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Shufang Xie

Shufang Xie contributes to research discovery and scholarly infrastructure.

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Artificial Intelligence Machine Learning Computation and Language Biomolecules

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preprint2026arXiv

FORGE: Fragment-Oriented Ranking and Generation for Context-Aware Molecular Optimization

Molecular optimization seeks to improve a molecule through small structural edits while preserving similarity to the starting compound. Recent language-model approaches typically treat this task as prompt-conditioned sequence generation. However, relying on natural language introduces an inherent data-scaling bottleneck, often leads to chemical hallucinations, and ignores the strong context dependence of fragment effects. We present FORGE, a two-stage framework that reformulates molecular optimization as context-aware local editing. By utilizing automatically mined, verified low-to-high edit pairs instead of expensive human text annotations, Stage 1 ranks candidate fragments by their property contribution under the full molecular context to inject chemical prior, and Stage 2 generates explicit fragment replacements. Built on a compact 0.6B language model, FORGE further adapts to unseen black-box objectives through in-context demonstrations. Across Prompt-MolOpt, PMO-1k and ChemCoTBench, FORGE consistently outperforms prior methods, including substantially larger language models and graph methods. These results highlight the value of explicit fragment-level supervision as a more easily obtainable, scalable, and hallucination-less alternative to natural language training.

preprint2026arXiv

SciCustom: A Framework for Custom Evaluation of Scientific Capabilities in Large Language Models

Large language models (LLMs) are increasingly applied to scientific research, yet existing evaluations often fail to reflect the fine-grained capabilities required in practice. Most benchmarks are manually curated or domain-generic, limiting scalability and alignment with real scientific use cases. In this paper, we propose a new framework named SciCustom to address the problem. It enables the custom construction of benchmarks from large-scale scientific data to evaluate application-specific scientific capabilities in LLMs. SciCustom first organizes scientific knowledge into ontology-grounded knowledge units with controlled granularity and trains a tagger to map large-scale data instances into this knowledge space. Given a custom requirement, relevant knowledge units are identified via voting-based multi-model consensus. These units enable relevance-aware benchmark retrieval via binary search, followed by proxy subset selection and data-grounded benchmark generation for efficient evaluation. Experiments in chemistry and healthcare demonstrate that SciCustom reveals fine-grained differences in LLM scientific capabilities that standard benchmarks overlook, while requiring neither expert annotation nor synthetic question generation. This work provides a scalable and application-aware foundation for benchmarking scientific capabilities in LLMs. The source code is available at https://github.com/yjwtheonly/SciCustom.

preprint2024arXiv

FABind: Fast and Accurate Protein-Ligand Binding

Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this challenge, with sampling-based and regression-based methods emerging as two prominent approaches. However, these methods have notable limitations. Sampling-based methods often suffer from low efficiency due to the need for generating multiple candidate structures for selection. On the other hand, regression-based methods offer fast predictions but may experience decreased accuracy. Additionally, the variation in protein sizes often requires external modules for selecting suitable binding pockets, further impacting efficiency. In this work, we propose $\mathbf{FABind}$, an end-to-end model that combines pocket prediction and docking to achieve accurate and fast protein-ligand binding. $\mathbf{FABind}$ incorporates a unique ligand-informed pocket prediction module, which is also leveraged for docking pose estimation. The model further enhances the docking process by incrementally integrating the predicted pocket to optimize protein-ligand binding, reducing discrepancies between training and inference. Through extensive experiments on benchmark datasets, our proposed $\mathbf{FABind}$ demonstrates strong advantages in terms of effectiveness and efficiency compared to existing methods. Our code is available at https://github.com/QizhiPei/FABind

preprint2022arXiv

Building Multilingual Machine Translation Systems That Serve Arbitrary X-Y Translations

