META2 improves taxonomic classification and abundance estimation in metagenomics with deep learning and memory efficiency.
problem Memory constraints and inefficiencies in taxonomic classification and abundance estimation for metagenomics.
method Developed a novel memory-efficient read classification technique combining deep learning and locality-sensitive hashing, and formulated abundance estimation as a Multiple Instance Learning problem.
result Our approach outperforms conventional methods in both single-read taxonomic classification and abundance estimation, especially when memory is limited.
The step of expert taxa recognition currently slows down the response time of many bioassessments. Shifting to quicker and cheaper state-of-the-art machine learning approaches is still met with expert scepticism towards the ability and logic of machines. In our study, we investigate both the differences in accuracy and…
Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is assigned to a taxonomic clade. Due to the large volume of metagenomics datasets,…
Knowledge graphs are used to represent relational information in terms of triples. To enable learning about domains, embedding models, such as tensor factorization models, can be used to make predictions of new triples. Often there is background taxonomic information (in terms of subclasses and subproperties) that shou…
Traditional disease surveillance can be augmented with a wide variety of real-time sources such as, news and social media. However, these sources are in general unstructured and, construction of surveillance tools such as taxonomical correlations and trace mapping involves considerable human supervision. In this paper,…
Image classification system identifies bumble bee species from images.
problem Manual identification of bumble bee species is time-consuming and requires expert knowledge.
method Transfer learning using Inception, VGG16, VGG19, and ResNet models.
result Inception and VGG classifiers achieved up to 23% accuracy for single species identification.
Vision models are interpretable when they classify objects on the basis of features that a person can directly understand. Recently, methods relying on visual feature prototypes have been developed for this purpose. However, in contrast to how humans categorize objects, these approaches have not yet made use of any tax…
Generative model for high-dimensional categorical data using Gaussian-Dirichlet fields.
problem Efficiently modeling and predicting high-dimensional categorical data.
method Combines Dirichlet and Gaussian processes for spatio-temporal modeling.
result Model accurately approximates categorical data in unobserved locations.
To study how mental object representations are related to behavior, we estimated sparse, non-negative representations of objects using human behavioral judgments on images representative of 1,854 object categories. These representations predicted a latent similarity structure between objects, which captured most of the…
Pruning unimportant parameters can allow deep neural networks (DNNs) to reduce their heavy computation and memory requirements. A saliency metric estimates which parameters can be safely pruned with little impact on the classification performance of the DNN. Many saliency metrics have been proposed, each within the con…
We introduce a method to provide vectorial representations of visual classification tasks which can be used to reason about the nature of those tasks and their relations. Given a dataset with ground-truth labels and a loss function defined over those labels, we process images through a "probe network" and compute an em…
ProGen models protein sequences for synthetic biology.
problem Generating proteins without structural annotations.
method Trained a 1.2B-parameter language model on 280M protein sequences.
result ProGen generates proteins with fine-grained control and accuracy.
Adaptive and sequential experiment design is a well-studied area in numerous domains. We survey and synthesize the work of the online statistical learning paradigm referred to as multi-armed bandits integrating the existing research as a resource for a certain class of online experiments. We first explore the tradition…
Artificial neural networks (ANNs) have achieved significant success in tackling classical and modern machine learning problems. As learning problems grow in scale and complexity, and expand into multi-disciplinary territory, a more modular approach for scaling ANNs will be needed. Modular neural networks (MNNs) are neu…
Semantic segmentation was seen as a challenging computer vision problem few years ago. Due to recent advancements in deep learning, relatively accurate solutions are now possible for its use in automated driving. In this paper, the semantic segmentation problem is explored from the perspective of automated driving. Mos…
Electronic health record (EHR) systems are used extensively throughout the healthcare domain. However, data interchangeability between EHR systems is limited due to the use of different coding standards across systems. Existing methods of mapping coding standards based on manual human experts mapping, dictionary mappin…
Study re-evaluates MIMIC-III codes, finding many are under-coded.
problem Validity of MIMIC-III clinical codes is questionable.
method Open-source, reproducible methodology for assessing codes.
result Most frequently assigned codes are under-coded up to 35%
AI enhances microbiology and microbiome research through machine learning.
problem Understanding microbial life and its impact on health and the environment.
method AI-driven approaches including machine learning and deep learning.
result Transformative role in enhancing microbial life understanding.
