Amortized Inference for Heterogeneous Reconstruction in Cryo-EM

Cryo-electron microscopy (cryo-EM) is an imaging modality that provides unique insights into the dynamics of proteins and other building blocks of life. The algorithmic challenge of jointly estimating the poses, 3D structure, and conformational heterogeneity of a biomolecule from millions of noisy and randomly oriented 2D projections in a computationally efficient manner, however, remains unsolved. Our method, cryoFIRE, performs ab initio heterogeneous reconstruction with unknown poses in an amortized framework, thereby avoiding the computationally expensive step of pose search while enabling the analysis of conformational heterogeneity. Poses and conformation are jointly estimated by an encoder while a physics-based decoder aggregates the images into an implicit neural representation of the conformational space. We show that our method can provide one order of magnitude speedup on datasets containing millions of images without any loss of accuracy. We validate that the joint estimation of poses and conformations can be amortized over the size of the dataset. For the first time, we prove that an amortized method can extract interpretable dynamic information from experimental datasets.

Query Expansion Using Contextual Clue Sampling with Language Models

Query expansion is an effective approach for mitigating vocabulary mismatch between queries and documents in information retrieval. One recent line of research uses language models to generate query-related contexts for expansion. Along this line, we argue that expansion terms from these contexts should balance two key aspects: diversity and relevance. The obvious way to increase diversity is to sample multiple contexts from the language model. However, this comes at the cost of relevance, because there is a well-known tendency of models to hallucinate incorrect or irrelevant contexts. To balance these two considerations, we propose a combination of an effective filtering strategy and fusion of the retrieved documents based on the generation probability of each context. Our lexical matching based approach achieves a similar top-5/top-20 retrieval accuracy and higher top-100 accuracy compared with the well-established dense retrieval model DPR, while reducing the index size by more than 96%. For end-to-end QA, the reader model also benefits from our method and achieves the highest Exact-Match score against several competitive baselines.

Threshold Treewidth and Hypertree Width

Treewidth and hypertree width have proven to be highly successful structural parameters in the context of the Constraint Satisfaction Problem (CSP). When either of these parameters is bounded by a constant, then CSP becomes solvable in polynomial time. However, here the order of the polynomial in the running time depends on the width, and this is known to be unavoidable; therefore, the problem is not fixed-parameter tractable parameterized by either of these width measures. Here we introduce an enhancement of tree and hypertree width through a novel notion of thresholds, allowing the associated decompositions to take into account information about the computational costs associated with solving the given CSP instance. Aside from introducing these notions, we obtain efficient theoretical as well as empirical algorithms for computing threshold treewidth and hypertree width and show that these parameters give rise to fixed-parameter algorithms for CSP as well as other, more general problems. We complement our theoretical results with experimental evaluations in terms of heuristics as well as exact methods based on SAT/SMT encodings.

Sapling Similarity outperforms other local similarity metrics in collaborative filtering

Many bipartite networks describe systems where a link represents a relation between a user and an item. Measuring the similarity between either users or items is the basis of memory-based collaborative filtering, a widely used method to build a recommender system with the purpose of proposing items to users. When the edges of the network are unweighted, traditional approaches allow only positive similarity values, so neglecting the possibility and the effect of two users (or two items) being very dissimilar. Here we propose a method to compute similarity that allows also negative values, the Sapling Similarity. The key idea is to look at how the information that a user is connected to an item influences our prior estimation of the probability that another user is connected to the same item: if it is reduced, then the similarity between the two users will be negative, otherwise it will be positive. Using different datasets, we show that the Sapling Similarity outperforms other similarity metrics when it is used to recommend new items to users.

Interpreting Neural Policies with Disentangled Tree Representations

Compact neural networks used in policy learning and closed-loop end-to-end control learn representations from data that encapsulate agent dynamics and potentially the agent-environment's factors of variation. A formal and quantitative understanding and interpretation of these explanatory factors in neural representations is difficult to achieve due to the complex and intertwined correspondence of neural activities with emergent behaviors. In this paper, we design a new algorithm that programmatically extracts tree representations from compact neural policies, in the form of a set of logic programs grounded by the world state. To assess how well networks uncover the dynamics of the task and their factors of variation, we introduce interpretability metrics that measure the disentanglement of learned neural dynamics from a concentration of decisions, mutual information, and modularity perspectives. Moreover, our method allows us to quantify how accurate the extracted decision paths (explanations) are and computes cross-neuron logic conflict. We demonstrate the effectiveness of our approach with several types of compact network architectures on a series of end-to-end learning to control tasks.

Virtual-Reality based Vestibular Ocular Motor Screening for Concussion Detection using Machine-Learning

Sport-related concussion (SRC) depends on sensory information from visual, vestibular, and somatosensory systems. At the same time, the current clinical administration of Vestibular/Ocular Motor Screening (VOMS) is subjective and deviates among administrators. Therefore, for the assessment and management of concussion detection, standardization is required to lower the risk of injury and increase the validation among clinicians. With the advancement of technology, virtual reality (VR) can be utilized to advance the standardization of the VOMS, increasing the accuracy of testing administration and decreasing overall false positive rates. In this paper, we experimented with multiple machine learning methods to detect SRC on VR-generated data using VOMS. In our observation, the data generated from VR for smooth pursuit (SP) and the Visual Motion Sensitivity (VMS) tests are highly reliable for concussion detection. Furthermore, we train and evaluate these models, both qualitatively and quantitatively. Our findings show these models can reach high true-positive-rates of around 99.9 percent of symptom provocation on the VR stimuli-based VOMS vs. current clinical manual VOMS.