Multilingual Neural Machine Translation (MNMT) enables one system to translate sentences from multiple source languages to multiple target languages, greatly reducing deployment costs compared with conventional bilingual systems. The MNMT training benefit, however, is often limited to many-to-one directions. The model suffers from poor performance in one-to-many and many-to-many with zero-shot setup. To address this issue, this paper discusses how to practically build MNMT systems that serve arbitrary X-Y translation directions while leveraging multilinguality with a two-stage training strategy of pretraining and finetuning. Experimenting with the WMT'21 multilingual translation task, we demonstrate that our systems outperform the conventional baselines of direct bilingual models and pivot translation models for most directions, averagely giving +6.0 and +4.1 BLEU, without the need for architecture change or extra data collection. Moreover, we also examine our proposed approach in an extremely large-scale data setting to accommodate practical deployment scenarios.

preprint2022arXiv

Direct Molecular Conformation Generation

Molecular conformation generation aims to generate three-dimensional coordinates of all the atoms in a molecule and is an important task in bioinformatics and pharmacology. Previous methods usually first predict the interatomic distances, the gradients of interatomic distances or the local structures (e.g., torsion angles) of a molecule, and then reconstruct its 3D conformation. How to directly generate the conformation without the above intermediate values is not fully explored. In this work, we propose a method that directly predicts the coordinates of atoms: (1) the loss function is invariant to roto-translation of coordinates and permutation of symmetric atoms; (2) the newly proposed model adaptively aggregates the bond and atom information and iteratively refines the coordinates of the generated conformation. Our method achieves the best results on GEOM-QM9 and GEOM-Drugs datasets. Further analysis shows that our generated conformations have closer properties (e.g., HOMO-LUMO gap) with the groundtruth conformations. In addition, our method improves molecular docking by providing better initial conformations. All the results demonstrate the effectiveness of our method and the great potential of the direct approach. The code is released at https://github.com/DirectMolecularConfGen/DMCG

preprint2022arXiv

RetroGraph: Retrosynthetic Planning with Graph Search

Retrosynthetic planning, which aims to find a reaction pathway to synthesize a target molecule, plays an important role in chemistry and drug discovery. This task is usually modeled as a search problem. Recently, data-driven methods have attracted many research interests and shown promising results for retrosynthetic planning. We observe that the same intermediate molecules are visited many times in the searching process, and they are usually independently treated in previous tree-based methods (e.g., AND-OR tree search, Monte Carlo tree search). Such redundancies make the search process inefficient. We propose a graph-based search policy that eliminates the redundant explorations of any intermediate molecules. As searching over a graph is more complicated than over a tree, we further adopt a graph neural network to guide the search over graphs. Meanwhile, our method can search a batch of targets together in the graph and remove the inter-target duplication in the tree-based search methods. Experimental results on two datasets demonstrate the effectiveness of our method. Especially on the widely used USPTO benchmark, we improve the search success rate to 99.47%, advancing previous state-of-the-art performance for 2.6 points.

preprint2022arXiv

Tailoring Molecules for Protein Pockets: a Transformer-based Generative Solution for Structured-based Drug Design

Structure-based drug design is drawing growing attentions in computer-aided drug discovery. Compared with the virtual screening approach where a pre-defined library of compounds are computationally screened, de novo drug design based on the structure of a target protein can provide novel drug candidates. In this paper, we present a generative solution named TamGent (Target-aware molecule generator with Transformer) that can directly generate candidate drugs from scratch for a given target, overcoming the limits imposed by existing compound libraries. Following the Transformer framework (a state-of-the-art framework in deep learning), we design a variant of Transformer encoder to process 3D geometric information of targets and pre-train the Transformer decoder on 10 million compounds from PubChem for candidate drug generation. Systematical evaluation on candidate compounds generated for targets from DrugBank shows that both binding affinity and drugability are largely improved. TamGent outperforms previous baselines in terms of both effectiveness and efficiency. The method is further verified by generating candidate compounds for the SARS-CoV-2 main protease and the oncogenic mutant KRAS G12C. The results show that our method not only re-discovers previously verified drug molecules , but also generates novel molecules with better docking scores, expanding the compound pool and potentially leading to the discovery of novel drugs.

