arXiv subjects

Doina Precup

Publications and source records attributed to Doina Precup.

At least 91 records · Page 5Linked to original sources

arXiv2024

MUDiff: Unified Diffusion for Complete Molecule Generation

Molecule generation is a very important practical problem, with uses in drug discovery and material design, and AI methods promise to provide useful solutions. However, existing methods for molecule generation focus either on 2D graph structure or on 3D geometric structure, which is not sufficient to represent a complete molecule as 2D graph captures mainly topology while 3D geometry captures mainly spatial atom arrangements. Combining these representations is essential to better represent a molecule. In this paper, we present a new model for generating a comprehensive representation of molecules, including atom features, 2D discrete molecule structures, and 3D continuous molecule coordinates, by combining discrete and continuous diffusion processes. The use of diffusion processes allows for capturing the probabilistic nature of molecular processes and exploring the effect of different factors on molecular structures. Additionally, we propose a novel graph transformer architecture to denoise the diffusion process. The transformer adheres to 3D roto-translation equivariance constraints, allowing it to learn invariant atom and edge representations while preserving the equivariance of atom coordinates. This transformer can be used to learn molecular representations robust to geometric transformations. We evaluate the performance of our model through experiments and comparisons with existing methods, showing its ability to generate more stable and valid molecules. Our model is a promising approach for designing stable and diverse molecules and can be applied to a wide range of tasks in molecular modeling.

cs.LG↗

arXiv2024

Effective Protein-Protein Interaction Exploration with PPIretrieval

Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the challenge has shifted towards effectively navigating the vast complex universe to identify potential PPIs. Herein, we propose PPIretrieval, the first deep learning-based model for protein-protein interaction exploration, which leverages existing PPI data to effectively search for potential PPIs in an embedding space, capturing rich geometric and chemical information of protein surfaces. When provided with an unseen query protein with its associated binding site, PPIretrieval effectively identifies a potential binding partner along with its corresponding binding site in an embedding space, facilitating the formation of protein-protein complexes.

q-bio.BM↗

arXiv2024

When Do Graph Neural Networks Help with Node Classification? Investigating the Impact of Homophily Principle on Node Distinguishability

Homophily principle, i.e., nodes with the same labels are more likely to be connected, has been believed to be the main reason for the performance superiority of Graph Neural Networks (GNNs) over Neural Networks on node classification tasks. Recent research suggests that, even in the absence of homophily, the advantage of GNNs still exists as long as nodes from the same class share similar neighborhood patterns. However, this argument only considers intra-class Node Distinguishability (ND) but neglects inter-class ND, which provides incomplete understanding of homophily on GNNs. In this paper, we first demonstrate such deficiency with examples and argue that an ideal situation for ND is to have smaller intra-class ND than inter-class ND. To formulate this idea and study ND deeply, we propose Contextual Stochastic Block Model for Homophily (CSBM-H) and define two metrics, Probabilistic Bayes Error (PBE) and negative generalized Jeffreys divergence, to quantify ND. With the metrics, we visualize and analyze how graph filters, node degree distributions and class variances influence ND, and investigate the combined effect of intra- and inter-class ND. Besides, we discovered the mid-homophily pitfall, which occurs widely in graph datasets. Furthermore, we verified that, in real-work tasks, the superiority of GNNs is indeed closely related to both intra- and inter-class ND regardless of homophily levels. Grounded in this observation, we propose a new hypothesis-testing based performance metric beyond homophily, which is non-linear, feature-based and can provide statistical threshold value for GNNs' the superiority. Experiments indicate that it is significantly more effective than the existing homophily metrics on revealing the advantage and disadvantage of graph-aware modes on both synthetic and benchmark real-world datasets.

cs.SI↗

arXiv2023

Prediction and Control in Continual Reinforcement Learning

Temporal difference (TD) learning is often used to update the estimate of the value function which is used by RL agents to extract useful policies. In this paper, we focus on value function estimation in continual reinforcement learning. We propose to decompose the value function into two components which update at different timescales: a permanent value function, which holds general knowledge that persists over time, and a transient value function, which allows quick adaptation to new situations. We establish theoretical results showing that our approach is well suited for continual learning and draw connections to the complementary learning systems (CLS) theory from neuroscience. Empirically, this approach improves performance significantly on both prediction and control problems.

