts of experience, mitigating the sample inefficiency problem in RL. However, while meta-RL agents can adapt quickly to new tasks at test time after experiencing only a few trajectories, the meta-…
Learning to perform tasks by leveraging a dataset of expert observations, also known as imitation learning from observations (ILO), is an important paradigm for learning skills without access to the expert reward function or the expert actions. We consider ILO in the setting where the expert and the…
Many practical applications of reinforcement learning require agents to learn from sparse and delayed rewards. It challenges the ability of agents to attribute their actions to future outcomes. In this paper, we consider the problem formulation of episodic reinforcement learning with trajectory feed…
We study deep reinforcement learning (RL) algorithms with delayed rewards. In many real-world tasks, instant rewards are often not readily accessible or even defined immediately after the agent performs actions. In this work, we first formally define the environment with delayed rewards and discuss…
Deep generative models have achieved tremendous success in designing novel drug molecules in recent years. A new thread of works have shown potential in advancing the specificity and success rate of in silico drug design by considering the structure of protein pockets. This setting posts fundamental…
Designing protein sequences with a particular biological function is a long-lasting challenge for protein engineering. Recent advances in machine-learning-guided approaches focus on building a surrogate sequence-function model to reduce the burden of expensive in-lab experiments. In this paper, we s…
We study a fundamental problem in structure-based drug design --- generating molecules that bind to specific protein binding sites. While we have witnessed the great success of deep generative models in drug design, the existing methods are mostly string-based or graph-based. They are limited by the…
This paper presents a detection-aware pre-training (DAP) approach, which leverages only weakly-labeled classification-style datasets (e.g., ImageNet) for pre-training, but is specifically tailored to benefit object detection tasks. In contrast to the widely used image classification-based pre-traini…
We study how to generate molecule conformations (i.e., 3D structures) from a molecular graph. Traditional methods, such as molecular dynamics, sample conformations via computationally expensive simulations. Recently, machine learning methods have shown great potential by training on a large collecti…
Protein sequence alignment is a fundamental problem in computational structure biology and popular for protein 3D structural prediction and protein homology detection. Most of the developed programs for detecting protein sequence alignments are based upon the likelihood information of amino acids an…
We present a novel semi-supervised semantic segmentation method which jointly achieves two desiderata of segmentation model regularities: the label-space consistency property between image augmentations and the feature-space contrastive property among different pixels. We leverage the pixel-level L2…
Deep generative modeling has achieved many successes for continuous data generation, such as producing realistic images and controlling their properties (e.g., styles). However, the development of generative modeling techniques for optimizing discrete data, such as sequences or strings, still lags b…
In this paper, we study the Bayesian thresholding bandit problem (BTBP), where the goal is to adaptively make a budget of $Q$ queries to $n$ stochastic arms and determine the label for each arm (whether its mean reward is closer to $0$ or $1$). We present a polynomial-time approximation scheme for t…
In this paper, we propose an effective knowledge transfer framework to boost the weakly supervised object detection accuracy with the help of an external fully-annotated source dataset, whose categories may not overlap with the target domain. This setting is of great practical value due to the exist…
In many vision-based reinforcement learning (RL) problems, the agent controls a movable object in its visual field, e.g., the player's avatar in video games and the robotic arm in visual grasping and manipulation. Leveraging action-conditioned video prediction, we propose an end-to-end learning fram…
Quality-Diversity (QD) is a concept from Neuroevolution with some intriguing applications to Reinforcement Learning. It facilitates learning a population of agents where each member is optimized to simultaneously accumulate high task-returns and exhibit behavioral diversity compared to other members
Long-term temporal credit assignment is an important challenge in deep reinforcement learning (RL). It refers to the ability of the agent to attribute actions to consequences that may occur after a long time interval. Existing policy-gradient and Q-learning algorithms typically rely on dense environ…
Deep reinforcement learning (RL) algorithms have achieved great success on a wide variety of sequential decision-making tasks. However, many of these algorithms suffer from high sample complexity when learning from scratch using environmental rewards, due to issues such as credit-assignment and high…
Off-policy evaluation provides an essential tool for evaluating the effects of different policies or treatments using only observed data. When applied to high-stakes scenarios such as medical diagnosis or financial decision-making, it is essential to provide provably correct upper and lower bounds o…
