We study multi-label prediction for structured output spaces, a problem that occurs, for example, in object detection in images, secondary structure prediction in computational biology, and graph matching with symmetries. Conventional multi-label classification techniques are typically not applicable in this situation, because they require explicit enumeration of the label space, which is infeasible in case of structured outputs. Relying on techniques originally designed for single- label structured prediction, in particular structured support vector machines, results in reduced prediction accuracy, or leads to infeasible optimization problems. In this work we derive a maximum-margin training formulation for multi-label structured prediction that remains computationally tractable while achieving high prediction accuracy. It also shares most beneficial properties with single-label maximum-margin approaches, in particular a formulation as a convex optimization problem, efficient working set training, and PAC-Bayesian generalization bounds.

Word embeddings that map words into a fixed-dimensional vector space are the backbone of modern NLP. Most word embedding methods encode semantic information. However, phonetic information, which is important for some tasks, is often overlooked. In this work, we develop several novel methods which leverage articulatory features to build phonetically informed word embeddings, and present a set of phonetic word embeddings to encourage their community development, evaluation and use. While several methods for learning phonetic word embeddings already exist, there is a lack of consistency in evaluating their effectiveness. Thus, we also proposes several ways to evaluate both intrinsic aspects of phonetic word embeddings, such as word retrieval and correlation with sound similarity, and extrinsic performances, such as rhyme and cognate detection and sound analogies. We hope that our suite of tasks will promote reproducibility and provide direction for future research on phonetic word embeddings.

Representation learning is an important step in the machine learning pipeline. Given the current biological sequencing data volume, learning an explicit representation is prohibitive due to the dimensionality of the resulting feature vectors. Kernel-based methods, e.g., SVM, are a proven efficient and useful alternative for several machine learning (ML) tasks such as sequence classification. Three challenges with kernel methods are (i) the computation time, (ii) the memory usage (storing an $n\times n$ matrix), and (iii) the usage of kernel matrices limited to kernel-based ML methods (difficult to generalize on non-kernel classifiers). While (i) can be solved using approximate methods, challenge (ii) remains for typical kernel methods. Similarly, although non-kernel-based ML methods can be applied to kernel matrices by extracting principal components (kernel PCA), it may result in information loss, while being computationally expensive. In this paper, we propose a general-purpose representation learning approach that embodies kernel methods' qualities while avoiding computation, memory, and generalizability challenges. This involves computing a low-dimensional embedding of each sequence, using random projections of its $k$-mer frequency vectors, significantly reducing the computation needed to compute the dot product and the memory needed to store the resulting representation. Our proposed fast and alignment-free embedding method can be used as input to any distance (e.g., $k$ nearest neighbors) and non-distance (e.g., decision tree) based ML method for classification and clustering tasks. Using different forms of biological sequences as input, we perform a variety of real-world classification tasks, such as SARS-CoV-2 lineage and gene family classification, outperforming several state-of-the-art embedding and kernel methods in predictive performance.

Extreme multilabel classification or XML, is an active area of interest in machine learning. Compared to traditional multilabel classification, here the number of labels is extremely large, hence, the name extreme multilabel classification. Using classical one versus all classification wont scale in this case due to large number of labels, same is true for any other classifiers. Embedding of labels as well as features into smaller label space is an essential first step. Moreover, other issues include existence of head and tail labels, where tail labels are labels which exist in relatively smaller number of given samples. The existence of tail labels creates issues during embedding. This area has invited application of wide range of approaches ranging from bit compression motivated from compressed sensing, tree based embeddings, deep learning based latent space embedding including using attention weights, linear algebra based embeddings such as SVD, clustering, hashing, to name a few. The community has come up with a useful set of metrics to identify correctly the prediction for head or tail labels.

We define the bigraded persistent homology modules and the bigraded barcodes of a finite pseudo-metric space X using the ordinary and double homology of the moment-angle complex associated with the Vietoris-Rips filtration of X. We prove the stability theorem for the bigraded persistent double homology modules and barcodes.

