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Researcher profile

Shengchao Liu

Shengchao Liu contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine LearningArtificial IntelligenceBiomoleculesComputation and LanguageComputational Engineering, Finance, and ScienceComputer Visioncond-mat.mtrl-scicond-mat.stat-mecheess.IVQuantitative MethodsSocial and Information Networks

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Published work

9 published item(s)

preprint2026arXiv

On Distinguishing Capability Elicitation from Capability Creation in Post-Training: A Free-Energy Perspective

Debates about large language model post-training often treat supervised fine-tuning (SFT) as imitation and reinforcement learning (RL) as discovery. But this distinction is too coarse. What matters is whether a training procedure increases the probability of behaviors the pretrained model could already produce, or whether it changes what the model can practically reach. We argue that post-training research should distinguish between capability elicitation and capability creation. We make this distinction operational by introducing the notion of accessible support: the set of behaviors that a model can practically produce under finite budgets. Post-training that reweights behaviors within this support is capability elicitation; whereas changing the support itself corresponds to capability creation. We develop this argument through a free-energy view of post-training. SFT and RL can both be seen as reweighting a pretrained reference distribution, only with different external signals. Demonstration signals define low-energy behavior for SFT, and reward signals define low-energy behavior for RL. When the update remains close to the base model, the main effect is local reweighting, not capability creation. Within this framework, the central question is no longer whether post-training is framed as SFT or RL, but whether it reweights behaviors already within reach, or instead expands the model's reachable behavioral space through search, interaction, tool use, or the incorporation of new information.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Scalable Dielectric Tensor Predictions for Inorganic Materials using Equivariant Graph Neural Networks

Accurate prediction of dielectric tensors is essential for accelerating the discovery of next-generation inorganic dielectric materials. Existing machine learning approaches, such as equivariant graph neural networks, typically rely on specially-designed network architectures to enforce O(3) equivariance. However, to preserve equivariance, these specially-designed models restrict the update of equivariant features during message passing to linear transformations or gated equivariant nonlinearities. The inability to implicitly characterize more complex nonlinear structures may reduce the predictive accuracy of the model. In this study, we introduce a frame-averaging-based approach to achieve equivariant dielectric tensor prediction. We propose GoeCTP, an O(3)-equivariant framework that predicts dielectric tensors without imposing any structural restrictions on the backbone network. We benchmark its performance against several state-of-the-art models and further employ it for large-scale virtual screening of thermodynamically stable materials from the Materials Project database. GoeCTP successfully identifies various promising candidates, such as Zr(InBr$_3$)$_2$ (band gap $E_g = 2.41$ eV, dielectric constant $\overline{\varepsilon} = 194.72$) and SeI$_2$ (anisotropy ratio $α_r = 96.763$), demonstrating its accuracy and efficiency in accelerating the discovery of advanced inorganic dielectric materials.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Attentive Walk-Aggregating Graph Neural Networks

Graph neural networks (GNNs) have been shown to possess strong representation power, which can be exploited for downstream prediction tasks on graph-structured data, such as molecules and social networks. They typically learn representations by aggregating information from the $K$-hop neighborhood of individual vertices or from the enumerated walks in the graph. Prior studies have demonstrated the effectiveness of incorporating weighting schemes into GNNs; however, this has been primarily limited to $K$-hop neighborhood GNNs so far. In this paper, we aim to design an algorithm incorporating weighting schemes into walk-aggregating GNNs and analyze their effect. We propose a novel GNN model, called AWARE, that aggregates information about the walks in the graph using attention schemes. This leads to an end-to-end supervised learning method for graph-level prediction tasks in the standard setting where the input is the adjacency and vertex information of a graph, and the output is a predicted label for the graph. We then perform theoretical, empirical, and interpretability analyses of AWARE. Our theoretical analysis in a simplified setting identifies successful conditions for provable guarantees, demonstrating how the graph information is encoded in the representation, and how the weighting schemes in AWARE affect the representation and learning performance. Our experiments demonstrate the strong performance of AWARE in graph-level prediction tasks in the standard setting in the domains of molecular property prediction and social networks. Lastly, our interpretation study illustrates that AWARE can successfully capture the important substructures of the input graph. The code is available on $\href{https://github.com/mehmetfdemirel/aware}{GitHub}$.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design

Molecule design is a fundamental problem in molecular science and has critical applications in a variety of areas, such as drug discovery, material science, etc. However, due to the large searching space, it is impossible for human experts to enumerate and test all molecules in wet-lab experiments. Recently, with the rapid development of machine learning methods, especially generative methods, molecule design has achieved great progress by leveraging machine learning models to generate candidate molecules. In this paper, we systematically review the most relevant work in machine learning models for molecule design. We start with a brief review of the mainstream molecule featurization and representation methods (including 1D string, 2D graph, and 3D geometry) and general generative methods (deep generative and combinatorial optimization methods). Then we summarize all the existing molecule design problems into several venues according to the problem setup, including input, output types and goals. Finally, we conclude with the open challenges and point out future opportunities of machine learning models for molecule design in real-world applications.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Pre-training Molecular Graph Representation with 3D Geometry

