Miracle-dz/UniFAR-FTUs huggingface dataset:
Global Transformer U-Nets for Label-Free Prediction of Fluorescence Images

Visualizing the details of different cellular structures is of great importance to elucidate cellular functions. However, it is challenging to obtain high quality images of different structures directly due to complex cellular environments. Fluorescence microscopy is a popular technique to label different structures but has several drawbacks. In particular, labeling is time consuming and may affect cell morphology, and simultaneous labels are inherently limited. This raises the need of building computational models to learn relationships between unlabeled and labeled fluorescence images, and to infer fluorescent labels of other unlabeled fluorescence images. We propose to develop a novel deep model for fluorescence image prediction. We first propose a novel network layer, known as the global transformer layer, that fuses global information from inputs effectively. The proposed global transformer layer can generate outputs with arbitrary dimensions, and can be employed for all the regular, down-sampling, and up-sampling operators. We then incorporate our proposed global transformer layers and dense blocks to build an U-Net like network. We believe such a design can promote feature reusing between layers. In addition, we propose a multi-scale input strategy to encourage networks to capture features at different scales. We conduct evaluations across various label-free prediction tasks to demonstrate the effectiveness of our approach. Both quantitative and qualitative results show that our method outperforms the state-of-the-art approach significantly. It is also shown that our proposed global transformer layer is useful to improve the fluorescence image prediction results.
Self-Propelled Rods: Insights and Perspectives for Active Matter

A wide range of experimental systems including gliding, swarming and swimming bacteria, in vitro motility assays, and shaken granular media are commonly described as self-propelled rods. Large ensembles of those entities display a large variety of self-organized, collective phenomena, including the formation of moving polar clusters, polar and nematic dynamic bands, mobility-induced phase separation, topological defects, and mesoscale turbulence, among others. Here, we give a brief survey of experimental observations and review the theoretical description of self-propelled rods. Our focus is on the emergent pattern formation of ensembles of dry self-propelled rods governed by short-ranged, contact mediated interactions and their wet counterparts that are also subject to long-ranged hydrodynamic flows. Altogether, self-propelled rods provide an overarching theme covering many aspects of active matter containing well-explored limiting cases. Their collective behavior not only bridges the well-studied regimes of polar self-propelled particles and active nematics, and includes active phase separation, but also reveals a rich variety of new patterns.
Splitting Algorithms of Common Solutions Between Equilibrium and Inclusion Problems on Hadamard Manifolds

The aim of this article is to introduce an iterative algorithm for finding a common solution from the set of an equilibrium point for a bifunction and the set of a singularity of an inclusion problem on an Hadamard manifold. We also discuss some particular cases of the problem by the proposed algorithm. The convergence of a sequence generated by the proposed algorithm is proved under mild assumptions. Moreover, we apply our results to solving minimization problems and minimax problems.
Unveiling Dust Aggregate Structure in Protoplanetary Disks by Millimeter-wave Scattering Polarization

Dust coagulation in a protoplanetary disk is the first step in planetesimal formation. However, the pathway from dust aggregates to planetesimals remains unclear. Both numerical simulations and laboratory experiments have suggested the importance of dust structure in planetesimal formation, but it is not well constrained by observations. We study how the dust structure and porosity alter polarimetric images at millimeter wavelengths by performing 3D radiative transfer simulations. Aggregates with different porosities and fractal dimensions are considered. As a result, we find that dust aggregates with lower porosity and/or higher fractal dimension are favored to explain the observed millimeter-wave scattering polarization of disks. Although we cannot rule out the presence of aggregates with extremely high porosity, a population of dust particles with relatively compact structure is at least necessary to explain polarized-scattered waves. In addition, we show that particles with moderate porosity show a weak wavelength dependence of the scattering polarization, indicating that multiwavelength polarimetry is useful to constrain dust porosity. Finally, we discuss implications for dust evolution and planetesimal formation in disks.
A Development of Continuous-Time Transfer Entropy.

Transfer entropy (TE) was introduced by Schreiber in 2000 as a measurement of the predictive capacity of one stochastic process with respect to another. Originally stated for discrete time processes, we expand the theory in line with recent work of Spinney, Prokopenko, and Lizier to define TE for stochastic processes indexed over a compact interval taking values in a Polish state space. We provide a definition for continuous time TE using the Radon-Nikodym Theorem, random measures, and projective limits of probability spaces. As our main result, we provide necessary and sufficient conditions to obtain this definition as a limit of discrete time TE, as well as illustrate its application via an example involving Poisson point processes. As a derivative of continuous time TE, we also define the transfer entropy rate between two processes and show that (under mild assumptions) their stationarity implies a constant rate. We also investigate TE between homogeneous Markov jump processes and discuss some open problems and possible future directions.
Mismatched Guesswork

