Search Results for author:
Found 29 papers, 20 papers with code
mixSeq: A Simple Data Augmentation Methodfor Neural Machine Translation
Data augmentation, which refers to manipulating the inputs (e. g., adding random noise, masking specific parts) to enlarge the dataset, has been widely adopted in machine learning.
Building Multilingual Machine Translation Systems That Serve Arbitrary XY 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.
BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning
However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e. g., IUPAC).
Ranked #1 on
Molecule Captioning
on ChEBI-20
Are We Falling in a Middle-Intelligence Trap? An Analysis and Mitigation of the Reversal Curse
Recent studies have highlighted a phenomenon in large language models (LLMs) known as "the reversal curse," in which the order of knowledge entities in the training data biases the models' comprehension.
Re-evaluating Retrosynthesis Algorithms with Syntheseus
The planning of how to synthesize molecules, also known as retrosynthesis, has been a growing focus of the machine learning and chemistry communities in recent years.
FABind: Fast and Accurate Protein-Ligand Binding
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.
Retrosynthesis Prediction with Local Template Retrieval
Furthermore, we propose a lightweight adapter to adjust the weights when combing neural network and KNN predictions conditioned on the hidden representation and the retrieved templates.
MolXPT: Wrapping Molecules with Text for Generative Pre-training
Considering that text is the most important record for scientific discovery, in this paper, we propose MolXPT, a unified language model of text and molecules pre-trained on SMILES (a sequence representation of molecules) wrapped by text.
Ranked #1 on
Molecular Property Prediction
on ClinTox
What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization
Summarization models often generate text that is poorly calibrated to quality metrics because they are trained to maximize the likelihood of a single reference (MLE).
O-GNN: Incorporating Ring Priors into Molecular Modeling
Despite the recent success of molecular modeling with graph neural networks (GNNs), few models explicitly take rings in compounds into consideration, consequently limiting the expressiveness of the models.
Ranked #1 on
Graph Regression
on PCQM4M-LSC
(Validation MAE metric)
ResiDual: Transformer with Dual Residual Connections
In this paper, we propose ResiDual, a novel Transformer architecture with Pre-Post-LN (PPLN), which fuses the connections in Post-LN and Pre-LN together and inherits their advantages while avoids their limitations.
De Novo Molecular Generation via Connection-aware Motif Mining
The obtained motif vocabulary consists of not only molecular motifs (i. e., the frequent fragments), but also their connection information, indicating how the motifs are connected with each other.
Retrosynthetic Planning with Dual Value Networks
Retrosynthesis, which aims to find a route to synthesize a target molecule from commercially available starting materials, is a critical task in drug discovery and materials design.
Ranked #1 on
Multi-step retrosynthesis
on USPTO-190
Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-design
Specifically, we first pre-train an antibody language model based on the sequence data, then propose a one-shot way for sequence and structure generation of CDR to avoid the heavy cost and error propagation from an autoregressive manner, and finally leverage the pre-trained antibody model for the antigen-specific antibody generation model with some carefully designed modules.
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.
Unified 2D and 3D Pre-Training of Molecular Representations
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.
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.
RetroGraph: Retrosynthetic Planning with Graph Search
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).
Ranked #2 on
Multi-step retrosynthesis
on USPTO-190
SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction
Accurate prediction of Drug-Target Affinity (DTA) is of vital importance in early-stage drug discovery, facilitating the identification of drugs that can effectively interact with specific targets and regulate their activities.
Ranked #1 on
Drug Discovery
on KIBA
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.
Target-Side Data Augmentation for Sequence Generation
Autoregressive sequence generation, a prevalent task in machine learning and natural language processing, generates every target token conditioned on both a source input and previously generated target tokens.
Discovering Drug-Target Interaction Knowledge from Biomedical Literature
We regard the DTI triplets as a sequence and use a Transformer-based model to directly generate them without using the detailed annotations of entities and relations.
Distance-Enhanced Graph Neural Network for Link Prediction
To overcome this difficulty, we propose an anchorbased distance: First, we randomly select K anchor vertices from the graph and then calculate the shortest distances of all vertices in the graph to them.
Ranked #1 on
Link Property Prediction
on ogbl-ddi
UniDrop: A Simple yet Effective Technique to Improve Transformer without Extra Cost
Therefore, in this paper, we integrate different dropout techniques into the training of Transformer models.
Ranked #4 on
Machine Translation
on IWSLT2014 English-German
IOT: Instance-wise Layer Reordering for Transformer Structures
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.
Learning to Use Future Information in Simultaneous Translation
For wait-k inference, we observe that wait-m training with $m>k$ in simultaneous NMT (i. e., using more future information for training than inference) generally outperforms wait-k training.
Temporally Correlated Task Scheduling for Sequence Learning
In many applications, a sequence learning task is usually associated with multiple temporally correlated auxiliary tasks, which are different in terms of how much input information to use or which future step to predict.
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.
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.
Ranked #4 on
Machine Translation
on WMT2014 English-German
(SacreBLEU metric)
