#cheminformatics
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cbirt · 7 months ago
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Centuries of scientific invention have been driven by the search for new drugs to fight against diseases. Since medicinal plants became valuable sources of medicine from synthetic chemistry, we have consistently improved our capacity to design molecules with therapeutic potential. However, the traditional drug discovery process is time-consuming, costly, and fraught with challenges. It is here that ETH Zurich Chemists develop DRAGONFLY (Drug-target interActome-based GeneratiON oF noveL biologicallY active molecules), a novel de novo drug design method, promising to make the creation of new therapeutics easier.
The conventional drug discovery pipeline is a slow process involving target identification, hit discovery, lead optimization, and pre-clinical and clinical development. It has produced numerous drugs that have saved millions of lives, but there are limitations.
Sequential Nature: The conventional drug discovery pipeline is a slow process involving target identification, hit discovery, lead optimization, and pre-clinical and clinical development. It has produced numerous drugs that have saved millions of lives, but there are limitations.
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reionized · 3 months ago
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also chat im gonna have to roleplay as a cs student so hard this semester its unreal wym 2 math classes AND computational physics on top of that
im hoping to get into molecular simulations though / cheminformatics so hopefully itll all be worth it in the end !!!!!!
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diegolopez1995 · 1 year ago
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Artificial Intelligence: Unexpected Results
Artificial intelligence (AI) is on the rise. Until now, AI applications generally have “black box” character: How AI arrives at its results remains hidden. Prof. Dr. Jürgen Bajorath, a cheminformatics scientist at the University of Bonn, and his team have developed a method that reveals how certain AI applications work in pharmaceutical research. more...
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industrynewsupdates · 1 month ago
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Bioinformatics Market: A Deep Dive into Predictive Modeling Applications
The global bioinformatics market was valued at USD 10.1 billion in 2022 and is projected to experience substantial growth, with an anticipated compound annual growth rate (CAGR) of 13.7% from 2023 to 2030. This growth is primarily driven by increasing demand for novel drug research and development (R&D) and the support of both private and public funding initiatives aimed at advancing R&D activities. Additionally, the emergence of user-friendly and accessible bioinformatics software, such as RasMol, AUTODOCK, BALL, and Bioclipse, is contributing to the market's expansion. These tools are widely utilized for the precise and effective analysis of biomarker discovery programs, which are essential for toxicity detection in the early stages of drug development.
Bioinformatics software and tools serve as integrated solutions that provide sophisticated algorithms and statistical methodologies for data analysis. They facilitate the integration of data management and analysis for a variety of applications, including next-generation sequencing, genomic and proteomic structuring, modeling, and three-dimensional drug design. The rising number of R&D initiatives in the proteomics and genomics sectors, along with other related '-omics' fields, is expected to bolster market growth by addressing increasing demands for data storage and analysis.
According to a study published by Stanford Medicine in January 2022, research conducted by Stanford scientists demonstrated that a DNA sequencing technique could sequence a human genome in approximately eight hours. Such technological advancements are likely to enhance the demand for genomics and, consequently, the bioinformatics sector. Applications in bioinformatics are capable of storing vast amounts of genomic and proteomic data, which supports research activities across various fields, including aging, carcinogenesis, and preventive therapies for genetic diseases. This capability is projected to significantly contribute to the industry's growth throughout the forecast period.
Gather more insights about the market drivers, restrains and growth of the Bioinformatics Market
Application Insights
In 2022, the genomics application segment accounted for a considerable share of the revenue in the bioinformatics market. The rising demand for pharmacogenomics in drug development, alongside advancements in technology aimed at managing extensive genomic data sets, are key factors driving this significant market share. The market is categorized into several application segments, including genomics, molecular phylogenetics, metabolomics, proteomics, transcriptomics, cheminformatics, drug designing, and others.
The cheminformatics segment is anticipated to expand notably during the forecast period, primarily driven by the increasing demand for biomarker discovery and development. Cost reductions in the drug development process, shortened timelines for introducing new drugs to market, and enhanced success rates in drug discovery attributed to cheminformatics and drug design are expected to further fuel the growth of this segment.
