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.
KEEL improves causal discovery with fuzzy knowledge and complex data.
Many machine learning tasks can be expressed as the transformation---or \emph{transduction}---of input sequences into output sequences: speech recognition, machine translation, protein secondary structure prediction and text-to-speech to name but a few. One of the key challenges in sequence transduction is learning to …
We present graph attention networks (GATs), novel neural network architectures that operate on graph-structured data, leveraging masked self-attentional layers to address the shortcomings of prior methods based on graph convolutions or their approximations. By stacking layers in which nodes are able to attend over thei…
Signaling proteins are an important topic in drug development due to the increased importance of finding fast, accurate and cheap methods to evaluate new molecular targets involved in specific diseases. The complexity of the protein structure hinders the direct association of the signaling activity with the molecular s…
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 …
Smoothed fitness landscape improves protein optimization.
Protein Thoughts interprets protein interactions with clear reasoning, improving prediction accuracy.
From social networks to protein complexes to disease genomes to visual data, hypergraphs are everywhere. However, the scope of research studying deep learning on hypergraphs is still quite sparse and nascent, as there has not yet existed an effective, unified framework for using hyperedge and vertex embeddings jointly …
Graph Neural Networks (GNNs) have been popularly used for analyzing non-Euclidean data such as social network data and biological data. Despite their success, the design of graph neural networks requires a lot of manual work and domain knowledge. In this paper, we propose a Graph Neural Architecture Search method (Grap…
BayReL learns molecular interactions across multi-omics data.
Nuclear magnetic resonance (NMR) spectroscopy is one of the leading techniques for protein studies. The method features a number of properties, allowing to explain macromolecular interactions mechanistically and resolve structures with atomic resolution. However, due to laborious data analysis, a full potential of NMR …
We present a machine learning framework for modeling protein dynamics. Our approach uses L1-regularized, reversible hidden Markov models to understand large protein datasets generated via molecular dynamics simulations. Our model is motivated by three design principles: (1) the requirement of massive scalability; (2) t…
Study on tradeoffs between mistakes and ERM oracle calls in online and transductive learning.
Perfect adaptation in systems is identified and tested using graphical tools.
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…
Examines WENDy-IRLS algorithm's noise robustness and efficiency in various differential equations.
We develop a technique for deriving data-dependent error bounds for transductive learning algorithms based on transductive Rademacher complexity. Our technique is based on a novel general error bound for transduction in terms of transductive Rademacher complexity, together with a novel bounding technique for Rademacher…
The paper establishes bounds for transductive learning using information theory.
Convolutional neural networks (CNNs) have achieved great success on grid-like data such as images, but face tremendous challenges in learning from more generic data such as graphs. In CNNs, the trainable local filters enable the automatic extraction of high-level features. The computation with filters requires a fixed …
Local regularization fails in transductive learning for some multiclass problems.
RG-VFM extends VFM to curved manifolds for better material and protein design.
New method uses sufficient statistics to infer causal relationships from observational data.
Improved mistake bounds for transductive online learning.
New method TLC improves transductive learning bounds.
We study the challenges of applying deep learning to gene expression data. We find experimentally that there exists non-linear signal in the data, however is it not discovered automatically given the noise and low numbers of samples used in most research. We discuss how gene interaction graphs (same pathway, protein-pr…
Transductive learning considers situations when a learner observes labelled training points and unlabelled test points with the final goal of giving correct answers for the test points. This paper introduces a new complexity measure for transductive learning called Permutational Rademacher Complexity (PRC) and …
The paper finds a fundamental trade-off between confidence and efficiency in transductive conformal prediction.
Transductive learning considers a training set of labeled samples and a test set of unlabeled samples, with the goal of best labeling that particular test set. Conversely, inductive learning considers a training set of labeled samples drawn iid from , with the goal of best labeling any future sample…
Extractive compression is a challenging natural language processing problem. This work contributes by formulating neural extractive compression as a parse tree transduction problem, rather than a sequence transduction task. Motivated by this, we introduce a deep neural model for learning structure-to-substructure tree …
Adversarial robust learning improved for transductive setting.
Proposes a framework for compositional generalization in language models.
Multi-group learners suffer a penalty in transductive learning.
Study shows transductive learning is equivalent to PAC learning for most natural loss functions.
The paper surveys recent extensions of the Long-Short Term Memory networks to handle tree structures from the perspective of learning non-trivial forms of isomorph structured transductions. It provides a discussion of modern TreeLSTM models, showing the effect of the bias induced by the direction of tree processing. An…
In this paper we consider the problem of graph-based transductive classification, and we are particularly interested in the directed graph scenario which is a natural form for many real world applications. Different from existing research efforts that either only deal with undirected graphs or circumvent directionality…
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…
Novel method identifies proteomic risk markers for Alzheimer disease.
Proposes a transductive matrix completion method with calibration for multi-task learning.
A new framework uses text descriptions to improve protein design.
New bounds improve graph node classification using optimal transport.
Most traditional online learning algorithms are based on variants of mirror descent or follow-the-leader. In this paper, we present an online algorithm based on a completely different approach, tailored for transductive settings, which combines "random playout" and randomized rounding of loss subgradients. As an applic…
Standard methods in supervised learning separate training and prediction: the model is fit independently of any test points it may encounter. However, can knowledge of the next test point be exploited to improve prediction accuracy? We address this question in the context of linear prediction, show…
PAC learning simplified as bipartite matching.
Deep learning models optimize protein sequences.
Mathematical pipeline identifies structural homology of knotted proteins.
We present transductive Boltzmann machines (TBMs), which firstly achieve transductive learning of the Gibbs distribution. While exact learning of the Gibbs distribution is impossible by the family of existing Boltzmann machines due to combinatorial explosion of the sample space, TBMs overcome the problem by adaptively …
We show two novel concentration inequalities for suprema of empirical processes when sampling without replacement, which both take the variance of the functions into account. While these inequalities may potentially have broad applications in learning theory in general, we exemplify their significance by studying the t…
TIM maximizes mutual information for few-shot learning, outperforming state-of-the-art methods.