GEFA predicts drug-target affinity using graph neural networks.
problem Accurate prediction of drug-target interactions for rapid drug repurposing.
method GEFA (Graph Early Fusion Affinity) is a novel graph-in-graph neural network with attention mechanism.
result GEFA effectively models drug-target interactions, demonstrating the effectiveness of pre-trained protein embedding and nested graph representation.
PLUS pre-trains protein sequences with structural info, improving performance.
problem Lack of labeled protein sequences for training models.
method PLUS combines masked language modeling with same-family prediction for pre-training.
result PLUS-RNN outperforms other models in protein biology tasks.
Paper improves Tm prediction of protein fragments using sparsity and probabilistic models.
problem Improving accuracy of melting temperature prediction for protein fragments.
method Promoting sparsity in pre-trained transformer models and adopting probabilistic frameworks.
result Mean absolute error of 0.23C for predicting melting temperature.
CogMol designs novel drug-like molecules for SARS-CoV-2 targets.
problem Designing efficient drugs for novel viral proteins.
method End-to-end framework combining VAE, controlled sampling, and predictors.
result Highly selective and affinity molecules for SARS-CoV-2 targets.
PGEL learns embeddings to diversify protein motifs while maintaining biological function.
problem Generating diverse protein structures while preserving biological function.
method Embedding learning framework that enhances motif diversity in a diffusion model's frozen denoiser.
result PGEL achieves greater structural diversity, better designability, and improved self-consistency compared to partial diffusion.
Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for understanding function. Existing approaches for detecting structural similarity between prot…
Protein Thoughts interprets protein interactions with clear reasoning, improving prediction accuracy.
problem Lack of mechanistic justification in protein-protein interaction predictions.
method Interpretable search problem reformulation, hypothesis-guided entropy-regularized Tree-of-Thoughts search, embedding-space flow matching.
result Improves mean best-binder rank from 47.7 to 11.2 on SHS148k benchmark.
Graph embedding method captures both local and global network structure.
problem Representing and analyzing complex graph networks.
method Spectral embedding based on a generalized graph Laplacian.
result Significant improvement in data analysis tasks.
ProtTrans models predict protein features without evolutionary info.
problem Predicting protein features from amino acid sequences.
method Self-supervised deep learning on large protein datasets.
result ProtT5 embeddings outperform state-of-the-art for per-residue predictions.
Deep learning predicts protein structures accurately.
problem Predicting the 3D structure of proteins from amino acid sequences.
method Embeddings and deep learning models for backbone atom distance matrices and torsion angles.
result Competitive results in CASP13 and CASP12, surpassing previous winners.
The effective representation of proteins is a crucial task that directly affects the performance of many bioinformatics problems. Related proteins usually bind to similar ligands. Chemical characteristics of ligands are known to capture the functional and mechanistic properties of proteins suggesting that a ligand base…
Low-dimensional embeddings of nodes in large graphs have proved extremely useful in a variety of prediction tasks, from content recommendation to identifying protein functions. However, most existing approaches require that all nodes in the graph are present during training of the embeddings; these previous approaches …
Automated protein structure prediction from cryo-EM data.
problem Challenging to build atomic models from cryo-EM densities without prior structure.
method Uses GCN and LSTM to automate model building from amino acid identities and candidate locations.
result Automated approach reduces time and eliminates human intervention for protein structure determination.
Flexible Kernels for Protein Property Prediction
problem Predicting protein properties from sparse experimental data
method Sequence kernels using evolutionary substitution matrices and local linearity
result Data-efficient models of protein property landscapes
Many applications of machine learning require a model to make accurate pre-dictions on test examples that are distributionally different from training ones, while task-specific labels are scarce during training. An effective approach to this challenge is to pre-train a model on related tasks where data is abundant, and…
New Performer model tackles long-sequence protein modeling.
problem Challenges of training complex Transformer models for long sequences.
method Linearly scalable long-context Transformer architecture, Performer.
result Performer provides strong theoretical guarantees and is effective for protein sequence modeling.