In a model extraction attack, an adversary steals a copy of a remotely deployed machine learning model, given oracle prediction access. We taxonomize model extraction attacks around two objectives: *accuracy*, i.e., performing well on the underlying learning task, and *fidelity*, i.e., matching the predictions of the r…
The paper introduces a method to control false splits in tree-based data aggregation.
problem Identifying the correct subgroups to treat as a single entity in tree-based data.
method Introduces the 'false split rate' and proposes a multiple hypothesis testing algorithm for tree-based aggregation.
result The proposed algorithm controls the false split rate, demonstrating its effectiveness on stock volatility and taxi fare data.
A model predicts how hyperparameters affect pruning performance.
problem Predicting the impact of hyperparameters on pruning performance.
method Phenomenological model using temperature-like and load-like parameters.
result A sharp transition phenomenon in pruning performance.
Adversarial examples are malicious inputs crafted to cause a model to misclassify them. Their most common instantiation, "perturbation-based" adversarial examples introduce changes to the input that leave its true label unchanged, yet result in a different model prediction. Conversely, "invariance-based" adversarial ex…
New statistical models for predicting ranked preferences from partial orders.
problem Statistical models overlook information in list length.
method Composite and augmented ranking models for joint modeling of partial orders and list lengths.
result Augmented ranking models best predict both length and preferences.
Machine learning predicts plant phenotypes from soil microbiome data.
problem Predicting plant phenotypes from soil microbiome data.
method Two models (random forest and Bayesian neural network) were used to predict plant phenotypes from soil properties and microbial population density.
result Human decisions and normalization strategies significantly impact model performance.
Framework uncovers symmetric and asymmetric species associations from data.
problem Retrieving bidirectional species associations from co-occurrence data.
method Machine learning framework modeling latent embeddings and joint generative model.
result Framework successfully recovers known symmetric and asymmetric associations.
DeepMaxent uses neural networks to improve species distribution models.
problem Sampling biases and lack of absence data in presence-only observations.
method DeepMaxent employs neural networks to learn shared features among species using the maximum entropy principle.
result DeepMaxent outperforms traditional methods in predicting species distributions, especially in unevenly sampled regions.
Dual-stage sEMG classification improves gesture recognition accuracy.
problem Improving accuracy in hand gesture recognition from sEMG signals.
method Dual-stage classification approach: first stage groups similar activities, second stage classifies within groups.
result Dual-stage classification yields significantly higher accuracy than single-stage approach.
A novel method for classification with rejection using ensemble of cost-sensitive classifiers.
problem Avoid risky misclassification in error-critical applications.
method Learning an ensemble of cost-sensitive classifiers.
result Improved classification accuracy and flexibility in loss selection.
The number of possible methods of generalizing binary classification to multi-class classification increases exponentially with the number of class labels. Often, the best method of doing so will be highly problem dependent. Here we present classification software in which the partitioning of multi-class classification…
Sequence classification is an important data mining task in many real world applications. Over the past few decades, many sequence classification methods have been proposed from different aspects. In particular, the pattern-based method is one of the most important and widely studied sequence classification methods in …
Few-shot image classification is improved by correcting CNNs' texture bias.
problem Few-shot image classification performance is hindered by CNNs' texture bias.
method Corrected CNNs' texture bias using a simpler method than state-of-the-art approaches.
result State-of-the-art performance on miniImageNet task achieved.
New NHCAs improve multi-category classification efficiency.
problem Efficient multi-category classification for real-world problems.
method Twin SVM (TWSVM), Generalized eigenvalue proximal SVM (GEPSVM), Regularized GEPSVM (RegGEPSVM), and Improved GEPSVM (IGEPSVM) with OAA, BT, and TDS approaches.
result TDS-TWSVM outperforms other methods in classification accuracy.
Paper compares XGB and BPNN for music style classification.
problem Efficient music style classification using different methods.
method Feature extraction for timbral texture, rhythmic content, and pitch content; comparative evaluation of XGB and BPNN.
result XGB outperforms BPNN for small datasets in music classification.
