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Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot be explained via a gene tree that both contains the depicted orthologs/paralogs, and that is consistent with a species tree $S$. This idea of detecting errors through inconsistency with a species tree has mostly been studied in the presence of speciation and duplication events only. In this work, we ask: could the given set of relations be consistent if we allow lateral gene transfers in the evolutionary model? We formalize this question and provide a variety of algorithmic results regarding the underlying problems. Namely, we show that deciding if a relation graph $R$ is consistent with a given species network $N$ is NP-hard, and that it is W[1]-hard under the parameter "minimum number of transfers". However, we present an FPT algorithm based on the degree of the $DS$-tree associated with $R$. We also study analogous problems in the case that the transfer highways on a species tree are unknown.

Today's scientific high performance computing (HPC) applications or advanced instruments are producing vast volumes of data across a wide range of domains, which introduces a serious burden on data transfer and storage. Error-bounded lossy compression has been developed and widely used in scientific community, because not only can it significantly reduce the data volumes but it can also strictly control the data distortion based on the use-specified error bound. Existing lossy compressors, however, cannot offer ultra-fast compression speed, which is highly demanded by quite a few applications or use-cases (such as in-memory compression and online instrument data compression). In this paper, we propose a novel ultra-fast error-bounded lossy compressor, which can obtain fairly high compression performance on both CPU and GPU, also with reasonably high compression ratios. The key contributions are three-fold: (1) We propose a novel, generic ultra-fast error-bounded lossy compression framework -- called UFZ, by confining our design to be composed of only super-lightweight operations such as bitwise and addition/subtraction operation, still keeping a certain high compression ratio. (2) We implement UFZ on both CPU and GPU and optimize the performance according to their architectures carefully. (3) We perform a comprehensive evaluation with 6 real-world production-level scientific datasets on both CPU and GPU. Experiments show that UFZ is 2~16X as fast as the second-fastest existing error-bounded lossy compressor (either SZ or ZFP) on CPU and GPU, with respect to both compression and decompression.

Neural compression algorithms are typically based on autoencoders that require specialized encoder and decoder architectures for different data modalities. In this paper, we propose COIN++, a neural compression framework that seamlessly handles a wide range of data modalities. Our approach is based on converting data to implicit neural representations, i.e. neural functions that map coordinates (such as pixel locations) to features (such as RGB values). Then, instead of storing the weights of the implicit neural representation directly, we store modulations applied to a meta-learned base network as a compressed code for the data. We further quantize and entropy code these modulations, leading to large compression gains while reducing encoding time by two orders of magnitude compared to baselines. We empirically demonstrate the effectiveness of our method by compressing various data modalities, from images to medical and climate data.

We present a polynomial-time algorithm that discovers all maximal patterns in a point set, $D\subset\mathbb{R}^k$, that are related by transformations in a user-specified class, $F$, of bijections over $\mathbb{R}^k$. We also present a second algorithm that discovers the set of occurrences for each of these maximal patterns and then uses compact encodings of these occurrence sets to compute a losslessly compressed encoding of the input point set. This encoding takes the form of a set of pairs, $E=\left\lbrace\left\langle P_1, T_1\right\rangle,\left\langle P_2, T_2\right\rangle,\ldots\left\langle P_{\ell}, T_{\ell}\right\rangle\right\rbrace$, where each $\langle P_i,T_i\rangle$ consists of a maximal pattern, $P_i\subseteq D$, and a set, $T_i\subset F$, of transformations that map $P_i$ onto other subsets of $D$. Each transformation is encoded by a vector of real values that uniquely identifies it within $F$ and the length of this vector is used as a measure of the complexity of $F$. We evaluate the new compression algorithm with three transformation classes of differing complexity, on the task of classifying folk-song melodies into tune families. The most complex of the classes tested includes all combinations of the musical transformations of transposition, inversion, retrograde, augmentation and diminution. We found that broadening the transformation class improved performance on this task. However, it did not, on average, improve compression factor, which may be due to the datasets (in this case, folk-song melodies) being too short and simple to benefit from the potentially greater number of pattern relationships that are discoverable with larger transformation classes.

In spite of considerable practical importance, current algorithmic fairness literature lacks technical methods to account for underlying geographic dependency while evaluating or mitigating bias issues for spatial data. We initiate the study of bias in spatial applications in this paper, taking the first step towards formalizing this line of quantitative methods. Bias in spatial data applications often gets confounded by underlying spatial autocorrelation. We propose hypothesis testing methodology to detect the presence and strength of this effect, then account for it by using a spatial filtering-based approach -- in order to enable application of existing bias detection metrics. We evaluate our proposed methodology through numerical experiments on real and synthetic datasets, demonstrating that in the presence of several types of confounding effects due to the underlying spatial structure our testing methods perform well in maintaining low type-II errors and nominal type-I errors.

