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Reproducibility of research is essential for science. However, in the way modern computational biology research is done, it is easy to lose track of small, but extremely critical, details. Key details, such as the specific version of a software used or iteration of a genome can easily be lost in the shuffle, or perhaps not noted at all. Much work is being done on the database and storage side of things, ensuring that there exists a space to store experiment-specific details, but current mechanisms for recording details are cumbersome for scientists to use. We propose a new metadata description language, named MEDFORD, in which scientists can record all details relevant to their research. Human-readable, easily-editable, and templatable, MEDFORD serves as a collection point for all notes that a researcher could find relevant to their research, be it for internal use or for future replication. MEDFORD has been applied to coral research, documenting research from RNA-seq analyses to photo collections.

Non-autoregressive (NAR) generation, which is first proposed in neural machine translation (NMT) to speed up inference, has attracted much attention in both machine learning and natural language processing communities. While NAR generation can significantly accelerate inference speed for machine translation, the speedup comes at the cost of sacrificed translation accuracy compared to its counterpart, auto-regressive (AR) generation. In recent years, many new models and algorithms have been designed/proposed to bridge the accuracy gap between NAR generation and AR generation. In this paper, we conduct a systematic survey with comparisons and discussions of various non-autoregressive translation (NAT) models from different aspects. Specifically, we categorize the efforts of NAT into several groups, including data manipulation, modeling methods, training criterion, decoding algorithms, and the benefit from pre-trained models. Furthermore, we briefly review other applications of NAR models beyond machine translation, such as dialogue generation, text summarization, grammar error correction, semantic parsing, speech synthesis, and automatic speech recognition. In addition, we also discuss potential directions for future exploration, including releasing the dependency of KD, dynamic length prediction, pre-training for NAR, and wider applications, etc. We hope this survey can help researchers capture the latest progress in NAR generation, inspire the design of advanced NAR models and algorithms, and enable industry practitioners to choose appropriate solutions for their applications. The web page of this survey is at \url{//github.com/LitterBrother-Xiao/Overview-of-Non-autoregressive-Applications}.

We introduce a new distortion measure for point processes called functional-covering distortion. It is inspired by intensity theory and is related to both the covering of point processes and logarithmic loss distortion. We obtain the distortion-rate function with feedforward under this distortion measure for a large class of point processes. For Poisson processes, the rate-distortion function is obtained under a general condition called constrained functional-covering distortion, of which both covering and functional-covering are special cases. Also for Poisson processes, we characterize the rate-distortion region for a two-encoder CEO problem and show that feedforward does not enlarge this region.

Current practices in metric evaluation focus on one single dataset, e.g., Newstest dataset in each year's WMT Metrics Shared Task. However, in this paper, we qualitatively and quantitatively show that the performances of metrics are sensitive to data. The ranking of metrics varies when the evaluation is conducted on different datasets. Then this paper further investigates two potential hypotheses, i.e., insignificant data points and the deviation of Independent and Identically Distributed (i.i.d) assumption, which may take responsibility for the issue of data variance. In conclusion, our findings suggest that when evaluating automatic translation metrics, researchers should take data variance into account and be cautious to claim the result on a single dataset, because it may leads to inconsistent results with most of other datasets.

Emerging distributed cloud architectures, e.g., fog and mobile edge computing, are playing an increasingly important role in the efficient delivery of real-time stream-processing applications such as augmented reality, multiplayer gaming, and industrial automation. While such applications require processed streams to be shared and simultaneously consumed by multiple users/devices, existing technologies lack efficient mechanisms to deal with their inherent multicast nature, leading to unnecessary traffic redundancy and network congestion. In this paper, we establish a unified framework for distributed cloud network control with generalized (mixed-cast) traffic flows that allows optimizing the distributed execution of the required packet processing, forwarding, and replication operations. We first characterize the enlarged multicast network stability region under the new control framework (with respect to its unicast counterpart). We then design a novel queuing system that allows scheduling data packets according to their current destination sets, and leverage Lyapunov drift-plus-penalty theory to develop the first fully decentralized, throughput- and cost-optimal algorithm for multicast cloud network flow control. Numerical experiments validate analytical results and demonstrate the performance gain of the proposed design over existing cloud network control techniques.