cs.LG↗

arXiv2023

A Definition of Continual Reinforcement Learning

In a standard view of the reinforcement learning problem, an agent's goal is to efficiently identify a policy that maximizes long-term reward. However, this perspective is based on a restricted view of learning as finding a solution, rather than treating learning as endless adaptation. In contrast, continual reinforcement learning refers to the setting in which the best agents never stop learning. Despite the importance of continual reinforcement learning, the community lacks a simple definition of the problem that highlights its commitments and makes its primary concepts precise and clear. To this end, this paper is dedicated to carefully defining the continual reinforcement learning problem. We formalize the notion of agents that "never stop learning" through a new mathematical language for analyzing and cataloging agents. Using this new language, we define a continual learning agent as one that can be understood as carrying out an implicit search process indefinitely, and continual reinforcement learning as the setting in which the best agents are all continual learning agents. We provide two motivating examples, illustrating that traditional views of multi-task reinforcement learning and continual supervised learning are special cases of our definition. Collectively, these definitions and perspectives formalize many intuitive concepts at the heart of learning, and open new research pathways surrounding continual learning agents.

cs.LG↗

arXiv2023

Learning domain-invariant classifiers for infant cry sounds

The issue of domain shift remains a problematic phenomenon in most real-world datasets and clinical audio is no exception. In this work, we study the nature of domain shift in a clinical database of infant cry sounds acquired across different geographies. We find that though the pitches of infant cries are similarly distributed regardless of the place of birth, other characteristics introduce peculiar biases into the data. We explore methodologies for mitigating the impact of domain shift in a model for identifying neurological injury from cry sounds. We adapt unsupervised domain adaptation methods from computer vision which learn an audio representation that is domain-invariant to hospitals and is task discriminative. We also propose a new approach, target noise injection (TNI), for unsupervised domain adaptation which requires neither labels nor training data from the target domain. Our best-performing model significantly improves target accuracy by 7.2%, without negatively affecting the source domain.

eess.AS↗

arXiv2023

A Deep Reinforcement Learning Approach to Marginalized Importance Sampling with the Successor Representation

Marginalized importance sampling (MIS), which measures the density ratio between the state-action occupancy of a target policy and that of a sampling distribution, is a promising approach for off-policy evaluation. However, current state-of-the-art MIS methods rely on complex optimization tricks and succeed mostly on simple toy problems. We bridge the gap between MIS and deep reinforcement learning by observing that the density ratio can be computed from the successor representation of the target policy. The successor representation can be trained through deep reinforcement learning methodology and decouples the reward optimization from the dynamics of the environment, making the resulting algorithm stable and applicable to high-dimensional domains. We evaluate the empirical performance of our approach on a variety of challenging Atari and MuJoCo environments.

cs.LG↗

arXiv2023

DGFN: Double Generative Flow Networks

Deep learning is emerging as an effective tool in drug discovery, with potential applications in both predictive and generative models. Generative Flow Networks (GFlowNets/GFNs) are a recently introduced method recognized for the ability to generate diverse candidates, in particular in small molecule generation tasks. In this work, we introduce double GFlowNets (DGFNs). Drawing inspiration from reinforcement learning and Double Deep Q-Learning, we introduce a target network used to sample trajectories, while updating the main network with these sampled trajectories. Empirical results confirm that DGFNs effectively enhance exploration in sparse reward domains and high-dimensional state spaces, both challenging aspects of de-novo design in drug discovery.

cs.LG↗

arXiv2023

For SALE: State-Action Representation Learning for Deep Reinforcement Learning

In the field of reinforcement learning (RL), representation learning is a proven tool for complex image-based tasks, but is often overlooked for environments with low-level states, such as physical control problems. This paper introduces SALE, a novel approach for learning embeddings that model the nuanced interaction between state and action, enabling effective representation learning from low-level states. We extensively study the design space of these embeddings and highlight important design considerations. We integrate SALE and an adaptation of checkpoints for RL into TD3 to form the TD7 algorithm, which significantly outperforms existing continuous control algorithms. On OpenAI gym benchmark tasks, TD7 has an average performance gain of 276.7% and 50.7% over TD3 at 300k and 5M time steps, respectively, and works in both the online and offline settings.

cs.LG↗

arXiv2023

Training Matters: Unlocking Potentials of Deeper Graph Convolutional Neural Networks

The performance limit of Graph Convolutional Networks (GCNs) and the fact that we cannot stack more of them to increase the performance, which we usually do for other deep learning paradigms, are pervasively thought to be caused by the limitations of the GCN layers, including insufficient expressive power, etc. However, if so, for a fixed architecture, it would be unlikely to lower the training difficulty and to improve performance by changing only the training procedure, which we show in this paper not only possible but possible in several ways. This paper first identify the training difficulty of GCNs from the perspective of graph signal energy loss. More specifically, we find that the loss of energy in the backward pass during training nullifies the learning of the layers closer to the input. Then, we propose several methodologies to mitigate the training problem by slightly modifying the GCN operator, from the energy perspective. After empirical validation, we confirm that these changes of operator lead to significant decrease in the training difficulties and notable performance boost, without changing the composition of parameters. With these, we conclude that the root cause of the problem is more likely the training difficulty than the others.

cs.LG↗

arXiv2023

When Do We Need Graph Neural Networks for Node Classification?