By integrating bioinformatics with cheminformatics and drug design, researchers can quickly analyze and interpret large volumes of chemical and biological data. This integration leads to more targeted and effective drug development efforts. For example, in June 2021, the U.S. Food and Drug Administration (FDA) and the Center for Drug Evaluation and Research (CDER) approved 26 new molecular entities (NMEs), which will further stimulate growth in research and development activities.
The field of proteomics has also seen significant R&D investments in recent years, and bioinformatics plays a crucial role in analyzing and managing the resulting data. This integration simplifies the handling of heterogeneous and large datasets, allows for the introduction of innovative algorithms, and enhances the knowledge discovery process. Overall, the bioinformatics market is poised for substantial growth, driven by technological advancements, increased funding, and an expanding array of applications across various scientific fields.
Order a free sample PDF of the Bioinformatics Market Intelligence Study, published by Grand View Research.
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atplblog · 1 month ago
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Price: [price_with_discount] (as of [price_update_date] - Details) [ad_1] A one-stop guide to teach chemists how to use Python for coding and iterations in a hands-on and practical mannerDescription Python is a versatile and powerful computer language without a steep learning curve. It can be deployed to simulate various physicochemical parameters or to analyze complex molecular, bio-molecular, and crystalline structures. The objective of this book is to give a gentle introduction to Python programming with relevant algorithms, iterations, and basic simulations from a chemist’s perspective. This book outlines the fundamentals of Python coding through the built-in functions, libraries, and modules as well as with a few selected external packages for physical/materials/inorganic/analytical/organic/ nuclear chemistry in terms of numerical, symbolic, structural, and graphical data analysis using the default, Integrated Development and Learning Environment. You will also learn about the Structural Elucidation of organic molecules and inorganic complexes with specific Cheminformatics modules. In addition to this, the book covers chemical data analysis with Numpy and also includes topics such as SymPy and Matplotlib for Symbolic calculations and Plotting. By the end of the book, you will be able to use Python as a graphical tool or a calculator for numerical and symbolic computations in the interdisciplinary areas of chemistry. What you will learn ● To fetch elemental, nuclear, atomic or molecular data with list or dictionary functions. ● Understanding the algorithms for the computation of Thermodynamic, Electrochemical, Kinetics, Molecular and Spectral parameters. Who this book is for This book is for Chemists, Chemical Engineers, Material Scientists, Bio-chemists, Biotechnologists, and Physicists. Students of Chemistry, Chemical Engineering, Materials Chemistry, Biochemistry, Biotechnology, and Physics will find this book resourceful. Publisher ‏ : ‎ BPB Publications (1 May 2023) Language ‏ : ‎ English Paperback ‏ : ‎ 368 pages ISBN-10 ‏ : ‎ 9355517971 ISBN-13 ‏ : ‎ 978-9355517975 Reading age ‏ : ‎ 18 years and up Item Weight ‏ : ‎ 550 g Dimensions ‏ : ‎ 19.05 x 2.11 x 23.5 cm Country of Origin ‏ : ‎ India [ad_2]
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crimsonpublishers-oabb · 3 months ago
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Artificial Cell Membranes as Bioinformation Hubs: Unraveling Therapeutic Networks through Nano-Informatics
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The living cells are composed of bio-membranes which construct lipid bilayers composed mainly of phospholipids with proteins and cholesterol embedded in them. The internal organelles of the cell are composed of intracellular membranes and their unique structure modulates the permeation of molecules, like water, ions, and oxygen. Bio-membranes are considered as complex systems, and their state of matter is the liquid crystalline state corresponds to the fluid mosaic model of Singer & Nicolson [1]. Such state of matter undergoes a huge number of metastable phases that are named as ‘lipid rafts’ that are considered to act as information hubs.
These ‘lipid rafts’ are thermodynamic driven bioinformation hubs essential for the cell functions and for the survival of the organism [2]. The convergence of various scientific disciplines, including bioinformatics, cheminformatics, medical informatics, and nanoinformatics, has given rise to novel approaches in understanding and harnessing the potential of artificial cell membranes as bioinformation hubs. This paper delves into the intricate interplay between bio-membranes, lipid rafts, and thermodynamic-driven bioinformation, elucidating their pivotal role in establishing therapeutic networks.
Read More About This Article: https://crimsonpublishers.com/oabb/fulltext/OABB.000566.php
Read More About Crimson Publishers: https://crimsonpublishers.com/oabb/index.php
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twinkl22004 · 5 months ago
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“Food Compounds”, PART TWO (II).