Embedding matrices are key components in neural natural language processing (NLP) models that are responsible to provide numerical representations of input tokens.\footnote{In this paper words and subwords are referred to as \textit{tokens} and the term \textit{embedding} only refers to embeddings of inputs.} In this paper, we analyze the impact and utility of such matrices in the context of neural machine translation (NMT). We show that detracting syntactic and semantic information from word embeddings and running NMT systems with random embeddings is not as damaging as it initially sounds. We also show how incorporating only a limited amount of task-specific knowledge from fully-trained embeddings can boost the performance NMT systems. Our findings demonstrate that in exchange for negligible deterioration in performance, any NMT model can be run with partially random embeddings. Working with such structures means a minimal memory requirement as there is no longer need to store large embedding tables, which is a significant gain in industrial and on-device settings. We evaluated our embeddings in translating {English} into {German} and {French} and achieved a $5.3$x compression rate. Despite having a considerably smaller architecture, our models in some cases are even able to outperform state-of-the-art baselines.

In the interdependent values (IDV) model introduced by Milgrom and Weber [1982], agents have private signals that capture their information about different social alternatives, and the valuation of every agent is a function of all agent signals. While interdependence has been mainly studied for auctions, it is extremely relevant for a large variety of social choice settings, including the canonical setting of public projects. The IDV model is very challenging relative to standard independent private values, and welfare guarantees have been achieved through two alternative conditions known as {\em single-crossing} and {\em submodularity over signals (SOS)}. In either case, the existing theory falls short of solving the public projects setting. Our contribution is twofold: (i) We give a workable characterization of truthfulness for IDV public projects for the largest class of valuations for which such a characterization exists, and term this class \emph{decomposable valuations}; (ii) We provide possibility and impossibility results for welfare approximation in public projects with SOS valuations. Our main impossibility result is that, in contrast to auctions, no universally truthful mechanism performs better for public projects with SOS valuations than choosing a project at random. Our main positive result applies to {\em excludable} public projects with SOS, for which we establish a constant factor approximation similar to auctions. Our results suggest that exclusion may be a key tool for achieving welfare guarantees in the IDV model.

A High-dimensional and sparse (HiDS) matrix is frequently encountered in a big data-related application like an e-commerce system or a social network services system. To perform highly accurate representation learning on it is of great significance owing to the great desire of extracting latent knowledge and patterns from it. Latent factor analysis (LFA), which represents an HiDS matrix by learning the low-rank embeddings based on its observed entries only, is one of the most effective and efficient approaches to this issue. However, most existing LFA-based models perform such embeddings on a HiDS matrix directly without exploiting its hidden graph structures, thereby resulting in accuracy loss. To address this issue, this paper proposes a graph-incorporated latent factor analysis (GLFA) model. It adopts two-fold ideas: 1) a graph is constructed for identifying the hidden high-order interaction (HOI) among nodes described by an HiDS matrix, and 2) a recurrent LFA structure is carefully designed with the incorporation of HOI, thereby improving the representa-tion learning ability of a resultant model. Experimental results on three real-world datasets demonstrate that GLFA outperforms six state-of-the-art models in predicting the missing data of an HiDS matrix, which evidently supports its strong representation learning ability to HiDS data.

Due to the success of pre-trained language models, versions of languages other than English have been released in recent years. This fact implies the need for resources to evaluate these models. In the case of Spanish, there are few ways to systematically assess the models' quality. In this paper, we narrow the gap by building two evaluation benchmarks. Inspired by previous work (Conneau and Kiela, 2018; Chen et al., 2019), we introduce Spanish SentEval and Spanish DiscoEval, aiming to assess the capabilities of stand-alone and discourse-aware sentence representations, respectively. Our benchmarks include considerable pre-existing and newly constructed datasets that address different tasks from various domains. In addition, we evaluate and analyze the most recent pre-trained Spanish language models to exhibit their capabilities and limitations. As an example, we discover that for the case of discourse evaluation tasks, mBERT, a language model trained on multiple languages, usually provides a richer latent representation than models trained only with documents in Spanish. We hope our contribution will motivate a fairer, more comparable, and less cumbersome way to evaluate future Spanish language models.

Human-in-the-loop aims to train an accurate prediction model with minimum cost by integrating human knowledge and experience. Humans can provide training data for machine learning applications and directly accomplish some tasks that are hard for computers in the pipeline with the help of machine-based approaches. In this paper, we survey existing works on human-in-the-loop from a data perspective and classify them into three categories with a progressive relationship: (1) the work of improving model performance from data processing, (2) the work of improving model performance through interventional model training, and (3) the design of the system independent human-in-the-loop. Using the above categorization, we summarize major approaches in the field, along with their technical strengths/ weaknesses, we have simple classification and discussion in natural language processing, computer vision, and others. Besides, we provide some open challenges and opportunities. This survey intends to provide a high-level summarization for human-in-the-loop and motivates interested readers to consider approaches for designing effective human-in-the-loop solutions.