Paper provides conditions for reliable use of pre-trained embeddings in econometrics.
problem Uncertainty in using pre-trained embeddings for econometric tasks.
method Derives sufficient conditions and convergence rates for machine learning models with pre-trained embeddings.
result Establishes theoretical foundations for reliable use of pre-trained embeddings in econometrics.
E-Stitchup augments pre-trained embeddings for better model performance and confidence calibration.
problem Improving classification accuracy and confidence calibration of models using pre-trained embeddings.
method Data augmentation methods inspired by Mixup combined with label softening.
result Significantly increased classification accuracy and reduced training time.
Knot theory applied to proteins, distinguishing folded linear chains.
problem Classifying proteins as unknots when intra-chain interactions are ignored.
method Developing knot theory for folded linear molecular chains, considering self-bonding, and using Gauss codes and quandles.
result Extended knot theory to distinguish topologies of proteins with intra-chain bonds.
Improved pre-trained embeddings through effective entropy maximization.
problem Developing high-quality pre-trained embeddings for future tasks.
method E2MC criterion defined in terms of low-dimensional constraints.
result Significant improvement in downstream performance.
POLAR framework interprets word embeddings using polar opposites.
problem Lack of interpretability in pre-trained word embeddings.
method Adopt semantic differentials and polar opposites to transform embeddings.
result Interpretable word embeddings maintain performance comparable to original embeddings.
Method curates cost-effective, high-quality datasets using AI models.
problem Costly manual labeling of datasets.
method Probably Approximately Correct Labels (PACL) method.
result Curates high-quality datasets with low overall labeling error.
Persistent homology provides a new, efficient molecular descriptor for protein dynamics.
problem Designing effective molecular descriptors for high-dimensional MD trajectories.
method Introduced masked Flood complex, a protein-tailored modification of simplicial complexes, for persistent homology.
result Persistent homology-based descriptors are competitive across protein dynamics tasks, including frame-level observable regression and MSM estimation.
Identification of high affinity drug-target interactions is a major research question in drug discovery. Proteins are generally represented by their structures or sequences. However, structures are available only for a small subset of biomolecules and sequence similarity is not always correlated with functional similar…
Unified model learns from proteins and ligands for drug design.
problem Disjoint data sources and modeling assumptions limit joint use of structure- and ligand-based drug design.
method Contrastive Geometric Learning for Unified Computational Drug Design (ConGLUDe)
result Unified model achieves competitive zero-shot virtual screening performance and state-of-the-art ligand-conditioned pocket selection.
Motivation: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy, and interpretability. Results: We present a seamless integration of domain knowledges and …
Protein modeling is an increasingly popular area of machine learning research. Semi-supervised learning has emerged as an important paradigm in protein modeling due to the high cost of acquiring supervised protein labels, but the current literature is fragmented when it comes to datasets and standardized evaluation tec…
Pre-training improves Bayesian optimization efficiency.
problem Optimizing complex machine learning models with hyperparameters.
method Pre-training a tighter Gaussian process prior from similar functions.
result 3 times more efficient hyperparameter tuning on average.
Transformer models improve query-document retrieval efficiency and accuracy.
problem Efficiently retrieve relevant documents from large corpora for query matching.
method Designed paragraph-level pre-training tasks to optimize embedding-based Transformer models.
result Transformer models significantly outperform BM-25 and non-Transformer embedding models.
Pre-trained GPs improve Bayesian optimization efficiency.
problem Optimizing complex machine learning models requires domain knowledge but is challenging.
method Developed HyperBO framework using pre-trained Gaussian processes.
result HyperBO achieves up to 3x better efficiency in hyperparameter tuning.
Interactive machine learning with weak supervision and pre-trained embeddings.
problem Training machine learning models with limited labeled data.
method Use pre-trained embeddings to define a distance function and extend source votes to nearby points.
result Significantly outperforms traditional weakly-supervised and fully-supervised methods.