We study the problem of mismatched guesswork, where we evaluate the number of symbols $y \in \mathcal{Y}$ which have higher likelihood than $X \sim \mu$ according to a mismatched distribution $\nu$. We discuss the role of the tilted/exponential families of the source distribution $\mu$ and of the mismatched distribution $\nu$. We show that the value of guesswork can be characterized using the tilted family of the mismatched distribution $\nu$, while the probability of guessing is characterized by an exponential family which passes through $\mu$. Using this characterization, we demonstrate that the mismatched guesswork follows a large deviation principle (LDP), where the rate function is described implicitly using information theoretic quantities. We apply these results to one-to-one source coding (without prefix free constraint) to obtain the cost of mismatch in terms of average codeword length. We show that the cost of mismatch in one-to-one codes is no larger than that of the prefix-free codes, i.e., $D(\mu\| \nu)$. Further, the cost of mismatch vanishes if and only if $\nu$ lies on the tilted family of the true distribution $\mu$, which is in stark contrast to the prefix-free codes. These results imply that one-to-one codes are inherently more robust to mismatch.
A Fusion Adversarial Underwater Image Enhancement Network with a Public Test Dataset

Underwater image enhancement algorithms have attracted much attention in underwater vision task. However, these algorithms are mainly evaluated on different data sets and different metrics. In this paper, we set up an effective and pubic underwater test dataset named U45 including the color casts, low contrast and haze-like effects of underwater degradation and propose a fusion adversarial network for enhancing underwater images. Meanwhile, the well-designed the adversarial loss including Lgt loss and Lfe loss is presented to focus on image features of ground truth, and image features of the image enhanced by fusion enhance method, respectively. The proposed network corrects color casts effectively and owns faster testing time with fewer parameters. Experiment results on U45 dataset demonstrate that the proposed method achieves better or comparable performance than the other state-of-the-art methods in terms of qualitative and quantitative evaluations. Moreover, an ablation study demonstrates the contributions of each component, and the application test further shows the effectiveness of the enhanced images.
Prediction is very hard, especially about conversion. Predicting user purchases from clickstream data in fashion e-commerce

Knowing if a user is a buyer vs window shopper solely based on clickstream data is of crucial importance for ecommerce platforms seeking to implement real-time accurate NBA (next best action) policies. However, due to the low frequency of conversion events and the noisiness of browsing data, classifying user sessions is very challenging. In this paper, we address the clickstream classification problem in the fashion industry and present three major contributions to the burgeoning field of AI in fashion: first, we collected, normalized and prepared a novel dataset of live shopping sessions from a major European e-commerce fashion website; second, we use the dataset to test in a controlled environment strong baselines and SOTA models from the literature; finally, we propose a new discriminative neural model that outperforms neural architectures recently proposed at Rakuten labs.
Empirical Evaluation of Sequence-to-Sequence Models for Word Discovery in Low-resource Settings

Since Bahdanau et al. [1] first introduced attention for neural machine translation, most sequence-to-sequence models made use of attention mechanisms [2, 3, 4]. While they produce soft-alignment matrices that could be interpreted as alignment between target and source languages, we lack metrics to quantify their quality, being unclear which approach produces the best alignments. This paper presents an empirical evaluation of 3 main sequence-to-sequence models (CNN, RNN and Transformer-based) for word discovery from unsegmented phoneme sequences. This task consists in aligning word sequences in a source language with phoneme sequences in a target language, inferring from it word segmentation on the target side [5]. Evaluating word segmentation quality can be seen as an extrinsic evaluation of the soft-alignment matrices produced during training. Our experiments in a low-resource scenario on Mboshi and English languages (both aligned to French) show that RNNs surprisingly outperform CNNs and Transformer for this task. Our results are confirmed by an intrinsic evaluation of alignment quality through the use of Average Normalized Entropy (ANE). Lastly, we improve our best word discovery model by using an alignment entropy confidence measure that accumulates ANE over all the occurrences of a given alignment pair in the collection.
From Bilingual to Multilingual Neural Machine Translation by Incremental Training

Multilingual Neural Machine Translation approaches are based on the use of task specific models and the addition of one more language can only be done by retraining the whole system. In this work, we propose a new training schedule that allows the system to scale to more languages without modification of the previous components based on joint training and language-independent encoder/decoder modules allowing for zero-shot translation. This work in progress shows close results to state-of-the-art in the WMT task.
Estimating Information-Theoretic Quantities with Random Forests