Classification outperforms regression in portfolio construction, yielding higher Sharpe ratios.
problem Determining which machine learning approach (classification vs. regression) is more effective for portfolio construction.
method Used stacking ensemble of gradient boosted tree, random forest, and neural network models.
result Classification yields higher Sharpe ratios and economically significant alphas compared to regression.
C-HMCNN(h) improves HMC classification by leveraging class hierarchy.
problem Hierarchical multi-label classification with class hierarchy constraints.
method Exploits class hierarchy to produce coherent predictions for multi-label classification.
result C-HMCNN(h) outperforms state-of-the-art models in HMC classification.
Advances few-shot classification by treating it as supervised learning and proposing new training techniques.
problem Formulating the ability of humans to learn from limited data in machine learning.
method Formulated few-shot classification as a supervised learning problem and introduced multi-episode and cross-way training techniques.
result Proposed training strategies accelerate the training process without accuracy loss.
Improves NILM with multi-label SRC, outperforming state-of-the-art.
problem Non-intrusive load monitoring (NILM) for energy disaggregation.
method Modified multi-label sparse representation based classification (SRC).
result Significant improvement over state-of-the-art techniques with minimal training data.
New approach improves classification guarantees by focusing on direction rather than regression risk.
problem Improving classification guarantees in binary classification problems.
method Establishing a geometric distinction between classification and regression, leveraging scale invariance.
result Improved guarantees for classification risk compared to regression risk.
We study realizations of Lie algebras by vector fields. A correspondence between classification of transitive local realizations and classification of subalgebras is generalized to the case of regular local realizations. A reasonable classification problem for general realizations is rigorously formulated and an algori…
Study selective classification with halfspaces, achieving error bounds under Gaussian distributions.
problem Modeling relationships in subsets of data defined by selection rules.
method Sparse linear classifiers for subsets defined by halfspaces, focusing on Gaussian feature distributions.
result First PAC-learning algorithm for homogeneous halfspace selectors with error guarantee $\bigO*{\sqrt{\mathrm{opt}}}$.
A new network-based high-level data classification method using betweenness centrality.
problem Traditional data classification techniques focus on physical features, while high-level classification considers semantic meaning.
method Proposes a network-based high-level classification technique using betweenness centrality.
result Competent classification performance in nine real datasets compared to traditional models.
This thesis evaluates text-based vs audio-based classification of mental health interviews.
problem Classifying psychiatric illness using text-based methods.
method Design and evaluate a text classification network on mental health interviews, using belabBERT.
result Text-based classification is a strong alternative to audio-based methods.
Study on error probability for classification of heavy-tailed renewal processes.
problem Error probability in classification of heavy-tailed renewal processes.
method Asymptotic expressions for Bhattacharyya bound on misclassification error probabilities.
result Obtained asymptotic expressions for misclassification error probabilities.
Directly compute classification by learning features with class scores.
problem Classification efficiency and accuracy on various datasets.
method PCA for feature encoding, supervised learning model with encoder-decoder structure.
result Effective classification performance on multiple datasets.
This review explores resampling techniques for imbalanced binary classification.
problem Imbalanced classes lead to poor prediction results in classification.
method Classical, cost-sensitive, and Neyman-Pearson paradigms with resampling techniques and classification methods.
result Complex dynamics among resampling techniques, base methods, metrics, and imbalance ratios.
Conventional techniques for supervised classification constrain the classification rules considered and use surrogate losses for classification 0-1 loss. Favored families of classification rules are those that enjoy parametric representations suitable for surrogate loss minimization, and low complexity properties suita…
This paper tackles tweet classification by identifying purpose and position.
problem Difficulties in determining user intention and attitude in short, informal tweets.
method Transformed tweet classification into a multi-label problem and applied a multi-label classification method with post-processing.
result The method effectively classifies tweet purpose and position, outperforming individual classification methods.
Text classification on drug SMILES strings yields competitive drug type classification results.
problem Classifying drug types using conventional text classification methods.
method Treated drug SMILES as sentences and applied basic NLP methods for classification.
result Competitive drug type classification results achieved.