  National Research Council,“Food Chemical Codex”, 3rd edition, Washington DC, 1981 was the topic of an earlier blog post. Samuel Yannai(editor), “Dictionary of Food Compounds”, 2003 was also the topic of an earlier blog post. Here I present: “Food Compounds”, PART TWO (II). INTRODUCTION. Chemical space is a concept in cheminformatics referring to the property space spanned by all possible…
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wellnessweb · 5 months ago
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The Rising Bioinformatics  Market Size: Key Drivers and Insights
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The Bioinformatics Market Size was valued at USD 11.58 billion in 2023 and is expected to reach USD 34.69 billion by 2031, and grow at a CAGR of 14.7% over the forecast period 2024-2031.The bioinformatics market is experiencing robust growth, driven by the escalating integration of computational tools in biological research and the increasing volume of complex biological data. Advances in next-generation sequencing technologies and precision medicine are propelling the demand for sophisticated bioinformatics solutions. Key players in this market are investing heavily in developing innovative software and algorithms to enhance data analysis capabilities, thereby improving outcomes in genomics, proteomics, and drug discovery. Additionally, collaborations between academic institutions, research organizations, and pharmaceutical companies are fostering a conducive environment for market expansion. As healthcare continues to evolve towards more personalized approaches, the bioinformatics market is poised for substantial growth, underscored by its critical role in bridging the gap between data and actionable biological insights.
Get Sample of This Report @ https://www.snsinsider.com/sample-request/1755
Market Scope & Overview 
The market research report highlights the important regulatory organizations as well as the important international rules and regulations put in place to regulate this industry. Interviews, questionnaires, and the observation of well-known industry experts are all used in the main study. The market research for Bioinformatics  Market includes market size predictions, verifiable data from reliable sources, and in-depth qualitative analysis. The predictions are supported by an established research methodology. In order to develop the market analysis, primary and secondary data were used.
The research uses the Ansoff Matrix and Porter's Five Forces model to carry out a complete market analysis. An innovative method for examining and assessing a company's position that combines a market performance score with an industry position score is called a competitive quadrant. The Bioinformatics Market study also discusses the sector's regulatory environment, which will help you make a wise decision.
Market Segmentation Analysis
By Product
Bioinformatics Platforms
Sequence Analysis Platforms
Sequence Manipulation Platforms
Sequence Alignment Platforms
Structural and Functional Analysis Platforms
Others
Bioinformatics Services
Sequencing
Database Management
Data Analysis
Others
Biocontent Management
Generalized Biocontent
Specialized Biocontent
By Application
Genomics
Molecular Phylogenetics
Metabolomics
Proteomics
Transcriptomics
Cheminformatics and drug designing
Others
Russia-Ukraine Conflict Impact Analysis
Recent market research on the target market discusses how the crisis between Russia and Ukraine has affected that market. The Bioinformatics Market  research focuses on both the emerging prospects and the significant problems that the market is currently experiencing as a result of these disagreements.
Regional Outlook
Numerous aspects, including the financial performance of the prior year, growth objectives, innovation score, new product releases, investments, market share growth, and others are all taken into consideration when conducting research on different areas of the Bioinformatics  Market  throughout the world.
Competitive Analysis
The top market participants are carefully investigated, with information on their histories, SWOT analyses, most recent successes, and corporate objectives included. Every aspect of the market is looked at, with a focus on important players such market leaders, followers, and entrants. By offering a thorough comparative analysis of the major players in the Bioinformatics  Market based on their offerings, prices, financial standing, product portfolios, growth strategies, and geographic reach, the report serves as a buyer's guide for investors.
Key Reasons to Purchase Bioinformatics  Market  Report
To track the development of the worldwide market competition, keep an eye on new product releases, collaborations, market expansions, and acquisitions.
Insights into the company's goods, applications, important areas and countries, market size, historical data, and forecast estimates.
Conclusion
The data and figures in the report will assist multinational corporations in defining, clarifying, and evaluating their product sales volume, value, and market share, as well as market competition, SWOT analysis, and long-term growth strategies.