A critical challenge to image-text retrieval is how to learn accurate correspondences between images and texts. Most existing methods mainly focus on coarse-grained correspondences based on co-occurrences of semantic objects, while failing to distinguish the fine-grained local correspondences. In this paper, we propose a novel Scene Graph based Fusion Network (dubbed SGFN), which enhances the images'/texts' features through intra- and cross-modal fusion for image-text retrieval. To be specific, we design an intra-modal hierarchical attention fusion to incorporate semantic contexts, such as objects, attributes, and relationships, into images'/texts' feature vectors via scene graphs, and a cross-modal attention fusion to combine the contextual semantics and local fusion via contextual vectors. Extensive experiments on public datasets Flickr30K and MSCOCO show that our SGFN performs better than quite a few SOTA image-text retrieval methods.

As a present to Mizar on its 50th anniversary, we develop an AI/TP system that automatically proves about 60 % of the Mizar theorems in the hammer setting. We also automatically prove 75 % of the Mizar theorems when the automated provers are helped by using only the premises used in the human-written Mizar proofs. We describe the methods and large-scale experiments leading to these results. This includes in particular the E and Vampire provers, their ENIGMA and Deepire learning modifications, a number of learning-based premise selection methods, and the incremental loop that interleaves growing a corpus of millions of ATP proofs with training increasingly strong AI/TP systems on them. We also present a selection of Mizar problems that were proved automatically.

The recently proposed Joint Energy-based Model (JEM) interprets discriminatively trained classifier $p(y|x)$ as an energy model, which is also trained as a generative model describing the distribution of the input observations $p(x)$. The JEM training relies on "positive examples" (i.e. examples from the training data set) as well as on "negative examples", which are samples from the modeled distribution $p(x)$ generated by means of Stochastic Gradient Langevin Dynamics (SGLD). Unfortunately, SGLD often fails to deliver negative samples of sufficient quality during the standard JEM training, which causes a very unbalanced contribution from the positive and negative examples when calculating gradients for JEM updates. As a consequence, the standard JEM training is quite unstable requiring careful tuning of hyper-parameters and frequent restarts when the training starts diverging. This makes it difficult to apply JEM to different neural network architectures, modalities, and tasks. In this work, we propose a training procedure that stabilizes SGLD-based JEM training (ST-JEM) by balancing the contribution from the positive and negative examples. We also propose to add an additional "regularization" term to the training objective -- MI between the input observations $x$ and output labels $y$ -- which encourages the JEM classifier to make more certain decisions about output labels. We demonstrate the effectiveness of our approach on the CIFAR10 and CIFAR100 tasks. We also consider the task of classifying phonemes in a speech signal, for which we were not able to train JEM without the proposed stabilization. We show that a convincing speech can be generated from the trained model. Alternatively, corrupted speech can be de-noised by bringing it closer to the modeled speech distribution using a few SGLD iterations. We also propose and discuss additional applications of the trained model.

Recent advancements in explainable machine learning provide effective and faithful solutions for interpreting model behaviors. However, many explanation methods encounter efficiency issues, which largely limit their deployments in practical scenarios. Real-time explainer (RTX) frameworks have thus been proposed to accelerate the model explanation process by learning a one-feed-forward explainer. Existing RTX frameworks typically build the explainer under the supervised learning paradigm, which requires large amounts of explanation labels as the ground truth. Considering that accurate explanation labels are usually hard to obtain due to constrained computational resources and limited human efforts, effective explainer training is still challenging in practice. In this work, we propose a COntrastive Real-Time eXplanation (CoRTX) framework to learn the explanation-oriented representation and relieve the intensive dependence of explainer training on explanation labels. Specifically, we design a synthetic strategy to select positive and negative instances for the learning of explanation. Theoretical analysis show that our selection strategy can benefit the contrastive learning process on explanation tasks. Experimental results on three real-world datasets further demonstrate the efficiency and efficacy of our proposed CoRTX framework.

We present a general-purpose active learning scheme for data in metric spaces. The algorithm maintains a collection of neighborhoods of different sizes and uses label queries to identify those that have a strong bias towards one particular label; when two such neighborhoods intersect and have different labels, the region of overlap is treated as a ``known unknown'' and is a target of future active queries. We give label complexity bounds for this method that do not rely on assumptions about the data and we instantiate them in several cases of interest.