preprint2022arXiv

Unified 2D and 3D Pre-Training of Molecular Representations

Molecular representation learning has attracted much attention recently. A molecule can be viewed as a 2D graph with nodes/atoms connected by edges/bonds, and can also be represented by a 3D conformation with 3-dimensional coordinates of all atoms. We note that most previous work handles 2D and 3D information separately, while jointly leveraging these two sources may foster a more informative representation. In this work, we explore this appealing idea and propose a new representation learning method based on a unified 2D and 3D pre-training. Atom coordinates and interatomic distances are encoded and then fused with atomic representations through graph neural networks. The model is pre-trained on three tasks: reconstruction of masked atoms and coordinates, 3D conformation generation conditioned on 2D graph, and 2D graph generation conditioned on 3D conformation. We evaluate our method on 11 downstream molecular property prediction tasks: 7 with 2D information only and 4 with both 2D and 3D information. Our method achieves state-of-the-art results on 10 tasks, and the average improvement on 2D-only tasks is 8.3%. Our method also achieves significant improvement on two 3D conformation generation tasks.

preprint2021arXiv

IOT: Instance-wise Layer Reordering for Transformer Structures

With sequentially stacked self-attention, (optional) encoder-decoder attention, and feed-forward layers, Transformer achieves big success in natural language processing (NLP), and many variants have been proposed. Currently, almost all these models assume that the layer order is fixed and kept the same across data samples. We observe that different data samples actually favor different orders of the layers. Based on this observation, in this work, we break the assumption of the fixed layer order in the Transformer and introduce instance-wise layer reordering into the model structure. Our Instance-wise Ordered Transformer (IOT) can model variant functions by reordered layers, which enables each sample to select the better one to improve the model performance under the constraint of almost the same number of parameters. To achieve this, we introduce a light predictor with negligible parameter and inference cost to decide the most capable and favorable layer order for any input sequence. Experiments on 3 tasks (neural machine translation, abstractive summarization, and code generation) and 9 datasets demonstrate consistent improvements of our method. We further show that our method can also be applied to other architectures beyond Transformer. Our code is released at Github.

preprint2021arXiv

Learning to Reweight with Deep Interactions

Recently, the concept of teaching has been introduced into machine learning, in which a teacher model is used to guide the training of a student model (which will be used in real tasks) through data selection, loss function design, etc. Learning to reweight, which is a specific kind of teaching that reweights training data using a teacher model, receives much attention due to its simplicity and effectiveness. In existing learning to reweight works, the teacher model only utilizes shallow/surface information such as training iteration number and loss/accuracy of the student model from training/validation sets, but ignores the internal states of the student model, which limits the potential of learning to reweight. In this work, we propose an improved data reweighting algorithm, in which the student model provides its internal states to the teacher model, and the teacher model returns adaptive weights of training samples to enhance the training of the student model. The teacher model is jointly trained with the student model using meta gradients propagated from a validation set. Experiments on image classification with clean/noisy labels and neural machine translation empirically demonstrate that our algorithm makes significant improvement over previous methods.

preprint2020arXiv

Multi-branch Attentive Transformer

While the multi-branch architecture is one of the key ingredients to the success of computer vision tasks, it has not been well investigated in natural language processing, especially sequence learning tasks. In this work, we propose a simple yet effective variant of Transformer called multi-branch attentive Transformer (briefly, MAT), where the attention layer is the average of multiple branches and each branch is an independent multi-head attention layer. We leverage two training techniques to regularize the training: drop-branch, which randomly drops individual branches during training, and proximal initialization, which uses a pre-trained Transformer model to initialize multiple branches. Experiments on machine translation, code generation and natural language understanding demonstrate that such a simple variant of Transformer brings significant improvements. Our code is available at \url{https://github.com/HA-Transformer}.

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