Read Full Report @ https://www.snsinsider.com/reports/bioinformatics-market-1755
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jcmarchi · 7 months ago
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Supercharging Graph Neural Networks with Large Language Models: The Ultimate Guide
New Post has been published on https://thedigitalinsider.com/supercharging-graph-neural-networks-with-large-language-models-the-ultimate-guide/
Supercharging Graph Neural Networks with Large Language Models: The Ultimate Guide
Graphs are data structures that represent complex relationships across a wide range of domains, including social networks, knowledge bases, biological systems, and many more. In these graphs, entities are represented as nodes, and their relationships are depicted as edges.
The ability to effectively represent and reason about these intricate relational structures is crucial for enabling advancements in fields like network science, cheminformatics, and recommender systems.
Graph Neural Networks (GNNs) have emerged as a powerful deep learning framework for graph machine learning tasks. By incorporating the graph topology into the neural network architecture through neighborhood aggregation or graph convolutions, GNNs can learn low-dimensional vector representations that encode both the node features and their structural roles. This allows GNNs to achieve state-of-the-art performance on tasks such as node classification, link prediction, and graph classification across diverse application areas.
While GNNs have driven substantial progress, some key challenges remain. Obtaining high-quality labeled data for training supervised GNN models can be expensive and time-consuming. Additionally, GNNs can struggle with heterogeneous graph structures and situations where the graph distribution at test time differs significantly from the training data (out-of-distribution generalization).
In parallel, Large Language Models (LLMs) like GPT-4, and LLaMA have taken the world by storm with their incredible natural language understanding and generation capabilities. Trained on massive text corpora with billions of parameters, LLMs exhibit remarkable few-shot learning abilities, generalization across tasks, and commonsense reasoning skills that were once thought to be extremely challenging for AI systems.
The tremendous success of LLMs has catalyzed explorations into leveraging their power for graph machine learning tasks. On one hand, the knowledge and reasoning capabilities of LLMs present opportunities to enhance traditional GNN models. Conversely, the structured representations and factual knowledge inherent in graphs could be instrumental in addressing some key limitations of LLMs, such as hallucinations and lack of interpretability.
In this article, we will delve into the latest research at the intersection of graph machine learning and large language models. We will explore how LLMs can be used to enhance various aspects of graph ML, review approaches to incorporate graph knowledge into LLMs, and discuss emerging applications and future directions for this exciting field.
Graph Neural Networks and Self-Supervised Learning
To provide the necessary context, we will first briefly review the core concepts and methods in graph neural networks and self-supervised graph representation learning.
Graph Neural Network Architectures
Graph Neural Network Architecture – source
The key distinction between traditional deep neural networks and GNNs lies in their ability to operate directly on graph-structured data. GNNs follow a neighborhood aggregation scheme, where each node aggregates feature vectors from its neighbors to compute its own representation.
Numerous GNN architectures have been proposed with different instantiations of the message and update functions, such as Graph Convolutional Networks (GCNs), GraphSAGE, Graph Attention Networks (GATs), and Graph Isomorphism Networks (GINs) among others.
More recently, graph transformers have gained popularity by adapting the self-attention mechanism from natural language transformers to operate on graph-structured data. Some examples include GraphormerTransformer, and GraphFormers. These models are able to capture long-range dependencies across the graph better than purely neighborhood-based GNNs.
Self-Supervised Learning on Graphs
While GNNs are powerful representational models, their performance is often bottlenecked by the lack of large labeled datasets required for supervised training. Self-supervised learning has emerged as a promising paradigm to pre-train GNNs on unlabeled graph data by leveraging pretext tasks that only require the intrinsic graph structure and node features.
Self-Supervised Graph
Some common pretext tasks used for self-supervised GNN pre-training include:
Node Property Prediction: Randomly masking or corrupting a portion of the node attributes/features and tasking the GNN to reconstruct them.
Edge/Link Prediction: Learning to predict whether an edge exists between a pair of nodes, often based on random edge masking.
Contrastive Learning: Maximizing similarities between graph views of the same graph sample while pushing apart views from different graphs.
Mutual Information Maximization: Maximizing the mutual information between local node representations and a target representation like the global graph embedding.
Pretext tasks like these allow the GNN to extract meaningful structural and semantic patterns from the unlabeled graph data during pre-training. The pre-trained GNN can then be fine-tuned on relatively small labeled subsets to excel at various downstream tasks like node classification, link prediction, and graph classification.