In recent decades, the rapid growth of Internet adoption is offering opportunities for convenient and inexpensive access to scientific information. Wikipedia, one of the largest encyclopedias worldwide, has become a reference in this respect, and has attracted widespread attention from scholars. However, a clear understanding of the scientific sources underpinning Wikipedia's contents remains elusive. In this work, we rely on an open dataset of citations from Wikipedia to map the relationship between Wikipedia articles and scientific journal articles. We find that most journal articles cited from Wikipedia belong to STEM fields, in particular biology and medicine ($47.6$\% of citations; $46.1$\% of cited articles). Furthermore, Wikipedia's biographies play an important role in connecting STEM fields with the humanities, especially history. These results contribute to our understanding of Wikipedia's reliance on scientific sources, and its role as knowledge broker to the public.

Most data is automatically collected and only ever "seen" by algorithms. Yet, data compressors preserve perceptual fidelity rather than just the information needed by algorithms performing downstream tasks. In this paper, we characterize the bit-rate required to ensure high performance on all predictive tasks that are invariant under a set of transformations, such as data augmentations. Based on our theory, we design unsupervised objectives for training neural compressors. Using these objectives, we train a generic image compressor that achieves substantial rate savings (more than $1000\times$ on ImageNet) compared to JPEG on 8 datasets, without decreasing downstream classification performance.

Optimal $k$-thresholding algorithms are a class of sparse signal recovery algorithms that overcome the shortcomings of traditional hard thresholding algorithms caused by the oscillation of the residual function. In this paper, a novel convergence analysis for optimal $k$-thresholding algorithms is established, which reveals the data-time tradeoffs of these algorithms. Both the analysis and numerical results demonstrate that when the number of measurements is small, the algorithms cannot converge; when the number of measurements is suitably large, the number of iterations required for successful recovery has a negative correlation with the number of measurements, and the algorithms can achieve linear convergence. Furthermore, the main theorems indicate that the number of measurements required for successful recovery is on the order of $k \log({n}/{k})$, where $n$ is the dimension of the target signal.

This paper introduces video domain generalization where most video classification networks degenerate due to the lack of exposure to the target domains of divergent distributions. We observe that the global temporal features are less generalizable, due to the temporal domain shift that videos from other unseen domains may have an unexpected absence or misalignment of the temporal relations. This finding has motivated us to solve video domain generalization by effectively learning the local-relation features of different timescales that are more generalizable, and exploiting them along with the global-relation features to maintain the discriminability. This paper presents the VideoDG framework with two technical contributions. The first is a new deep architecture named the Adversarial Pyramid Network, which improves the generalizability of video features by capturing the local-relation, global-relation, and cross-relation features progressively. On the basis of pyramid features, the second contribution is a new and robust approach of adversarial data augmentation that can bridge different video domains by improving the diversity and quality of augmented data. We construct three video domain generalization benchmarks in which domains are divided according to different datasets, different consequences of actions, or different camera views, respectively. VideoDG consistently outperforms the combinations of previous video classification models and existing domain generalization methods on all benchmarks.

Referring expression comprehension aims to locate the object instance described by a natural language referring expression in an image. This task is compositional and inherently requires visual reasoning on top of the relationships among the objects in the image. Meanwhile, the visual reasoning process is guided by the linguistic structure of the referring expression. However, existing approaches treat the objects in isolation or only explore the first-order relationships between objects without being aligned with the potential complexity of the expression. Thus it is hard for them to adapt to the grounding of complex referring expressions. In this paper, we explore the problem of referring expression comprehension from the perspective of language-driven visual reasoning, and propose a dynamic graph attention network to perform multi-step reasoning by modeling both the relationships among the objects in the image and the linguistic structure of the expression. In particular, we construct a graph for the image with the nodes and edges corresponding to the objects and their relationships respectively, propose a differential analyzer to predict a language-guided visual reasoning process, and perform stepwise reasoning on top of the graph to update the compound object representation at every node. Experimental results demonstrate that the proposed method can not only significantly surpass all existing state-of-the-art algorithms across three common benchmark datasets, but also generate interpretable visual evidences for stepwisely locating the objects referred to in complex language descriptions.