Motivation: Understanding functions of proteins in specific human tissues is essential for insights into disease diagnostics and therapeutics, yet prediction of tissue-specific cellular function remains a critical challenge for biomedicine. Results: Here we present OhmNet, a hierarchy-aware unsupervised node feature le…
Author2Vec generates user embeddings from social media data.
problem Generating useful user embeddings from noisy social media data.
method End-to-end neural network with BERT sentence representations and unsupervised pre-training.
result Author2Vec outperforms traditional methods in user classification tasks.
Law explains how LLMs learn to predict next tokens.
problem Understanding how LLMs process input data internally.
method Introduced a precise law governing token embeddings in LLMs.
result Each layer equally contributes to next-token prediction accuracy.
Variational auto-encoder frameworks have demonstrated success in reducing complex nonlinear dynamics in molecular simulation to a single non-linear embedding. In this work, we illustrate how this non-linear latent embedding can be used as a collective variable for enhanced sampling, and present a simple modification th…
Enhanced word embeddings boost multiclass text classification accuracy.
problem Improving multiclass text classification accuracy using pre-trained embeddings.
method Proposed word-class embeddings (WCEs) to enhance pre-trained word embeddings.
result WCEs significantly improve multiclass text classification accuracy.
Proposes a thermodynamic work minimization framework for guiding generative models.
problem Guiding generative models in sparse-data regimes with limited target samples or constraints.
method Regularization framework inspired by thermodynamic work, introducing Path Guidance and Observable Guidance.
result Improves sample efficiency and reduces bias in molecular simulations.
Simplified image clustering achieves competitive results without text-based embeddings.
problem Complexity and resource requirements of state-of-the-art clustering methods.
method SCP: trains a small cluster head using pre-trained vision model features and positive data pairs.
result SCP achieves highly competitive performance on various benchmark datasets.
Low-dimensional embeddings of knowledge graphs and behavior graphs have proved remarkably powerful in varieties of tasks, from predicting unobserved edges between entities to content recommendation. The two types of graphs can contain distinct and complementary information for the same entities/nodes. However, previous…
Topic models are frequently used in machine learning owing to their high interpretability and modular structure. However, extending a topic model to include a supervisory signal, to incorporate pre-trained word embedding vectors and to include a nonlinear output function is not an easy task because one has to resort to…
A new framework uses text descriptions to improve protein design.
problem Lack of effective methods to incorporate textual descriptions in protein design.
method ProteinDT framework that combines text and protein structural information.
result ProteinDT significantly improves protein design accuracy and performance.
Researchers develop method to protect against 'weight poisoning' attacks on pre-trained models.
problem The security threat of downloading untrusted pre-trained weights that can be manipulated after fine-tuning.
method RIPPLe regularization method and Embedding Surgery initialization procedure.
result Demonstrated that weight poisoning attacks are possible even with limited knowledge of the dataset and fine-tuning procedure.
Deep learning models optimize protein sequences.
problem Optimizing protein properties through sequence design.
method Deep generative models guided by machine learning.
result Improved protein sequence generation from prior knowledge.
New method uses diffusion models for Bayesian inverse problems.
problem Solving Bayesian inverse problems with linear-Gaussian models.
method Decoupled Diffusion Sequential Monte Carlo (DDSMC) method.
result Asymptotically exact solution demonstrated on various data types.
Learning low-dimensional embeddings of knowledge graphs is a powerful approach used to predict unobserved or missing edges between entities. However, an open challenge in this area is developing techniques that can go beyond simple edge prediction and handle more complex logical queries, which might involve multiple un…
Protein interaction networks are a promising type of data for studying complex biological systems. However, despite the rich information embedded in these networks, they face important data quality challenges of noise and incompleteness that adversely affect the results obtained from their analysis. Here, we explore th…
Capturing sentence semantics plays a vital role in a range of text mining applications. Despite continuous efforts on the development of related datasets and models in the general domain, both datasets and models are limited in biomedical and clinical domains. The BioCreative/OHNLP organizers have made the first attemp…
Mathematical pipeline identifies structural homology of knotted proteins.
problem Quantification and classification of protein structures, especially knotted proteins, require noise-free and complete data.
method Developed a geometric framework using persistent homology to analyze protein structures.
result Persistent homology accurately represents structural homology of knotted proteins and identifies geometric features of protein entanglement.