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Labeling neural network submodules with human-legible descriptions is useful for many downstream tasks: such descriptions can surface failures, guide interventions, and perhaps even explain important model behaviors. To date, most mechanistic descriptions of trained networks have involved small models, narrowly delimited phenomena, and large amounts of human labor. Labeling all human-interpretable sub-computations in models of increasing size and complexity will almost certainly require tools that can generate and validate descriptions automatically. Recently, techniques that use learned models in-the-loop for labeling have begun to gain traction, but methods for evaluating their efficacy are limited and ad-hoc. How should we validate and compare open-ended labeling tools? This paper introduces FIND (Function INterpretation and Description), a benchmark suite for evaluating the building blocks of automated interpretability methods. FIND contains functions that resemble components of trained neural networks, and accompanying descriptions of the kind we seek to generate. The functions are procedurally constructed across textual and numeric domains, and involve a range of real-world complexities, including noise, composition, approximation, and bias. We evaluate new and existing methods that use language models (LMs) to produce code-based and language descriptions of function behavior. We find that an off-the-shelf LM augmented with only black-box access to functions can sometimes infer their structure, acting as a scientist by forming hypotheses, proposing experiments, and updating descriptions in light of new data. However, LM-based descriptions tend to capture global function behavior and miss local corruptions. These results show that FIND will be useful for characterizing the performance of more sophisticated interpretability methods before they are applied to real-world models.

Many downstream inference tasks for knowledge graphs, such as relation prediction, have been handled successfully by knowledge graph embedding techniques in the transductive setting. To address the inductive setting wherein new entities are introduced into the knowledge graph at inference time, more recent work opts for models which learn implicit representations of the knowledge graph through a complex function of a network's subgraph structure, often parametrized by graph neural network architectures. These come at the cost of increased parametrization, reduced interpretability and limited generalization to other downstream inference tasks. In this work, we bridge the gap between traditional transductive knowledge graph embedding approaches and more recent inductive relation prediction models by introducing a generalized form of harmonic extension which leverages representations learned through transductive embedding methods to infer representations of new entities introduced at inference time as in the inductive setting. This harmonic extension technique provides the best such approximation, can be implemented via an efficient iterative scheme, and can be employed to answer a family of conjunctive logical queries over the knowledge graph, further expanding the capabilities of transductive embedding methods. In experiments on a number of large-scale knowledge graph embedding benchmarks, we find that this approach for extending the functionality of transductive knowledge graph embedding models to perform knowledge graph completion and answer logical queries in the inductive setting is competitive with--and in some scenarios outperforms--several state-of-the-art models derived explicitly for such inductive tasks.

With the fast-growing and evolving omics data, the demand for streamlined and adaptable tools to handle the analysis continues to grow. In response to this need, we introduce Auto Bioinformatics Analysis (AutoBA), an autonomous AI agent based on a large language model designed explicitly for conventional omics data analysis. AutoBA simplifies the analytical process by requiring minimal user input while delivering detailed step-by-step plans for various bioinformatics tasks. Through rigorous validation by expert bioinformaticians, AutoBA's robustness and adaptability are affirmed across a diverse range of omics analysis cases, including whole genome sequencing (WGS), RNA sequencing (RNA-seq), single-cell RNA-seq, ChIP-seq, and spatial transcriptomics. AutoBA's unique capacity to self-design analysis processes based on input data variations further underscores its versatility. Compared with online bioinformatic services, AutoBA deploys the analysis locally, preserving data privacy. Moreover, different from the predefined pipeline, AutoBA has adaptability in sync with emerging bioinformatics tools. Overall, AutoBA represents a convenient tool, offering robustness and adaptability for complex omics data analysis.

Composed image retrieval, a task involving the search for a target image using a reference image and a complementary text as the query, has witnessed significant advancements owing to the progress made in cross-modal modeling. Unlike the general image-text retrieval problem with only one alignment relation, i.e., image-text, we argue for the existence of two types of relations in composed image retrieval. The explicit relation pertains to the reference image & complementary text-target image, which is commonly exploited by existing methods. Besides this intuitive relation, the observations during our practice have uncovered another implicit yet crucial relation, i.e., reference image & target image-complementary text, since we found that the complementary text can be inferred by studying the relation between the target image and the reference image. Regrettably, existing methods largely focus on leveraging the explicit relation to learn their networks, while overlooking the implicit relation. In response to this weakness, We propose a new framework for composed image retrieval, termed dual relation alignment, which integrates both explicit and implicit relations to fully exploit the correlations among the triplets. Specifically, we design a vision compositor to fuse reference image and target image at first, then the resulted representation will serve two roles: (1) counterpart for semantic alignment with the complementary text and (2) compensation for the complementary text to boost the explicit relation modeling, thereby implant the implicit relation into the alignment learning. Our method is evaluated on two popular datasets, CIRR and FashionIQ, through extensive experiments. The results confirm the effectiveness of our dual-relation learning in substantially enhancing composed image retrieval performance.

