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.
New method extracts biological concepts from cell microscopy images.
COMET learns concepts for few-shot learning, improving performance.
The technique of Formal Concept Analysis is applied to a dataset describing the traits of rodents, with the goal of identifying zoonotic disease carriers,or those species carrying infections that can spillover to cause human disease. The concepts identified among these species together provide rules-of-thumb about the …
This brief note highlights some basic concepts required toward understanding the evolution of machine learning and deep learning models. The note starts with an overview of artificial intelligence and its relationship to biological neuron that ultimately led to the evolution of todays intelligent models.
Deep neural networks (DNNs) transform stimuli across multiple processing stages to produce representations that can be used to solve complex tasks, such as object recognition in images. However, a full understanding of how they achieve this remains elusive. The complexity of biological neural networks substantially exc…
Evaluating, explaining, and visualizing high-level concepts in generative models, such as variational autoencoders (VAEs), is challenging in part due to a lack of known prediction classes that are required to generate saliency maps in supervised learning. While saliency maps may help identify relevant features (e.g., p…
Bioinformatics tools have been developed to interpret gene expression data at the gene set level, and these gene set based analyses improve the biologists' capability to discover functional relevance of their experiment design. While elucidating gene set individually, inter gene sets association is rarely taken into co…
The relationships between game theory and quantum mechanics let us propose certain quantization relationships through which we could describe and understand not only quantum but also classical, evolutionary and the biological systems that were described before through the replicator dynamics. Quantum mechanics could be…
There is a growing interest and literature on intrinsic motivations and open-ended learning in both cognitive robotics and machine learning on one side, and in psychology and neuroscience on the other. This paper aims to review some relevant contributions from the two literature threads and to draw links between them. …
Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been propos…
Optimal transport embedding learns feature sets efficiently.
Biclustering is an unsupervised data mining technique that aims to unveil patterns (biclusters) from gene expression data matrices. In the framework of this thesis, we propose new biclustering algorithms for microarray data. The latter is done using data mining techniques. The objective is to identify positively and ne…
This paper presents a constructive algorithm that achieves successful one-shot learning of hidden spike-patterns in a competitive detection task. It has previously been shown (Masquelier et al., 2008) that spike-timing-dependent plasticity (STDP) and lateral inhibition can result in neurons competitively tuned to repea…
MIK improves t-SNE's local structure preservation in biological sequence data.
Complex biological systems have been successfully modeled by biochemical and genetic interaction networks, typically gathered from high-throughput (HTP) data. These networks can be used to infer functional relationships between genes or proteins. Using the intuition that the topological role of a gene in a network rela…
Optimal algorithm selects biological models without prior info.
Inspired by the human visual perception system, hexagonal image processing in the context of machine learning deals with the development of image processing systems that combine the advantages of evolutionary motivated structures based on biological models. While conventional state-of-the-art image processing systems o…
An interesting toy model has recently been proposed on Schumpeterian economic dynamics by Thurner {\it et al.} following the idea of economist Joseph Schumpeter. Punctuated equilibrium dynamics is shown to emerge from this model and some detail analyses of the time series indicate SOC kind of behaviours. The focus in t…
Researchers develop flexible kernels for biological sequences with guaranteed reliability.
NESS improves neighbor embedding for smooth cell-state transitions in single-cell data.
New learning algorithm mimics biological neural networks.
SENA-discrepancy-VAE interprets latent causal factors in biological pathways.
Complex architectures of biological neural circuits, such as parallel processing pathways, has been behaviorally implicated in many cognitive studies. However, the theoretical consequences of circuit complexity on neural computation have only been explored in limited cases. Here, we introduce a mechanism by which direc…
Deep learning applied to biological data mining.
Several social, medical, engineering and biological challenges rely on discovering the functionality of networks from their structure and node metadata, when it is available. For example, in chemoinformatics one might want to detect whether a molecule is toxic based on structure and atomic types, or discover the resear…
Proposes a new method to better understand complex system interactions.
BDH model learns like the brain, rivaling Transformer performance.
Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and postgenomics data sets. Indeed, biological entities are not isolated, but are components of complex multi-level systems. We go one step further and advocate for the consideration of …
DCMIX learns channel importance for high content imaging.
Scalable GPLVM reduces complexity in scRNA-seq data, accounting for technical and biological confounders.
DeepSIBA predicts biological effects of chemical structures using graph neural networks.
A fundamental aspect of biological information processing is the ubiquity of sequence-function relationships -- functions that map the sequence of DNA, RNA, or protein to a biochemically relevant activity. Most sequence-function relationships in biology are quantitative, but only recently have experimental techniques f…
New methods improve uncertainty quantification in dynamic biological systems.
Proposes a novel network-based neighborhood regression for biological systems.
AR algorithm simplifies backpropagation with improved scalability and biological plausibility.
We solve a lifecycle model in which the consumer's chronological age does not move in lockstep with calendar time. Instead, biological age increases at a stochastic non-linear rate in time like a broken clock that might occasionally move backwards. In other words, biological age could actually decline. Our paper is ins…
In the brain, learning signals change over time and synaptic location, and are applied based on the learning history at the synapse, in the complex process of neuromodulation. Learning in artificial neural networks, on the other hand, is shaped by hyper-parameters set before learning starts, which remain static through…
Algorithm optimizes biological sequences using bootstrapped training with a score-conditioned generator.
Backpropagation is the workhorse of deep learning, however, several other biologically-motivated learning rules have been introduced, such as random feedback alignment and difference target propagation. None of these methods have produced a competitive performance against backpropagation. In this paper, we show that bi…
Fault-tolerant neural networks inspired by biological error correction codes.
Probabilistic graphical models (PGMs) have become a popular tool for computational analysis of biological data in a variety of domains. But, what exactly are they and how do they work? How can we use PGMs to discover patterns that are biologically relevant? And to what extent can PGMs help us formulate new hypotheses t…
VampPrior Mixture Model improves clustering in DLVMs.
Graph representations offer powerful and intuitive ways to describe data in a multitude of application domains. Here, we consider stochastic processes generating graphs and propose a methodology for detecting changes in stationarity of such processes. The methodology is general and considers a process generating attrib…
New learning rules for wide neural networks without backpropagation.
We present an analysis of the problem of identifying biological context and associating it with biochemical events in biomedical texts. This constitutes a non-trivial, inter-sentential relation extraction task. We focus on biological context as descriptions of the species, tissue type and cell type that are associated …
We introduce bio-inspired artificial neural networks consisting of neurons that are additionally characterized by spatial positions. To simulate properties of biological systems we add the costs penalizing long connections and the proximity of neurons in a two-dimensional space. Our experiments show that in the case wh…
Oja's rule improves neural network training without engineered tricks.
Graph auto-encoder predicts unobserved node features from biological networks and omics data.