Stochastic Simulation Algorithm (SSA) is crucial for modeling biochemical reactions and gene regulatory networks. Traditional SSA is characterized by Markovian property and cannot naturally model systems with time delays. Several algorithms have already been designed to handle delayed reactions, yet few easy-to-use implementations exist. To address these challenges, we have developed DelaySSA, an R package that implements currently available algorithms for SSA with or without delays. Meanwhile, we also provided Matlab and Python versions to support wider applications. We demonstrated its accuracy and validity by simulating two classical models: the Bursty model and Refractory model. We then tested its capability to simulate the RNA Velocity model, where it successfully reproduced both the up- and down-regulation stages in the phase portrait. Finally, we extended its application to simulate a gene regulatory network of lung cancer adeno-to-squamous transition (AST) and qualitatively analyzed its bistability behavior by approximating the Waddington's landscape. Modeling the therapeutic intervention of a SOX2 degrader as a delayed degradation reaction, AST is effectively blocked and reprogrammed back to the adenocarcinoma state, providing a useful clue for targeting drug-resistant AST in the future. Taken together, DelaySSA is a powerful and easy-to-use software suite, facilitating accurate modeling of various kinds of biological systems and broadening the scope of stochastic simulations in systems biology.

Advancements in peptidomics have revealed numerous small open reading frames with coding potential and revealed that some of these micropeptides are closely related to human cancer. However, the systematic analysis and integration from sequence to structure and function remains largely undeveloped. Here, as a solution, we built a workflow for the collection and analysis of proteomic data, transcriptomic data, and clinical outcomes for cancer-associated micropeptides using publicly available datasets from large cohorts. We initially identified 19 586 novel micropeptides by reanalyzing proteomic profile data from 3753 samples across 8 cancer types. Further quantitative analysis of these micropeptides, along with associated clinical data, identified 3065 that were dysregulated in cancer, with 370 of them showing a strong association with prognosis. Moreover, we employed a deep learning framework to construct a micropeptide-protein interaction network for further bioinformatics analysis, revealing that micropeptides are involved in multiple biological processes as bioactive molecules. Taken together, our atlas provides a benchmark for high-throughput prediction and functional exploration of micropeptides, providing new insights into their biological mechanisms in cancer. The HMPA is freely available at http://hmpa.zju.edu.cn.

Building 3D perception systems for autonomous vehicles that do not rely on high-density LiDAR is a critical research problem because of the expense of LiDAR systems compared to cameras and other sensors. Recent research has developed a variety of camera-only methods, where features are differentiably “lifted” from the multi-camera images onto the 2D ground plane, yielding a “bird's eye view” (BEV) feature representation of the 3D space around the vehicle. This line of work has produced a variety of novel “lifting” methods, but we observe that other details in the training setups have shifted at the same time, making it unclear what really matters in top-performing methods. We also observe that using cameras alone is not a real-world constraint, considering that additional sensors like radar have been integrated into real vehicles for years already. In this paper, we first of all attempt to elucidate the high-impact factors in the design and training protocol of BEV perception models. We find that batch size and input resolution greatly affect performance, while lifting strategies have a more modest effect-even a simple parameter-free lifter works well. Second, we demonstrate that radar data can provide a substantial boost to performance, helping to close the gap between camera-only and LiDAR-enabled systems. We analyze the radar usage details that lead to good performance, and invite the community to re-consider this commonly-neglected part of the sensor platform.

RNA-seq technology is widely employed in various research areas related to transcriptome analyses, and the identification of all the expressed transcripts from short sequencing reads presents a considerable computational challenge. In this study, we introduce TransRef, a new computational algorithm for accurate transcriptome assembly by redefining a novel graph model, the neo-splicing graph, and then iteratively applying a constrained dynamic programming to reconstruct all the expressed transcripts for each graph. When TransRef is utilized to analyze both real and simulated datasets, its performance is notably better than those of several state-of-the-art assemblers, including StringTie2, Cufflinks and Scallop. In particular, the performance of TransRef is notably strong in identifying novel transcripts and transcripts with low-expression levels, while the other assemblers are less effective.