Imitation Learning (IL) is a popular paradigm for training agents to achieve complicated goals by leveraging expert behavior, rather than dealing with the hardships of designing a correct reward function. With the environment modeled as a Markov Decision Process (MDP), most of the existing IL algori…
Gradient-based approximate inference methods, such as Stein variational gradient descent (SVGD) \cite{liu2016stein}, provide simple and general-purpose inference engines for differentiable continuous distributions. However, existing forms of SVGD can not be directly applied to discrete distributions…
This paper provides a simple procedure to fit generative networks to target distributions, with the goal of a small Wasserstein distance (or other optimal transport costs). The approach is based on two principles: (a) if the source randomness of the network is a continuous distribution (the "semi-di…
Langevin diffusion is a powerful method for nonconvex optimization, which enables the escape from local minima by injecting noise into the gradient. In particular, the temperature parameter controlling the noise level gives rise to a tradeoff between ``global exploration'' and ``local exploitation''…
Goal-oriented reinforcement learning has recently been a practical framework for robotic manipulation tasks, in which an agent is required to reach a certain goal defined by a function on the state space. However, the sparsity of such reward definition makes traditional reinforcement learning algori…
A zoo of deep nets is available these days for almost any given task, and it is increasingly unclear which net to start with when addressing a new task, or which net to use as an initialization for fine-tuning a new model. To address this issue, in this paper, we develop knowledge flow which moves ‘…
Representing data in hyperbolic space can effectively capture latent hierarchical relationships. To enable accurate classification of points in hyperbolic space while respecting their hyperbolic geometry, we introduce hyperbolic SVM, a hyperbolic formulation of support vector machine classifiers, an…
We consider the problem of imitation learning from expert demonstrations in partially observable Markov decision processes (POMDPs). Belief representations, which characterize the distribution over the latent states in a POMDP, have been modeled using recurrent neural networks and probabilistic late…
The success of popular algorithms for deep reinforcement learning, such as policy-gradients and Q-learning, relies heavily on the availability of an informative reward signal at each timestep of the sequential decision-making process. When rewards are only sparsely available during an episode, or a…
When learning from a batch of logged bandit feedback, the discrepancy between the policy to be learned and the off-policy training data imposes statistical and computational challenges. Unlike classical supervised learning and online learning settings, in batch contextual bandit learning, one only h…
Batch Bayesian optimization has been shown to be an efficient and successful approach for black-box function optimization, especially when the evaluation of cost function is highly expensive but can be efficiently parallelized. In this paper, we introduce a novel variational framework for batch quer…
We consider the thresholding bandit problem, whose goal is to find arms of mean rewards above a given threshold $\theta$, with a fixed budget of $T$ trials. We introduce LSA, a new, simple and anytime algorithm that aims to minimize the aggregate regret (or the expected number of mis-classified arm…
Policy gradient methods have achieved remarkable successes in solving challenging reinforcement learning problems. However, it still often suffers from the large variance issue on policy gradient estimation, which leads to poor sample efficiency during training. In this work, we propose a control va…
Recent advances in recurrent neural nets (RNNs) have shown much promise in many applications in natural language processing. For most of these tasks, such as sentiment analysis of customer reviews, a recurrent neural net model parses the entire review before forming a decision. We argue that reading…
The performance of off-policy learning, including deep Q-learning and deep deterministic policy gradient (DDPG), critically depends on the choice of the exploration policy. Existing exploration methods are mostly based on adding noise to the on-going actor policy and can only explore
Genetic algorithms have been widely used in many practical optimization problems. Inspired by natural selection, operators, including mutation, crossover and selection, provide effective heuristics for search and black-box optimization. However, they have not been shown useful for deep reinforcement…
We propose a novel training algorithm for reinforcement learning which combines the strength of deep Q-learning with a constrained optimization approach to tighten optimality and encourage faster reward propagation. Our novel technique makes deep reinforcement learning more practical by drastically…
We study the interpretability of conditional probability estimates for binary classification under the agnostic setting or scenario. Under the agnostic setting, conditional probability estimates do not necessarily reflect the true conditional probabilities. Instead, they have a certain calibration p…