By leveraging self-supervision, GNNs pre-trained on large unlabeled datasets exhibit better generalization, robustness to distribution shifts, and efficiency compared to training from scratch. However, some key limitations of traditional GNN-based self-supervised methods remain, which we will explore leveraging LLMs to address next.
Enhancing Graph ML with Large Language Models
Integration of Graphs and LLM –  source
The remarkable capabilities of LLMs in understanding natural language, reasoning, and few-shot learning present opportunities to enhance multiple aspects of graph machine learning pipelines. We explore some key research directions in this space:
A key challenge in applying GNNs is obtaining high-quality feature representations for nodes and edges, especially when they contain rich textual attributes like descriptions, titles, or abstracts. Traditionally, simple bag-of-words or pre-trained word embedding models have been used, which often fail to capture the nuanced semantics.
Recent works have demonstrated the power of leveraging large language models as text encoders to construct better node/edge feature representations before passing them to the GNN. For example, Chen et al. utilize LLMs like GPT-3 to encode textual node attributes, showing significant performance gains over traditional word embeddings on node classification tasks.
Beyond better text encoders, LLMs can be used to generate augmented information from the original text attributes in a semi-supervised manner. TAPE generates potential labels/explanations for nodes using an LLM and uses these as additional augmented features. KEA extracts terms from text attributes using an LLM and obtains detailed descriptions for these terms to augment features.
By improving the quality and expressiveness of input features, LLMs can impart their superior natural language understanding capabilities to GNNs, boosting performance on downstream tasks.
Alleviating Reliance on Labeled Data
A key advantage of LLMs is their ability to perform reasonably well on new tasks with little to no labeled data, thanks to their pre-training on vast text corpora. This few-shot learning capability can be leveraged to alleviate the reliance of GNNs on large labeled datasets.
One approach is to use LLMs to directly make predictions on graph tasks by describing the graph structure and node information in natural language prompts. Methods like InstructGLM and GPT4Graph fine-tune LLMs like LLaMA and GPT-4 using carefully designed prompts that incorporate graph topology details like node connections, neighborhoods etc. The tuned LLMs can then generate predictions for tasks like node classification and link prediction in a zero-shot manner during inference.
While using LLMs as black-box predictors has shown promise, their performance degrades for more complex graph tasks where explicit modeling of the structure is beneficial. Some approaches thus use LLMs in conjunction with GNNs – the GNN encodes the graph structure while the LLM provides enhanced semantic understanding of nodes from their text descriptions.
Graph Understanding with LLM Framework – Source
GraphLLM explores two strategies: 1) LLMs-as-Enhancers where LLMs encode text node attributes before passing to the GNN, and 2) LLMs-as-Predictors where the LLM takes the GNN’s intermediate representations as input to make final predictions.
GLEM goes further by proposing a variational EM algorithm that alternates between updating the LLM and GNN components for mutual enhancement.
By reducing reliance on labeled data through few-shot capabilities and semi-supervised augmentation, LLM-enhanced graph learning methods can unlock new applications and improve data efficiency.
Enhancing LLMs with Graphs
While LLMs have been tremendously successful, they still suffer from key limitations like hallucinations (generating non-factual statements), lack of interpretability in their reasoning process, and inability to maintain consistent factual knowledge.
Graphs, especially knowledge graphs which represent structured factual information from reliable sources, present promising avenues to address these shortcomings. We explore some emerging approaches in this direction:
Knowledge Graph Enhanced LLM Pre-training
Similar to how LLMs are pre-trained on large text corpora, recent works have explored pre-training them on knowledge graphs to imbue better factual awareness and reasoning capabilities.
Some approaches modify the input data by simply concatenating or aligning factual KG triples with natural language text during pre-training. E-BERT aligns KG entity vectors with BERT’s wordpiece embeddings, while K-BERT constructs trees containing the original sentence and relevant KG triples.
The Role of LLMs in Graph Machine Learning:
Researchers have explored several ways to integrate LLMs into the graph learning pipeline, each with its unique advantages and applications. Here are some of the prominent roles LLMs can play:
LLM as an Enhancer: In this approach, LLMs are used to enrich the textual attributes associated with the nodes in a TAG. The LLM’s ability to generate explanations, knowledge entities, or pseudo-labels can augment the semantic information available to the GNN, leading to improved node representations and downstream task performance.
