2,963 research outputs found
Learning Multimodal Graph-to-Graph Translation for Molecular Optimization
We view molecular optimization as a graph-to-graph translation problem. The
goal is to learn to map from one molecular graph to another with better
properties based on an available corpus of paired molecules. Since molecules
can be optimized in different ways, there are multiple viable translations for
each input graph. A key challenge is therefore to model diverse translation
outputs. Our primary contributions include a junction tree encoder-decoder for
learning diverse graph translations along with a novel adversarial training
method for aligning distributions of molecules. Diverse output distributions in
our model are explicitly realized by low-dimensional latent vectors that
modulate the translation process. We evaluate our model on multiple molecular
optimization tasks and show that our model outperforms previous
state-of-the-art baselines
Analyzing Learned Molecular Representations for Property Prediction
Advancements in neural machinery have led to a wide range of algorithmic
solutions for molecular property prediction. Two classes of models in
particular have yielded promising results: neural networks applied to computed
molecular fingerprints or expert-crafted descriptors, and graph convolutional
neural networks that construct a learned molecular representation by operating
on the graph structure of the molecule. However, recent literature has yet to
clearly determine which of these two methods is superior when generalizing to
new chemical space. Furthermore, prior research has rarely examined these new
models in industry research settings in comparison to existing employed models.
In this paper, we benchmark models extensively on 19 public and 16 proprietary
industrial datasets spanning a wide variety of chemical endpoints. In addition,
we introduce a graph convolutional model that consistently matches or
outperforms models using fixed molecular descriptors as well as previous graph
neural architectures on both public and proprietary datasets. Our empirical
findings indicate that while approaches based on these representations have yet
to reach the level of experimental reproducibility, our proposed model
nevertheless offers significant improvements over models currently used in
industrial workflows
GIT-Mol: A Multi-modal Large Language Model for Molecular Science with Graph, Image, and Text
Large language models have made significant strides in natural language
processing, paving the way for innovative applications including molecular
representation and generation. However, most existing single-modality
approaches cannot capture the abundant and complex information in molecular
data. Here, we introduce GIT-Mol, a multi-modal large language model that
integrates the structure Graph, Image, and Text information, including the
Simplified Molecular Input Line Entry System (SMILES) and molecular captions.
To facilitate the integration of multi-modal molecular data, we propose
GIT-Former, a novel architecture capable of mapping all modalities into a
unified latent space. Our study develops an innovative any-to-language
molecular translation strategy and achieves a 10%-15% improvement in molecular
captioning, a 5%-10% accuracy increase in property prediction, and a 20% boost
in molecule generation validity compared to baseline or single-modality models.Comment: 16 pages, 5 figure
Geometric deep learning: going beyond Euclidean data
Many scientific fields study data with an underlying structure that is a
non-Euclidean space. Some examples include social networks in computational
social sciences, sensor networks in communications, functional networks in
brain imaging, regulatory networks in genetics, and meshed surfaces in computer
graphics. In many applications, such geometric data are large and complex (in
the case of social networks, on the scale of billions), and are natural targets
for machine learning techniques. In particular, we would like to use deep
neural networks, which have recently proven to be powerful tools for a broad
range of problems from computer vision, natural language processing, and audio
analysis. However, these tools have been most successful on data with an
underlying Euclidean or grid-like structure, and in cases where the invariances
of these structures are built into networks used to model them. Geometric deep
learning is an umbrella term for emerging techniques attempting to generalize
(structured) deep neural models to non-Euclidean domains such as graphs and
manifolds. The purpose of this paper is to overview different examples of
geometric deep learning problems and present available solutions, key
difficulties, applications, and future research directions in this nascent
field
BioBridge: Bridging Biomedical Foundation Models via Knowledge Graphs
Foundation models (FMs) are able to leverage large volumes of unlabeled data
to demonstrate superior performance across a wide range of tasks. However, FMs
developed for biomedical domains have largely remained unimodal, i.e.,
independently trained and used for tasks on protein sequences alone, small
molecule structures alone, or clinical data alone. To overcome this limitation
of biomedical FMs, we present BioBridge, a novel parameter-efficient learning
framework, to bridge independently trained unimodal FMs to establish multimodal
behavior. BioBridge achieves it by utilizing Knowledge Graphs (KG) to learn
transformations between one unimodal FM and another without fine-tuning any
underlying unimodal FMs. Our empirical results demonstrate that BioBridge can
beat the best baseline KG embedding methods (on average by around 76.3%) in
cross-modal retrieval tasks. We also identify BioBridge demonstrates
out-of-domain generalization ability by extrapolating to unseen modalities or
relations. Additionally, we also show that BioBridge presents itself as a
general purpose retriever that can aid biomedical multimodal question answering
as well as enhance the guided generation of novel drugs
MolFM: A Multimodal Molecular Foundation Model
Molecular knowledge resides within three different modalities of information
sources: molecular structures, biomedical documents, and knowledge bases.
Effective incorporation of molecular knowledge from these modalities holds
paramount significance in facilitating biomedical research. However, existing
multimodal molecular foundation models exhibit limitations in capturing
intricate connections between molecular structures and texts, and more
importantly, none of them attempt to leverage a wealth of molecular expertise
derived from knowledge graphs. In this study, we introduce MolFM, a multimodal
molecular foundation model designed to facilitate joint representation learning
from molecular structures, biomedical texts, and knowledge graphs. We propose
cross-modal attention between atoms of molecular structures, neighbors of
molecule entities and semantically related texts to facilitate cross-modal
comprehension. We provide theoretical analysis that our cross-modal
pre-training captures local and global molecular knowledge by minimizing the
distance in the feature space between different modalities of the same
molecule, as well as molecules sharing similar structures or functions. MolFM
achieves state-of-the-art performance on various downstream tasks. On
cross-modal retrieval, MolFM outperforms existing models with 12.13% and 5.04%
absolute gains under the zero-shot and fine-tuning settings, respectively.
Furthermore, qualitative analysis showcases MolFM's implicit ability to provide
grounding from molecular substructures and knowledge graphs. Code and models
are available on https://github.com/BioFM/OpenBioMed.Comment: 31 pages, 15 figures, and 15 table
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