Diversity and unpredictability of artifacts potentially presented to an iris sensor calls for presentation attack detection methods that are agnostic to specificity of presentation attack instruments. This article proposes a method that combines two-dimensional and three-dimensional properties of the observed iris to address the problem of spoof detection in case when some properties of artifacts are unknown. The 2D (textural) iris features are extracted by a state-of-the-art method employing Binary Statistical Image Features (BSIF) and an ensemble of classifiers is used to deliver 2D modality-related decision. The 3D (shape) iris features are reconstructed by a photometric stereo method from only two images captured under near-infrared illumination placed at two different angles, as in many current commercial iris recognition sensors. The map of normal vectors is used to assess the convexity of the observed iris surface. The combination of these two approaches has been applied to detect whether a subject is wearing a textured contact lens to disguise their identity. Extensive experiments with NDCLD'15 dataset, and a newly collected NDIris3D dataset show that the proposed method is highly robust under various open-set testing scenarios, and that it outperforms all available open-source iris PAD methods tested in identical scenarios. The source code and the newly prepared benchmark are made available along with this article.

Launched in 2013, LivDet-Iris is an international competition series open to academia and industry with the aim to assess and report advances in iris Presentation Attack Detection (PAD). This paper presents results from the fourth competition of the series: LivDet-Iris 2020. This year's competition introduced several novel elements: (a) incorporated new types of attacks (samples displayed on a screen, cadaver eyes and prosthetic eyes), (b) initiated LivDet-Iris as an on-going effort, with a testing protocol available now to everyone via the Biometrics Evaluation and Testing (BEAT)* open-source platform to facilitate reproducibility and benchmarking of new algorithms continuously, and (c) performance comparison of the submitted entries with three baseline methods (offered by the University of Notre Dame and Michigan State University), and three open-source iris PAD methods available in the public domain. The best performing entry to the competition reported a weighted average APCER of 59.10% and a BPCER of 0.46% over all five attack types. This paper serves as the latest evaluation of iris PAD on a large spectrum of presentation attack instruments.

This paper proposes the first known to us open source hardware and software iris recognition system with presentation attack detection (PAD), which can be easily assembled for about 75 USD using Raspberry Pi board and a few peripherals. The primary goal of this work is to offer a low-cost baseline for spoof-resistant iris recognition, which may (a) stimulate research in iris PAD and allow for easy prototyping of secure iris recognition systems, (b) offer a low-cost secure iris recognition alternative to more sophisticated systems, and (c) serve as an educational platform. We propose a lightweight image complexity-guided convolutional network for fast and accurate iris segmentation, domain-specific human-inspired Binarized Statistical Image Features (BSIF) to build an iris template, and to combine 2D (iris texture) and 3D (photometric stereo-based) features for PAD. The proposed iris recognition runs in about 3.2 seconds and the proposed PAD runs in about 4.5 seconds on Raspberry Pi 3B+. The hardware specifications and all source codes of the entire pipeline are made available along with this paper.

We present AlignNet, a model that synchronizes videos with reference audios undernon-uniform and irregularmis- alignments. AlignNet learns the end-to-end dense correspondence between each frame of a video and an audio. Our method is designed according to simple and well- established principles: attention, pyramidal processing, warping, and affinity function. Together with the model, we release a dancing dataset Dance50 for training and evaluation. Qualitative, quantitative and subjective evaluation results on dance-music alignment and speech-lip alignment demonstrate that our method far outperforms the state-of- the-art methods. Code, dataset and sample videos are available at our project page1.

We propose a new iris presentation attack detection method using three-dimensional features of an observed iris region estimated by photometric stereo. Our implementation uses a pair of iris images acquired by a common commercial iris sensor (LG 4000). No hardware modifications of any kind are required. Our approach should be applicable to any iris sensor that can illuminate the eye from two different directions. Each iris image in the pair is captured under near-infrared illumination at a different angle relative to the eye. Photometric stereo is used to estimate surface normal vectors in the non-occluded portions of the iris region. The variability of the normal vectors is used as the presentation attack detection score. This score is larger for a texture that is irregularly opaque and printed on a convex contact lens, and is smaller for an authentic iris texture. Thus the problem is formulated as binary classification into (a) an eye wearing textured contact lens and (b) the texture of an actual iris surface (possibly seen through a clear contact lens). Experiments were carried out on a database of approx. 2,900 iris image pairs acquired from approx. 100 subjects. Our method was able to correctly classify over 95% of samples when tested on contact lens brands unseen in training, and over 98% of samples when the contact lens brand was seen during training. The source codes of the method are made available to other researchers.