For example, the TAPE (Text Augmented Pre-trained Encoders) model leverages ChatGPT to generate explanations and pseudo-labels for citation network papers, which are then used to fine-tune a language model. The resulting embeddings are fed into a GNN for node classification and link prediction tasks, achieving state-of-the-art results.
LLM as a Predictor: Rather than enhancing the input features, some approaches directly employ LLMs as the predictor component for graph-related tasks. This involves converting the graph structure into a textual representation that can be processed by the LLM, which then generates the desired output, such as node labels or graph-level predictions.
One notable example is the GPT4Graph model, which represents graphs using the Graph Modelling Language (GML) and leverages the powerful GPT-4 LLM for zero-shot graph reasoning tasks.
GNN-LLM Alignment: Another line of research focuses on aligning the embedding spaces of GNNs and LLMs, allowing for a seamless integration of structural and semantic information. These approaches treat the GNN and LLM as separate modalities and employ techniques like contrastive learning or distillation to align their representations.
The MoleculeSTM model, for instance, uses a contrastive objective to align the embeddings of a GNN and an LLM, enabling the LLM to incorporate structural information from the GNN while the GNN benefits from the LLM’s semantic knowledge.
Challenges and Solutions
While the integration of LLMs and graph learning holds immense promise, several challenges need to be addressed:
Efficiency and Scalability: LLMs are notoriously resource-intensive, often requiring billions of parameters and immense computational power for training and inference. This can be a significant bottleneck for deploying LLM-enhanced graph learning models in real-world applications, especially on resource-constrained devices.
One promising solution is knowledge distillation, where the knowledge from a large LLM (teacher model) is transferred to a smaller, more efficient GNN (student model).
Data Leakage and Evaluation: LLMs are pre-trained on vast amounts of publicly available data, which may include test sets from common benchmark datasets, leading to potential data leakage and overestimated performance. Researchers have started collecting new datasets or sampling test data from time periods after the LLM’s training cut-off to mitigate this issue.
Additionally, establishing fair and comprehensive evaluation benchmarks for LLM-enhanced graph learning models is crucial to measure their true capabilities and enable meaningful comparisons.
Transferability and Explainability: While LLMs excel at zero-shot and few-shot learning, their ability to transfer knowledge across diverse graph domains and structures remains an open challenge. Improving the transferability of these models is a critical research direction.
Furthermore, enhancing the explainability of LLM-based graph learning models is essential for building trust and enabling their adoption in high-stakes applications. Leveraging the inherent reasoning capabilities of LLMs through techniques like chain-of-thought prompting can contribute to improved explainability.
Multimodal Integration: Graphs often contain more than just textual information, with nodes and edges potentially associated with various modalities, such as images, audio, or numeric data. Extending the integration of LLMs to these multimodal graph settings presents an exciting opportunity for future research.
Real-world Applications and Case Studies
The integration of LLMs and graph machine learning has already shown promising results in various real-world applications:
Molecular Property Prediction: In the field of computational chemistry and drug discovery, LLMs have been employed to enhance the prediction of molecular properties by incorporating structural information from molecular graphs. The LLM4Mol model, for instance, leverages ChatGPT to generate explanations for SMILES (Simplified Molecular-Input Line-Entry System) representations of molecules, which are then used to improve the accuracy of property prediction tasks.
Knowledge Graph Completion and Reasoning: Knowledge graphs are a special type of graph structure that represents real-world entities and their relationships. LLMs have been explored for tasks like knowledge graph completion and reasoning, where the graph structure and textual information (e.g., entity descriptions) need to be considered jointly.
Recommender Systems: In the domain of recommender systems, graph structures are often used to represent user-item interactions, with nodes representing users and items, and edges denoting interactions or similarities. LLMs can be leveraged to enhance these graphs by generating user/item side information or reinforcing interaction edges.
Conclusion
The synergy between Large Language Models and Graph Machine Learning presents an exciting frontier in artificial intelligence research. By combining the structural inductive bias of GNNs with the powerful semantic understanding capabilities of LLMs, we can unlock new possibilities in graph learning tasks, particularly for text-attributed graphs.