Molecular graph representation learning is a fundamental problem in modern drug and material discovery. Molecular graphs are typically modeled by their 2D topological structures, but it has been recently discovered that 3D geometric information plays a more vital role in predicting molecular functionalities. However, the lack of 3D information in real-world scenarios has significantly impeded the learning of geometric graph representation. To cope with this challenge, we propose the Graph Multi-View Pre-training (GraphMVP) framework where self-supervised learning (SSL) is performed by leveraging the correspondence and consistency between 2D topological structures and 3D geometric views. GraphMVP effectively learns a 2D molecular graph encoder that is enhanced by richer and more discriminative 3D geometry. We further provide theoretical insights to justify the effectiveness of GraphMVP. Finally, comprehensive experiments show that GraphMVP can consistently outperform existing graph SSL methods.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery

Machine learning has huge potential to revolutionize the field of drug discovery and is attracting increasing attention in recent years. However, lacking domain knowledge (e.g., which tasks to work on), standard benchmarks and data preprocessing pipelines are the main obstacles for machine learning researchers to work in this domain. To facilitate the progress of machine learning for drug discovery, we develop TorchDrug, a powerful and flexible machine learning platform for drug discovery built on top of PyTorch. TorchDrug benchmarks a variety of important tasks in drug discovery, including molecular property prediction, pretrained molecular representations, de novo molecular design and optimization, retrosynthsis prediction, and biomedical knowledge graph reasoning. State-of-the-art techniques based on geometric deep learning (or graph machine learning), deep generative models, reinforcement learning and knowledge graph reasoning are implemented for these tasks. TorchDrug features a hierarchical interface that facilitates customization from both novices and experts in this domain. Tutorials, benchmark results and documentation are available at https://torchdrug.ai. Code is released under Apache License 2.0.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Bad Global Minima Exist and SGD Can Reach Them

Several works have aimed to explain why overparameterized neural networks generalize well when trained by Stochastic Gradient Descent (SGD). The consensus explanation that has emerged credits the randomized nature of SGD for the bias of the training process towards low-complexity models and, thus, for implicit regularization. We take a careful look at this explanation in the context of image classification with common deep neural network architectures. We find that if we do not regularize \emph{explicitly}, then SGD can be easily made to converge to poorly-generalizing, high-complexity models: all it takes is to first train on a random labeling on the data, before switching to properly training with the correct labels. In contrast, we find that in the presence of explicit regularization, pretraining with random labels has no detrimental effect on SGD. We believe that our results give evidence that explicit regularization plays a far more important role in the success of overparameterized neural networks than what has been understood until now. Specifically, by penalizing complicated models independently of their fit to the data, regularization affects training dynamics also far away from optima, making simple models that fit the data well discoverable by local methods, such as SGD.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Neural Sentence Ordering Based on Constraint Graphs

Sentence ordering aims at arranging a list of sentences in the correct order. Based on the observation that sentence order at different distances may rely on different types of information, we devise a new approach based on multi-granular orders between sentences. These orders form multiple constraint graphs, which are then encoded by Graph Isomorphism Networks and fused into sentence representations. Finally, sentence order is determined using the order-enhanced sentence representations. Our experiments on five benchmark datasets show that our method outperforms all the existing baselines significantly, achieving a new state-of-the-art performance. The results demonstrate the advantage of considering multiple types of order information and using graph neural networks to integrate sentence content and order information for the task. Our code is available at https://github.com/DaoD/ConstraintGraph4NSO.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Learning To Navigate The Synthetically Accessible Chemical Space Using Reinforcement Learning

Over the last decade, there has been significant progress in the field of machine learning for de novo drug design, particularly in deep generative models. However, current generative approaches exhibit a significant challenge as they do not ensure that the proposed molecular structures can be feasibly synthesized nor do they provide the synthesis routes of the proposed small molecules, thereby seriously limiting their practical applicability. In this work, we propose a novel forward synthesis framework powered by reinforcement learning (RL) for de novo drug design, Policy Gradient for Forward Synthesis (PGFS), that addresses this challenge by embedding the concept of synthetic accessibility directly into the de novo drug design system. In this setup, the agent learns to navigate through the immense synthetically accessible chemical space by subjecting commercially available small molecule building blocks to valid chemical reactions at every time step of the iterative virtual multi-step synthesis process. The proposed environment for drug discovery provides a highly challenging test-bed for RL algorithms owing to the large state space and high-dimensional continuous action space with hierarchical actions. PGFS achieves state-of-the-art performance in generating structures with high QED and penalized clogP. Moreover, we validate PGFS in an in-silico proof-of-concept associated with three HIV targets. Finally, we describe how the end-to-end training conceptualized in this study represents an important paradigm in radically expanding the synthesizable chemical space and automating the drug discovery process.

0 citations0 reviewsNo code linkedOpen access