Textual Entailment Recognition with Semantic Features from Empirical Text Representation

Textual entailment recognition is one of the basic natural language understanding(NLU) tasks. Understanding the meaning of sentences is a prerequisite before applying any natural language processing(NLP) techniques to automatically recognize the textual entailment. A text entails a hypothesis if and only if the true value of the hypothesis follows the text. Classical approaches generally utilize the feature value of each word from word embedding to represent the sentences. In this paper, we propose a novel approach to identifying the textual entailment relationship between text and hypothesis, thereby introducing a new semantic feature focusing on empirical threshold-based semantic text representation. We employ an element-wise Manhattan distance vector-based feature that can identify the semantic entailment relationship between the text-hypothesis pair. We carried out several experiments on a benchmark entailment classification(SICK-RTE) dataset. We train several machine learning(ML) algorithms applying both semantic and lexical features to classify the text-hypothesis pair as entailment, neutral, or contradiction. Our empirical sentence representation technique enriches the semantic information of the texts and hypotheses found to be more efficient than the classical ones. In the end, our approach significantly outperforms known methods in understanding the meaning of the sentences for the textual entailment classification task.

Joint Multilingual Knowledge Graph Completion and Alignment

Knowledge graph (KG) alignment and completion are usually treated as two independent tasks. While recent work has leveraged entity and relation alignments from multiple KGs, such as alignments between multilingual KGs with common entities and relations, a deeper understanding of the ways in which multilingual KG completion (MKGC) can aid the creation of multilingual KG alignments (MKGA) is still limited. Motivated by the observation that structural inconsistencies -- the main challenge for MKGA models -- can be mitigated through KG completion methods, we propose a novel model for jointly completing and aligning knowledge graphs. The proposed model combines two components that jointly accomplish KG completion and alignment. These two components employ relation-aware graph neural networks that we propose to encode multi-hop neighborhood structures into entity and relation representations. Moreover, we also propose (i) a structural inconsistency reduction mechanism to incorporate information from the completion into the alignment component, and (ii) an alignment seed enlargement and triple transferring mechanism to enlarge alignment seeds and transfer triples during KGs alignment. Extensive experiments on a public multilingual benchmark show that our proposed model outperforms existing competitive baselines, obtaining new state-of-the-art results on both MKGC and MKGA tasks. We publicly release the implementation of our model at https://github.com/vinhsuhi/JMAC

DAGAD: Data Augmentation for Graph Anomaly Detection

Graph anomaly detection in this paper aims to distinguish abnormal nodes that behave differently from the benign ones accounting for the majority of graph-structured instances. Receiving increasing attention from both academia and industry, yet existing research on this task still suffers from two critical issues when learning informative anomalous behavior from graph data. For one thing, anomalies are usually hard to capture because of their subtle abnormal behavior and the shortage of background knowledge about them, which causes severe anomalous sample scarcity. Meanwhile, the overwhelming majority of objects in real-world graphs are normal, bringing the class imbalance problem as well. To bridge the gaps, this paper devises a novel Data Augmentation-based Graph Anomaly Detection (DAGAD) framework for attributed graphs, equipped with three specially designed modules: 1) an information fusion module employing graph neural network encoders to learn representations, 2) a graph data augmentation module that fertilizes the training set with generated samples, and 3) an imbalance-tailored learning module to discriminate the distributions of the minority (anomalous) and majority (normal) classes. A series of experiments on three datasets prove that DAGAD outperforms ten state-of-the-art baseline detectors concerning various mostly-used metrics, together with an extensive ablation study validating the strength of our proposed modules.

Rethinking Prototypical Contrastive Learning through Alignment, Uniformity and Correlation

Contrastive self-supervised learning (CSL) with a prototypical regularization has been introduced in learning meaningful representations for downstream tasks that require strong semantic information. However, to optimize CSL with a loss that performs the prototypical regularization aggressively, e.g., the ProtoNCE loss, might cause the "coagulation" of examples in the embedding space. That is, the intra-prototype diversity of samples collapses to trivial solutions for their prototype being well-separated from others. Motivated by previous works, we propose to mitigate this phenomenon by learning Prototypical representation through Alignment, Uniformity and Correlation (PAUC). Specifically, the ordinary ProtoNCE loss is revised with: (1) an alignment loss that pulls embeddings from positive prototypes together; (2) a uniformity loss that distributes the prototypical level features uniformly; (3) a correlation loss that increases the diversity and discriminability between prototypical level features. We conduct extensive experiments on various benchmarks where the results demonstrate the effectiveness of our method in improving the quality of prototypical contrastive representations. Particularly, in the classification down-stream tasks with linear probes, our proposed method outperforms the state-of-the-art instance-wise and prototypical contrastive learning methods on the ImageNet-100 dataset by 2.96% and the ImageNet-1K dataset by 2.46% under the same settings of batch size and epochs.