We derive optimality conditions for the optimum sample allocation problem in stratified sampling, formulated as the determination of the fixed strata sample sizes that minimize the total cost of the survey, under the assumed level of variance of the stratified $\pi$ estimator of the population total (or mean) and one-sided upper bounds imposed on sample sizes in strata. In this context, we presume that the variance function is of some generic form that, in particular, covers the case of the simple random sampling without replacement design in strata. The optimality conditions mentioned above will be derived from the Karush-Kuhn-Tucker conditions. Based on the established optimality conditions, we provide a formal proof of the optimality of the existing procedure, termed here as LRNA, which solves the allocation problem considered. We formulate the LRNA in such a way that it also provides the solution to the classical optimum allocation problem (i.e. minimization of the estimator's variance under a fixed total cost) under one-sided lower bounds imposed on sample sizes in strata. In this context, the LRNA can be considered as a counterparty to the popular recursive Neyman allocation procedure that is used to solve the classical problem of an optimum sample allocation with added one-sided upper bounds. Ready-to-use R-implementation of the LRNA is available through our stratallo package, which is published on the Comprehensive R Archive Network (CRAN) package repository.

Regularized m-estimators are widely used due to their ability of recovering a low-dimensional model in high-dimensional scenarios. Some recent efforts on this subject focused on creating a unified framework for establishing oracle bounds, and deriving conditions for support recovery. Under this same framework, we propose a new Generalized Information Criteria (GIC) that takes into consideration the sparsity pattern one wishes to recover. We obtain non-asymptotic model selection bounds and sufficient conditions for model selection consistency of the GIC. Furthermore, we show that the GIC can also be used for selecting the regularization parameter within a regularized $m$-estimation framework, which allows practical use of the GIC for model selection in high-dimensional scenarios. We provide examples of group LASSO in the context of generalized linear regression and low rank matrix regression.

Cellwise outliers are widespread in data and traditional robust methods may fail when applied to datasets under such contamination. We propose a variable selection procedure, that uses a pairwise robust estimator to obtain an initial empirical covariance matrix among the response and potentially many predictors. Then we replace the primary design matrix and the response vector with their robust counterparts based on the estimated covariance matrix. Finally, we adopt the adaptive Lasso to obtain variable selection results. The proposed approach is robust to cellwise outliers in regular and high dimensional settings and empirical results show good performance in comparison with recently proposed alternative robust approaches, particularly in the challenging setting when contamination rates are high but the magnitude of outliers is moderate. Real data applications demonstrate the practical utility of the proposed method.

Mediation analysis learns the causal effect transmitted via mediator variables between treatments and outcomes and receives increasing attention in various scientific domains to elucidate causal relations. Most existing works focus on point-exposure studies where each subject only receives one treatment at a single time point. However, there are a number of applications (e.g., mobile health) where the treatments are sequentially assigned over time and the dynamic mediation effects are of primary interest. Proposing a reinforcement learning (RL) framework, we are the first to evaluate dynamic mediation effects in settings with infinite horizons. We decompose the average treatment effect into an immediate direct effect, an immediate mediation effect, a delayed direct effect, and a delayed mediation effect. Upon the identification of each effect component, we further develop robust and semi-parametrically efficient estimators under the RL framework to infer these causal effects. The superior performance of the proposed method is demonstrated through extensive numerical studies, theoretical results, and an analysis of a mobile health dataset.

Embedding entities and relations into a continuous multi-dimensional vector space have become the dominant method for knowledge graph embedding in representation learning. However, most existing models ignore to represent hierarchical knowledge, such as the similarities and dissimilarities of entities in one domain. We proposed to learn a Domain Representations over existing knowledge graph embedding models, such that entities that have similar attributes are organized into the same domain. Such hierarchical knowledge of domains can give further evidence in link prediction. Experimental results show that domain embeddings give a significant improvement over the most recent state-of-art baseline knowledge graph embedding models.

Benefit from the quick development of deep learning techniques, salient object detection has achieved remarkable progresses recently. However, there still exists following two major challenges that hinder its application in embedded devices, low resolution output and heavy model weight. To this end, this paper presents an accurate yet compact deep network for efficient salient object detection. More specifically, given a coarse saliency prediction in the deepest layer, we first employ residual learning to learn side-output residual features for saliency refinement, which can be achieved with very limited convolutional parameters while keep accuracy. Secondly, we further propose reverse attention to guide such side-output residual learning in a top-down manner. By erasing the current predicted salient regions from side-output features, the network can eventually explore the missing object parts and details which results in high resolution and accuracy. Experiments on six benchmark datasets demonstrate that the proposed approach compares favorably against state-of-the-art methods, and with advantages in terms of simplicity, efficiency (45 FPS) and model size (81 MB).