Information-theoretic quantities, such as mutual information and conditional entropy, are useful statistics for measuring the dependence between two random variables. However, estimating these quantities in a non-parametric fashion is difficult, especially when the variables are high-dimensional, a mixture of continuous and discrete values, or both. In this paper, we propose a decision forest method, Conditional Forests (CF), to estimate these quantities. By combining quantile regression forests with honest sampling, and introducing a finite sample correction, CF improves finite sample bias in a range of settings. We demonstrate through simulations that CF achieves smaller bias and variance in both low- and high-dimensional settings for estimating posteriors, conditional entropy, and mutual information. We then use CF to estimate the amount of information between neuron class and other ceulluar feautres.
EGG: a toolkit for research on Emergence of lanGuage in Games

There is renewed interest in simulating language emergence among deep neural agents that communicate to jointly solve a task, spurred by the practical aim to develop language-enabled interactive AIs, as well as by theoretical questions about the evolution of human language. However, optimizing deep architectures connected by a discrete communication channel (such as that in which language emerges) is technically challenging. We introduce EGG, a toolkit that greatly simplifies the implementation of emergent-language communication games. EGG’s modular design provides a set of building blocks that the user can combine to create new games, easily navigating the optimization and architecture space. We hope that the tool will lower the technical barrier, and encourage researchers from various backgrounds to do original work in this exciting area.
Bridging the Architecture Gap: Abstracting Performance-Relevant Properties of Modern Server Processors

We describe a universal modeling approach for predicting single- and multicore runtime of steady-state loops on server processors. To this end we strictly differentiate between application and machine models: An application model comprises the loop code, problem sizes, and other runtime parameters, while a machine model is an abstraction of all performance-relevant properties of a CPU. We introduce a generic method for determining machine models and present results for relevant server-processor architectures by Intel, AMD, IBM, and Marvell/Cavium. Considering this wide range of architectures, the set of features required for adequate performance modeling is surprisingly small. To validate our approach, we compare performance predictions to empirical data for an OpenMP-parallel preconditioned CG algorithm, which includes compute- and memory-bound kernels. Both single- and multicore analysis shows that the model exhibits average and maximum relative errors of 5% and 10%. Deviations from the model and insights gained are discussed in detail.
Scalable isosurface visualization

Scientific data visualization assists users in understanding and analyzing large volumes of raw data by converting them into graphic representations. The main challenges in building a visualization system are large datasets, high-resolution displays, and the need to visualize remote datasets over slow networks. This dissertation focuses on visualizing isosurfaces efficiently under these challenges. First, to visualize large datasets efficiently on high-resolution displays, this dissertation proposes a new isosurface extraction algorithm that generates approximate results much faster than previous algorithms. The algorithm extracts portions of the isosurface in a view-dependent manner by ray casting and propagation. It casts rays through a volume to find visible active cells as seeds and then propagates their polygonal isosurface into the neighboring cells. Small pieces of the isosurface are generated by distance-limited propagation and joined together to form the final surface. Evaluation shows that this progressive algorithm generates an approximate result quickly before the final correct image is reached over time. In addition, the algorithm scales with the resolution of the display and supports adaptive-resolution visualization. This dissertation further discusses design options that are used for a fast implementation of the base algorithm. Finally, this dissertation presents a simple and effective protocol for remote isosurface visualization. The protocol breaks up the isosurface visualization pipeline at the 3D primitive stage for the server to send primitives to the client. Several techniques are introduced to reduce communication requirement and to provide interactive visualization. The server runs an efficient isosurface extraction algorithm that generates view-dependent portions of the isosurface. The resulting 3D primitives are organized into groups and sent to the client to be rendered. This approach uses primitive compression, progressive level-of-detail, and primitive caching techniques to improve the interactivity perceived by the user. This dissertation reports and compares the experiment results under different settings to show the effectiveness of these techniques. The results show that, when applied together, the techniques reduce both the amount of data transferred and time spent when the result becomes 90% correct by two orders of magnitude.
Design of Navigation Control Architecture for an Autonomous Mobile Robot Agent

Background/Objectives: To design a navigation control architecture which attempts to identify optimal path for a mobile robot agent to move from initial position to target position, in an environment where multiple path exists. Methods/ Statistical Analysis: The design of navigation control architecture determines how all the components are integrated and it is completely depends on its requirement and since, there is no standard reference architectures exists, we propose an architecture for mobile robot system, with three-tier user centric layer approach with hybrid methodology. The integration and interaction between the three layers are both centralized as well as distributed and, choice of selecting the path planner mechanism differs from existing system. Findings: In this paper, various existing robot architectures were reviewed in high level. A Hybrid methodology is used to adopt along with dynamic modelling approach for motion planning system and geometric modelling approach for path planning system, to suit the design complexity. The Path planner control system model proposed in this paper focuses much on agent based path planning system and motion planning system, which plays critical role in controlling the movement of a non-holonomic robot system. Application/Improvements: The efficiency of the proposed architecture is yet to be evaluated by applying this system in real time application
From Parameter Estimation to Dispersion of Nonstationary Gauss-Markov Processes