While significant progress has been made, challenges remain in areas such as efficiency, scalability, transferability, and explainability. Techniques like knowledge distillation, fair evaluation benchmarks, and multimodal integration are paving the way for practical deployment of LLM-enhanced graph learning models in real-world applications.
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jobrxiv · 10 months ago
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RESEARCH ASSISTANT/RESEARCH SCIENTIST - Cheminformatics Calibr at Scripps Research See the full job description on jobRxiv: https://jobrxiv.org/job/research-assistant-research-scientist-cheminformatics/?feed_id=70259 #ScienceJobs #hiring #research
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omkarpatel · 11 months ago
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Cheminformatics Market is Estimated to Witness High Growth Owing to Increasing Adoption of AI and Machine Learning
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Cheminformatics is a field of science that uses software tools to process chemical data and information to enable the discovery and development of new pharmaceutical drugs and chemical products. It helps in analyzing chemical structures and reactions.
Market Dynamics:
The growing adoption of artificial intelligence (AI) and machine learning technologies in the pharmaceutical and chemical industries is driving the growth of the cheminformatics market. AI and machine learning are increasingly being used for virtual screening, molecular generation and optimization, and predictive toxicology. They help speed up the drug discovery process and reduce costs by identifying promising drug candidates. Additionally, the increasing focus on reducing drug development costs is also fueling the demand for cheminformatics solutions. By integrating cheminformatics tools with AI, it is possible to analyze huge chemical databases and clinical trial data more efficiently.
Market Drivers: Increasing Demand for Computational Chemistry to Speed up Drug Discovery: Cheminformatics plays a key role in computational chemistry that helps automate various processes in drug discovery like development, screening, optimization and validation of lead compounds. With high attrition rates and mounting R&D costs faced by pharma companies, demand for computational chemistry techniques using cheminformatics tools is growing significantly to accelerate drug discovery and reduce failure rates. This shift towards in silico methods acts as a major driver for the cheminformatics market.
Need for Effective Management of Chemical Data Due to Growing Chemical Databases: With the explosion of chemical databases due to research activities in pharmaceutical and biotech industries, managing the huge volumes of chemical data has become a challenging task. Cheminformatics solutions help scientists and researchers organize, analyze and draw insights from extensive chemical information databases, facilitating data-driven decision making. The growing complexity of chemical data is boosting the demand for sophisticated cheminformatics software and services.
Market Restrain Lack of Adequately Skilled Workforce: While cheminformatics is a multidisciplinary field encompassing domains like chemistry, biology, computer science and mathematics, finding professionals with expertise across these diverse areas remains an issue. The technical skills required for developing and utilizing advanced cheminformatics tools are not widely available. The shortage of trained chemists and data scientists proficient in cheminformatics techniques poses challenges for organizations to leverage the full potential of cheminformatics and limits market growth to some extent.
 Market Opportunity: Scope for Outsourcing of Cheminformatics Services Given the specialized expertise and resources needed, developing in-house cheminformatics capabilities may not always be viable, especially for smaller companies. This provides opportunities for specialist cheminformatics service providers to tap into the outsourcing market. As pharmaceutical and biotech firms increasingly rely on outsourcing non-core activities, demand is growing for third-party cheminformatics consulting, custom software development and other outsourced services.
Market Trends Rise of Cloud-Based Cheminformatics Tools Cloud computing is revolutionizing various industries by offering highly scalable and flexible solutions. In cheminformatics as well, the trend is shifting towards cloud-based platforms and software-as-a-service models that provide on-demand access to applications and databases over the internet. Cloud delivery of cheminformatics eliminates the need for organizations to make huge upfront capital investments and maintain their own IT infrastructure. This emerging deployment model is attracting more users and propelling future market trends.
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cbirt · 9 months ago
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Deep learning-based virtual screening provides a more effective way to find molecules that resemble drugs, and virtual sources give chemists useful information. Leiden University researchers present PCMol, a multi-target model that trains the de novo generative model on target proteins using the latent embeddings extracted from AlphaFold. Protein descriptors are a useful tactic for expanding the quantitative structure-activity relation (QSAR) models’ prediction range and applicability. Using structural relationships between proteins, AlphaFold latent embeddings within a generative model for small molecules enable extrapolation on the target side based on similarities to other proteins and interpolation within the chemical space of known highly active compounds, which is especially relevant for understudied or novel targets.
