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Researcher profile

Daniel Kudenko

Daniel Kudenko contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine LearningArtificial IntelligenceMultiagent Systems

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Published work

5 published item(s)

preprint2026arXiv

Fine-tuning Pocket-Aware Diffusion Models via Denoising Policy Optimization

Structure-based drug design has been accelerated by pocket-aware 3D generative models, yet most methods primarily fit the training distribution and may fall short of satisfying multiple properties required in real-world therapeutic drug discovery. Recently, increasing attention has focused on structure-based molecule optimization (SBMO), which targets fine-grained control over multiple specified molecular properties. In this paper, we present DEPPA, a novel SBMO approach building upon Denoising Diffusion Policy Optimization for fine-tuning a pre-trained pocket-aware diffusion model via reinforcement learning. DEPPA enables optimization over multiple properties, including binding affinity, drug-likeness, synthesizability and diversity. We formulate the reverse denoising process of the pretrained pocket-aware diffusion model as a multi-step Markov Decision Process, where the desired properties that serve as reward signals are evaluated on the final generated ligand molecules. DEPPA incorporates a coarse denoising scheduler during the RL fine-tuning to achieve efficient and effective molecule optimization. Experimental results on the CrossDocked2020 benchmark demonstrate that DEPPA outperforms baselines in binding affinity (Vina Score -8.5 kcal/mol), drug-likeness and diversity while exhibiting competitive performance in synthesizability. The source code is available at https://github.com/xy9485/DePPA .

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Data Valuation for Offline Reinforcement Learning

The success of deep reinforcement learning (DRL) hinges on the availability of training data, which is typically obtained via a large number of environment interactions. In many real-world scenarios, costs and risks are associated with gathering these data. The field of offline reinforcement learning addresses these issues through outsourcing the collection of data to a domain expert or a carefully monitored program and subsequently searching for a batch-constrained optimal policy. With the emergence of data markets, an alternative to constructing a dataset in-house is to purchase external data. However, while state-of-the-art offline reinforcement learning approaches have shown a lot of promise, they currently rely on carefully constructed datasets that are well aligned with the intended target domains. This raises questions regarding the transferability and robustness of an offline reinforcement learning agent trained on externally acquired data. In this paper, we empirically evaluate the ability of the current state-of-the-art offline reinforcement learning approaches to coping with the source-target domain mismatch within two MuJoCo environments, finding that current state-of-the-art offline reinforcement learning algorithms underperform in the target domain. To address this, we propose data valuation for offline reinforcement learning (DVORL), which allows us to identify relevant and high-quality transitions, improving the performance and transferability of policies learned by offline reinforcement learning algorithms. The results show that our method outperforms offline reinforcement learning baselines on two MuJoCo environments.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Graph-based State Representation for Deep Reinforcement Learning

Deep RL approaches build much of their success on the ability of the deep neural network to generate useful internal representations. Nevertheless, they suffer from a high sample-complexity and starting with a good input representation can have a significant impact on the performance. In this paper, we exploit the fact that the underlying Markov decision process (MDP) represents a graph, which enables us to incorporate the topological information for effective state representation learning. Motivated by the recent success of node representations for several graph analytical tasks we specifically investigate the capability of node representation learning methods to effectively encode the topology of the underlying MDP in Deep RL. To this end we perform a comparative analysis of several models chosen from 4 different classes of representation learning algorithms for policy learning in grid-world navigation tasks, which are representative of a large class of RL problems. We find that all embedding methods outperform the commonly used matrix representation of grid-world environments in all of the studied cases. Moreoever, graph convolution based methods are outperformed by simpler random walk based methods and graph linear autoencoders.

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preprint2020arXiv

Uniform State Abstraction For Reinforcement Learning

Potential Based Reward Shaping combined with a potential function based on appropriately defined abstract knowledge has been shown to significantly improve learning speed in Reinforcement Learning. MultiGrid Reinforcement Learning (MRL) has further shown that such abstract knowledge in the form of a potential function can be learned almost solely from agent interaction with the environment. However, we show that MRL faces the problem of not extending well to work with Deep Learning. In this paper we extend and improve MRL to take advantage of modern Deep Learning algorithms such as Deep Q-Networks (DQN). We show that DQN augmented with our approach perform significantly better on continuous control tasks than its Vanilla counterpart and DQN augmented with MRL.

0 citations0 reviewsNo code linkedOpen access
preprint2019arXiv

Resource Abstraction for Reinforcement Learning in Multiagent Congestion Problems

Real-world congestion problems (e.g. traffic congestion) are typically very complex and large-scale. Multiagent reinforcement learning (MARL) is a promising candidate for dealing with this emerging complexity by providing an autonomous and distributed solution to these problems. However, there are three limiting factors that affect the deployability of MARL approaches to congestion problems. These are learning time, scalability and decentralised coordination i.e. no communication between the learning agents. In this paper we introduce Resource Abstraction, an approach that addresses these challenges by allocating the available resources into abstract groups. This abstraction creates new reward functions that provide a more informative signal to the learning agents and aid the coordination amongst them. Experimental work is conducted on two benchmark domains from the literature, an abstract congestion problem and a realistic traffic congestion problem. The current state-of-the-art for solving multiagent congestion problems is a form of reward shaping called difference rewards. We show that the system using Resource Abstraction significantly improves the learning speed and scalability, and achieves the highest possible or near-highest joint performance/social welfare for both congestion problems in large-scale scenarios involving up to 1000 reinforcement learning agents.

0 citations0 reviewsNo code linkedOpen access