A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
GEFA predicts drug-target affinity using graph neural networks.
Bridging the exponentially growing gap between the numbers of unlabeled and labeled protein sequences, several studies adopted semi-supervised learning for protein sequence modeling. In these studies, models were pre-trained with a substantial amount of unlabeled data, and the representations were transferred to variou…
Paper improves Tm prediction of protein fragments using sparsity and probabilistic models.
CogMol designs novel drug-like molecules for SARS-CoV-2 targets.
PGEL learns embeddings to diversify protein motifs while maintaining biological function.
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.
Graph embedding method captures both local and global network structure.
ProtTrans models predict protein features without evolutionary info.
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.
Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fundamental role in drug design. This motivates predicting the structure of a protein from its sequence of amino…
Flexible Kernels for Protein Property Prediction
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.
Paper provides conditions for reliable use of pre-trained embeddings in econometrics.
Proteins are linear molecular chains that often fold to function. The topology of folding is widely believed to define its properties and function, and knot theory has been applied to study protein structure and its implications. More that 97% of proteins are, however, classified as unknots when intra-chain interaction…
Improved pre-trained embeddings through effective entropy maximization.
We introduce POLAR - a framework that adds interpretability to pre-trained word embeddings via the adoption of semantic differentials. Semantic differentials are a psychometric construct for measuring the semantics of a word by analysing its position on a scale between two polar opposites (e.g., cold -- hot, soft -- ha…
Method curates cost-effective, high-quality datasets using AI models.
Persistent homology provides a new, efficient molecular descriptor for protein dynamics.
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.
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.
Pre-trained GPs improve Bayesian optimization efficiency.
We consider the large-scale query-document retrieval problem: given a query (e.g., a question), return the set of relevant documents (e.g., paragraphs containing the answer) from a large document corpus. This problem is often solved in two steps. The retrieval phase first reduces the solution space, returning a subset …
In this work, we propose data augmentation methods for embeddings from pre-trained deep learning models that take a weighted combination of a pair of input embeddings, as inspired by Mixup, and combine such augmentation with extra label softening. These methods are shown to significantly increase classification accurac…
Interactive machine learning with weak supervision and pre-trained embeddings.
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.
Law explains how LLMs learn to predict next tokens.
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…
Pre-trained word embeddings encode general word semantics and lexical regularities of natural language, and have proven useful across many NLP tasks, including word sense disambiguation, machine translation, and sentiment analysis, to name a few. In supervised tasks such as multiclass text classification (the focus of …
Proposes a thermodynamic work minimization framework for guiding generative models.
Simplified image clustering achieves competitive results without text-based embeddings.
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.
Deep learning models optimize protein sequences.
Researchers develop method to protect against 'weight poisoning' attacks on pre-trained models.
New method uses diffusion models for Bayesian inverse problems.
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…
Mathematical pipeline identifies structural homology of knotted proteins.
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…