Graph Neural Networks (GNNs) extend basic Neural Networks (NNs) by additionally making use of graph structure based on the relational inductive bias (edge bias), rather than treating the nodes as collections of independent and identically distributed (i.i.d.) samples. Though GNNs are believed to outperform basic NNs in real-world tasks, it is found that in some cases, GNNs have little performance gain or even underperform graph-agnostic NNs. To identify these cases, based on graph signal processing and statistical hypothesis testing, we propose two measures which analyze the cases in which the edge bias in features and labels does not provide advantages. Based on the measures, a threshold value can be given to predict the potential performance advantages of graph-aware models over graph-agnostic models.

cs.LG↗

arXiv2023

A cry for help: Early detection of brain injury in newborns

Since the 1960s, neonatal clinicians have known that newborns suffering from certain neurological conditions exhibit altered crying patterns such as the high-pitched cry in birth asphyxia. Despite an annual burden of over 1.5 million infant deaths and disabilities, early detection of neonatal brain injuries due to asphyxia remains a challenge, particularly in developing countries where the majority of births are not attended by a trained physician. Here we report on the first inter-continental clinical study to demonstrate that neonatal brain injury can be reliably determined from recorded infant cries using an AI algorithm we call Roseline. Previous and recent work has been limited by the lack of a large, high-quality clinical database of cry recordings, constraining the application of state-of-the-art machine learning. We develop a new training methodology for audio-based pathology detection models and evaluate this system on a large database of newborn cry sounds acquired from geographically diverse settings -- 5 hospitals across 3 continents. Our system extracts interpretable acoustic biomarkers that support clinical decisions and is able to accurately detect neurological injury from newborns' cries with an AUC of 92.5% (88.7% sensitivity at 80% specificity). Cry-based neurological monitoring opens the door for low-cost, easy-to-use, non-invasive and contact-free screening of at-risk babies, especially when integrated into simple devices like smartphones or neonatal ICU monitors. This would provide a reliable tool where there are no alternatives, but also curtail the need to regularly exert newborns to physically-exhausting or radiation-exposing assessments such as brain CT scans. This work sets the stage for embracing the infant cry as a vital sign and indicates the potential of AI-driven sound monitoring for the future of affordable healthcare.

eess.AS↗

arXiv2023

Forecaster: Towards Temporally Abstract Tree-Search Planning from Pixels

The ability to plan at many different levels of abstraction enables agents to envision the long-term repercussions of their decisions and thus enables sample-efficient learning. This becomes particularly beneficial in complex environments from high-dimensional state space such as pixels, where the goal is distant and the reward sparse. We introduce Forecaster, a deep hierarchical reinforcement learning approach which plans over high-level goals leveraging a temporally abstract world model. Forecaster learns an abstract model of its environment by modelling the transitions dynamics at an abstract level and training a world model on such transition. It then uses this world model to choose optimal high-level goals through a tree-search planning procedure. It additionally trains a low-level policy that learns to reach those goals. Our method not only captures building world models with longer horizons, but also, planning with such models in downstream tasks. We empirically demonstrate Forecaster's potential in both single-task learning and generalization to new tasks in the AntMaze domain.

cs.AI↗

arXiv2023

Acceleration in Policy Optimization

We work towards a unifying paradigm for accelerating policy optimization methods in reinforcement learning (RL) by integrating foresight in the policy improvement step via optimistic and adaptive updates. Leveraging the connection between policy iteration and policy gradient methods, we view policy optimization algorithms as iteratively solving a sequence of surrogate objectives, local lower bounds on the original objective. We define optimism as predictive modelling of the future behavior of a policy, and adaptivity as taking immediate and anticipatory corrective actions to mitigate accumulating errors from overshooting predictions or delayed responses to change. We use this shared lens to jointly express other well-known algorithms, including model-based policy improvement based on forward search, and optimistic meta-learning algorithms. We analyze properties of this formulation, and show connections to other accelerated optimization algorithms. Then, we design an optimistic policy gradient algorithm, adaptive via meta-gradient learning, and empirically highlight several design choices pertaining to acceleration, in an illustrative task.