This paper provides a precise error analysis for the maximum likelihood estimate $\hat a\left( {\boldsymbol{u}} \right)$ of the parameter a given samples u = (u1, … , un)⊤ drawn from a nonstationary Gauss-Markov process Ui = aUi−1 + Zi, i ≥ 1, where a > 1, U0 = 0, and Zi’s are independent Gaussian random variables with zero mean and variance σ2. We show a tight nonasymptotic exponentially decaying bound on the tail probability of the estimation error. Unlike previous works, our bound is tight already for a sample size of the order of hundreds. We apply the new estimation bound to find the dispersion for lossy compression of nonstationary Gauss-Markov sources. We show that the dispersion is given by the same integral formula derived in our previous work [1] for the (asymptotically) stationary Gauss-Markov sources, i.e., |a| < 1. New ideas in the nonstationary case include a deeper understanding of the scaling of the maximum eigenvalue of the covariance matrix of the source sequence, and new techniques in the derivation of our estimation error bound.
Evaluating Local Geometric Feature Representations for 3D Rigid Data Matching

Local geometric descriptors act as an essential component for 3D rigid data matching. A rotational invariant local geometric descriptor usually consists of two components: local reference frame (LRF) and feature representation. However, existing evaluation efforts have mainly been paid on the LRF or the overall descriptor and the quantitative comparison of feature representations remains unexplored. This paper fills the gap by comprehensively evaluating nine state-of-the-art local geometric feature representations. In particular, our evaluation assesses feature representations based on ground-truth LRFs such that the ranking of tested methods is more convincing as compared with existing studies. The experiments are deployed on six standard datasets with various application scenarios (shape retrieval, point cloud registration, and object recognition) and data modalities (LiDAR, Kinect, and Space Time) as well as perturbations including Gaussian noise, shot noise, data decimation, clutter, occlusion, and limited overlap. The evaluated terms cover the major concerns for a feature representation, e.g., distinctiveness, robustness, compactness, and efficiency. The outcomes present interesting findings that may shed new light on this community and provide complementary perspectives to existing evaluations on the topic of local geometric feature description. A summary of evaluated methods regarding their peculiarities is finally presented to guide real-world applications and new descriptor crafting.
Reinforcement Learning for Robotic Time-optimal Path Tracking Using Prior Knowledge

Time-optimal path tracking, as a significant tool for industrial robots, has attracted the attention of numerous researchers. In most time-optimal path tracking problems, the actuator torque constraints are assumed to be conservative, which ignores the motor characteristic; i.e., the actuator torque constraints are velocity-dependent, and the relationship between torque and velocity is piecewise linear. However, considering that the motor characteristics increase the solving difficulty, in this study, an improved Q-learning algorithm for robotic time-optimal path tracking using prior knowledge is proposed. After considering the limitations of the Q-learning algorithm, an improved action-value function is proposed to improve the convergence rate. The proposed algorithms use the idea of reward and penalty, rewarding the actions that satisfy constraint conditions and penalizing the actions that break constraint conditions, to finally obtain a time-optimal trajectory that satisfies the constraint conditions. The effectiveness of the algorithms is verified by experiments.
Developing a Data Mining Based Model to Extract Predictor Factors in Energy Systems: Application of Global Natural Gas Demand

Recently, the natural gas (NG) global market attracted much attention as it is cleaner than oil and, simultaneously in most regions, is cheaper than renewable energy sources. However, price fluctuations, environmental concerns, technological development, emerging unconventional resources, energy security challenges, and shipment are some of the forces made the NG market more dynamic and complex. From a policy-making perspective, it is vital to uncover demand-side future trends. This paper proposed an intelligent forecasting model to forecast NG global demand, however investigating a multi-dimensional purified input vector. The model starts with a data mining (DM) step to purify input features, identify the best time lags, and pre-processing selected input vector. Then a hybrid artificial neural network (ANN) which is equipped with genetic optimizer is applied to set up ANN’s characteristics. Among 13 available input features, six features (e.g., Alternative and Nuclear Energy, CO2 Emissions, GDP per Capita, Urban Population, Natural Gas Production, Oil Consumption) were selected as the most relevant feature via the DM step. Then, the hybrid learning prediction model is designed to extrapolate the consumption of future trends. The proposed model overcomes competitive models refer to different five error based evaluation statistics consist of R2, MAE, MAPE, MBE, and RMSE. In addition, as the model proposed the best input feature set, results compared to the model which used the raw input set, with no DM purification process. The comparison showed that DmGNn overcame dramatically a simple GNn. Also, a looser prediction model, such as a generalized neural network with purified input features obtained a larger R2 indicator (=0.9864) than the GNn (=0.9679).