Drug development research is increasingly concentrating on computational methods to choose novel candidate molecules in silico. These substances have to interact chemically in a certain way with the binding site residues of protein targets. These interactions can be confirmed using in vitro bioactivity testing; however, physics-based computational techniques such as molecular docking or QSAR models are frequently performed prior to thorough virtual molecule screening. Choosing compounds for virtual screening entails either creating them from scratch using de novo molecule generation models or choosing them from huge libraries of synthesizable chemicals like Enamine Real.
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nuadox · 1 year ago
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This AI model directly compares the properties of prospective new pharmaceuticals
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- By Nuadox Crew -
Researchers at Duke University have developed an AI platform named DeepDelta that compares molecules autonomously, learning from their variations to predict crucial property differences.
This tool aims to enhance the efficiency of designing pharmaceuticals and other chemicals by providing a more accurate means for researchers to understand and predict various molecular properties.
Traditionally, machine learning in this field focused on evaluating one molecule's properties at a time, limiting efficiency. DeepDelta stands out by simultaneously comparing two molecules, learning from their structural differences to predict their respective properties.
It outperforms existing models in predicting differences in ten essential molecular properties related to drug development, offering more accuracy and efficiency.
This innovation could revolutionize drug design by aiding in identifying safer and more effective therapeutic compounds. Its ability to compare molecules and predict properties efficiently could potentially save time and money in drug development by identifying compounds with desirable attributes and fewer adverse effects like liver toxicity.
--
Source: Duke University
Full study: Zachary Fralish et al, DeepDelta: predicting ADMET improvements of molecular derivatives with deep learning, Journal of Cheminformatics (2023). DOI: 10.1186/s13321-023-00769-x
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clcpapers · 1 year ago
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Cheminformatics approach for identification of N-HyMenatPimeMelly as a novel potential ligand against RAS and renal chloride channel
http://dlvr.it/Sy0LJB
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kenyatta · 3 years ago
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We are but one very small company in a universe of many hundreds of companies using AI software for drug discovery and de novo design. How many of them have even considered repurposing, or misuse, possibilities? Most will work on small molecules, and many of the companies are very well funded and likely using the global chemistry network to make their AI-designed molecules. How many people have the know-how to find the pockets of chemical space that can be filled with molecules predicted to be orders of magnitude more toxic than VX? We do not currently have answers to these questions.
There has not previously been significant discussion in the scientific community about this dual-use concern around the application of AI for de novo molecule design, at least not publicly. Discussion of societal impacts of AI has principally focused on aspects such as safety, privacy, discrimination and potential criminal misuse, but not on national and international security. When we think of drug discovery, we normally do not consider technology misuse potential. We are not trained to consider it, and it is not even required for machine learning research, but we can now share our experience with other companies and individuals.
AI generative machine learning tools are equally applicable to larger molecules (peptides, macrolactones, etc.) and to other industries, such as consumer products and agrochemicals, that also have interests in designing and making new molecules with specific physicochemical and biological properties. This greatly increases the breadth of the potential audience that should be paying attention to these concerns.
For us, the genie is out of the medicine bottle when it comes to repurposing our machine learning. We must now ask: what are the implications? Our own commercial tools, as well as open-source software tools and many datasets that populate public databases, are available with no oversight. If the threat of harm, or actual harm, occurs with ties back to machine learning, what impact will this have on how this technology is perceived? Will hype in the press on AI-designed drugs suddenly flip to concern about AI-designed toxins, public shaming and decreased investment in these technologies? As a field, we should open a conversation on this topic.
- Dual use of artificial-intelligence-powered drug discovery by Fabio Urbina, Filippa Lentzos, Cédric Invernizzi & Sean Ekins, Nature Machine Intelligence (2022)
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mahnoorz · 4 years ago
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2020.05.27
Yup... I tried the famous French macaroon... Ofcourse the supermarket ones. Still... Delicious and it was the first time I tried.
I had a meeting with the postdoc I am working under. She was really happy with my progress and provided me with great feedback.
I also gave German quiz and scored 15/16... Pretty good haan... But to be honest, it was easy.
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