cs.LG↗

arXiv2023

Policy composition in reinforcement learning via multi-objective policy optimization

We enable reinforcement learning agents to learn successful behavior policies by utilizing relevant pre-existing teacher policies. The teacher policies are introduced as objectives, in addition to the task objective, in a multi-objective policy optimization setting. Using the Multi-Objective Maximum a Posteriori Policy Optimization algorithm (Abdolmaleki et al. 2020), we show that teacher policies can help speed up learning, particularly in the absence of shaping rewards. In two domains with continuous observation and action spaces, our agents successfully compose teacher policies in sequence and in parallel, and are also able to further extend the policies of the teachers in order to solve the task. Depending on the specified combination of task and teacher(s), teacher(s) may naturally act to limit the final performance of an agent. The extent to which agents are required to adhere to teacher policies are determined by hyperparameters which determine both the effect of teachers on learning speed and the eventual performance of the agent on the task. In the humanoid domain (Tassa et al. 2018), we also equip agents with the ability to control the selection of teachers. With this ability, agents are able to meaningfully compose from the teacher policies to achieve a superior task reward on the walk task than in cases without access to the teacher policies. We show the resemblance of composed task policies with the corresponding teacher policies through videos.

cs.LG↗

arXiv2023

On the Convergence of Bounded Agents

When has an agent converged? Standard models of the reinforcement learning problem give rise to a straightforward definition of convergence: An agent converges when its behavior or performance in each environment state stops changing. However, as we shift the focus of our learning problem from the environment's state to the agent's state, the concept of an agent's convergence becomes significantly less clear. In this paper, we propose two complementary accounts of agent convergence in a framing of the reinforcement learning problem that centers around bounded agents. The first view says that a bounded agent has converged when the minimal number of states needed to describe the agent's future behavior cannot decrease. The second view says that a bounded agent has converged just when the agent's performance only changes if the agent's internal state changes. We establish basic properties of these two definitions, show that they accommodate typical views of convergence in standard settings, and prove several facts about their nature and relationship. We take these perspectives, definitions, and analysis to bring clarity to a central idea of the field.

cs.LG↗

arXiv2023

An Empirical Study of the Effectiveness of Using a Replay Buffer on Mode Discovery in GFlowNets

Reinforcement Learning (RL) algorithms aim to learn an optimal policy by iteratively sampling actions to learn how to maximize the total expected return, $R(x)$. GFlowNets are a special class of algorithms designed to generate diverse candidates, $x$, from a discrete set, by learning a policy that approximates the proportional sampling of $R(x)$. GFlowNets exhibit improved mode discovery compared to conventional RL algorithms, which is very useful for applications such as drug discovery and combinatorial search. However, since GFlowNets are a relatively recent class of algorithms, many techniques which are useful in RL have not yet been associated with them. In this paper, we study the utilization of a replay buffer for GFlowNets. We explore empirically various replay buffer sampling techniques and assess the impact on the speed of mode discovery and the quality of the modes discovered. Our experimental results in the Hypergrid toy domain and a molecule synthesis environment demonstrate significant improvements in mode discovery when training with a replay buffer, compared to training only with trajectories generated on-policy.

cs.LG↗

arXiv2023

Minimal Value-Equivalent Partial Models for Scalable and Robust Planning in Lifelong Reinforcement Learning

Learning models of the environment from pure interaction is often considered an essential component of building lifelong reinforcement learning agents. However, the common practice in model-based reinforcement learning is to learn models that model every aspect of the agent's environment, regardless of whether they are important in coming up with optimal decisions or not. In this paper, we argue that such models are not particularly well-suited for performing scalable and robust planning in lifelong reinforcement learning scenarios and we propose new kinds of models that only model the relevant aspects of the environment, which we call "minimal value-equivalent partial models". After providing a formal definition for these models, we provide theoretical results demonstrating the scalability advantages of performing planning with such models and then perform experiments to empirically illustrate our theoretical results. Then, we provide some useful heuristics on how to learn these kinds of models with deep learning architectures and empirically demonstrate that models learned in such a way can allow for performing planning that is robust to distribution shifts and compounding model errors. Overall, both our theoretical and empirical results suggest that minimal value-equivalent partial models can provide significant benefits to performing scalable and robust planning in lifelong reinforcement learning scenarios.

cs.LG↗