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Researcher profile

Yingce Xia

Yingce Xia contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine LearningArtificial IntelligenceComputation and LanguageBiomoleculesComputer Visioneess.IVMultimediaq-fin.GNq-fin.ST

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Published work

15 published item(s)

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.

0 citations0 reviewsNo code linkedOpen access
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

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

DDG-DA: Data Distribution Generation for Predictable Concept Drift Adaptation

In many real-world scenarios, we often deal with streaming data that is sequentially collected over time. Due to the non-stationary nature of the environment, the streaming data distribution may change in unpredictable ways, which is known as concept drift. To handle concept drift, previous methods first detect when/where the concept drift happens and then adapt models to fit the distribution of the latest data. However, there are still many cases that some underlying factors of environment evolution are predictable, making it possible to model the future concept drift trend of the streaming data, while such cases are not fully explored in previous work. In this paper, we propose a novel method DDG-DA, that can effectively forecast the evolution of data distribution and improve the performance of models. Specifically, we first train a predictor to estimate the future data distribution, then leverage it to generate training samples, and finally train models on the generated data. We conduct experiments on three real-world tasks (forecasting on stock price trend, electricity load and solar irradiance) and obtain significant improvement on multiple widely-used models.

0 citations0 reviewsNo code linkedOpen access
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

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

HIST: A Graph-based Framework for Stock Trend Forecasting via Mining Concept-Oriented Shared Information

Stock trend forecasting, which forecasts stock prices' future trends, plays an essential role in investment. The stocks in a market can share information so that their stock prices are highly correlated. Several methods were recently proposed to mine the shared information through stock concepts (e.g., technology, Internet Retail) extracted from the Web to improve the forecasting results. However, previous work assumes the connections between stocks and concepts are stationary, and neglects the dynamic relevance between stocks and concepts, limiting the forecasting results. Moreover, existing methods overlook the invaluable shared information carried by hidden concepts, which measure stocks' commonness beyond the manually defined stock concepts. To overcome the shortcomings of previous work, we proposed a novel stock trend forecasting framework that can adequately mine the concept-oriented shared information from predefined concepts and hidden concepts. The proposed framework simultaneously utilize the stock's shared information and individual information to improve the stock trend forecasting performance. Experimental results on the real-world tasks demonstrate the efficiency of our framework on stock trend forecasting. The investment simulation shows that our framework can achieve a higher investment return than the baselines.

0 citations0 reviewsNo code linkedOpen access
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.

0 citations0 reviewsNo code linkedOpen access
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.

0 citations0 reviewsNo code linkedOpen access
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.

0 citations0 reviewsNo code linkedOpen access
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.

0 citations0 reviewsNo code linkedOpen access
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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Dual Learning: Theoretical Study and an Algorithmic Extension

Dual learning has been successfully applied in many machine learning applications including machine translation, image-to-image transformation, etc. The high-level idea of dual learning is very intuitive: if we map an $x$ from one domain to another and then map it back, we should recover the original $x$. Although its effectiveness has been empirically verified, theoretical understanding of dual learning is still very limited. In this paper, we aim at understanding why and when dual learning works. Based on our theoretical analysis, we further extend dual learning by introducing more related mappings and propose multi-step dual learning, in which we leverage feedback signals from additional domains to improve the qualities of the mappings. We prove that multi-step dual learn-ing can boost the performance of standard dual learning under mild conditions. Experiments on WMT 14 English$\leftrightarrow$German and MultiUNEnglish$\leftrightarrow$French translations verify our theoretical findings on dual learning, and the results on the translations among English, French, and Spanish of MultiUN demonstrate the effectiveness of multi-step dual learning.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

DualLip: A System for Joint Lip Reading and Generation

Lip reading aims to recognize text from talking lip, while lip generation aims to synthesize talking lip according to text, which is a key component in talking face generation and is a dual task of lip reading. In this paper, we develop DualLip, a system that jointly improves lip reading and generation by leveraging the task duality and using unlabeled text and lip video data. The key ideas of the DualLip include: 1) Generate lip video from unlabeled text with a lip generation model, and use the pseudo pairs to improve lip reading; 2) Generate text from unlabeled lip video with a lip reading model, and use the pseudo pairs to improve lip generation. We further extend DualLip to talking face generation with two additionally introduced components: lip to face generation and text to speech generation. Experiments on GRID and TCD-TIMIT demonstrate the effectiveness of DualLip on improving lip reading, lip generation, and talking face generation by utilizing unlabeled data. Specifically, the lip generation model in our DualLip system trained with only10% paired data surpasses the performance of that trained with the whole paired data. And on the GRID benchmark of lip reading, we achieve 1.16% character error rate and 2.71% word error rate, outperforming the state-of-the-art models using the same amount of paired data.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Incorporating BERT into Neural Machine Translation

The recently proposed BERT has shown great power on a variety of natural language understanding tasks, such as text classification, reading comprehension, etc. However, how to effectively apply BERT to neural machine translation (NMT) lacks enough exploration. While BERT is more commonly used as fine-tuning instead of contextual embedding for downstream language understanding tasks, in NMT, our preliminary exploration of using BERT as contextual embedding is better than using for fine-tuning. This motivates us to think how to better leverage BERT for NMT along this direction. We propose a new algorithm named BERT-fused model, in which we first use BERT to extract representations for an input sequence, and then the representations are fused with each layer of the encoder and decoder of the NMT model through attention mechanisms. We conduct experiments on supervised (including sentence-level and document-level translations), semi-supervised and unsupervised machine translation, and achieve state-of-the-art results on seven benchmark datasets. Our code is available at \url{https://github.com/bert-nmt/bert-nmt}.

0 citations0 reviewsNo code linkedOpen access
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}.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

TuiGAN: Learning Versatile Image-to-Image Translation with Two Unpaired Images

An unsupervised image-to-image translation (UI2I) task deals with learning a mapping between two domains without paired images. While existing UI2I methods usually require numerous unpaired images from different domains for training, there are many scenarios where training data is quite limited. In this paper, we argue that even if each domain contains a single image, UI2I can still be achieved. To this end, we propose TuiGAN, a generative model that is trained on only two unpaired images and amounts to one-shot unsupervised learning. With TuiGAN, an image is translated in a coarse-to-fine manner where the generated image is gradually refined from global structures to local details. We conduct extensive experiments to verify that our versatile method can outperform strong baselines on a wide variety of UI2I tasks. Moreover, TuiGAN is capable of achieving comparable performance with the state-of-the-art UI2I models trained with sufficient data.

0 citations0 reviewsNo code linkedOpen access