How Does Fine-Tuning Impact Out-of-Distribution Detection for Vision-Language Models?

Recent large vision-language models such as CLIP have shown remarkable out-of-distribution (OOD) detection and generalization performance. However, their zero-shot in-distribution (ID) accuracy is often limited for downstream datasets. Recent CLIP-based fine-tuning methods such as prompt learning have demonstrated significant improvements in ID classification and OOD generalization where OOD labels are available. Nonetheless, it remains unclear whether the model is reliable to semantic shifts without OOD labels. In this paper, we aim to bridge the gap and present a comprehensive study to understand how fine-tuning impact OOD detection for few-shot downstream tasks. By framing OOD detection as multi-modal concept matching, we establish a connection between fine-tuning methods and various OOD scores. Our results suggest that a proper choice of OOD scores is essential for CLIP-based fine-tuning. In particular, the maximum concept matching (MCM) score provides a promising solution consistently. We also show that prompt learning demonstrates the state-of-the-art OOD detection performance over the zero-shot counterpart

Delving into Out-of-Distribution Detection with Vision-Language Representations

Recognizing out-of-distribution (OOD) samples is critical for machine learning systems deployed in the open world. The vast majority of OOD detection methods are driven by a single modality (e.g., either vision or language), leaving the rich information in multi-modal representations untapped. Inspired by the recent success of vision-language pre-training, this paper enriches the landscape of OOD detection from a single-modal to a multi-modal regime. Particularly, we propose Maximum Concept Matching (MCM), a simple yet effective zero-shot OOD detection method based on aligning visual features with textual concepts. We contribute in-depth analysis and theoretical insights to understand the effectiveness of MCM. Extensive experiments demonstrate that MCM achieves superior performance on a wide variety of real-world tasks. MCM with vision-language features outperforms a common baseline with pure visual features on a hard OOD task with semantically similar classes by 13.1% (AUROC). Code is available at https://github.com/deeplearning-wisc/MCM.Comment: 36th Conference on Neural Information Processing Systems (NeurIPS 2022

Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A

ABSTRACT Porcine epidemic diarrhea virus (PEDV) is a highly pathogenic alphacoronavirus. In the United States, highly virulent PEDV strains cause between 80 and 100% mortality in suckling piglets and are rapidly transmitted between animals and farms. To study the genetic factors that regulate pathogenesis and transmission, we developed a molecular clone of PEDV strain PC22A. The infectious-clone-derived PEDV (icPEDV) replicated as efficiently as the parental virus in cell culture and in pigs, resulting in lethal disease in vivo . Importantly, recombinant PEDV was rapidly transmitted to uninoculated pigs via indirect contact, demonstrating virulence and efficient transmission while replicating phenotypes seen in the wild-type virus. Using reverse genetics, we removed open reading frame 3 (ORF3) and replaced this region with a red fluorescent protein (RFP) gene to generate icPEDV-ΔORF3-RFP. icPEDV-ΔORF3-RFP replicated efficiently in vitro and in vivo , was efficiently transmitted among pigs, and produced lethal disease outcomes. However, the diarrheic scores in icPEDV-ΔORF3-RFP-infected pigs were lower than those in wild-type-virus- or icPEDV-infected pigs, and the virus formed smaller plaques than those of PC22A. Together, these data describe the development of a robust reverse-genetics platform for identifying genetic factors that regulate pathogenic outcomes and transmission efficiency in vivo , providing key infrastructural developments for developing and evaluating the efficacy of live attenuated vaccines and therapeutics in a clinical setting. IMPORTANCE Porcine epidemic diarrhea virus (PEDV) emerged in the United States in 2013 and has since killed 10% of U.S. farm pigs. Though the disease has been circulating internationally for decades, the lack of a rapid reverse-genetics platform for manipulating PEDV and identifying genetic factors that impact transmission and virulence has hindered the study of this important agricultural disease. Here, we present a DNA-based infectious-clone system that replicates the pathogenesis of circulating U.S. strain PC22A both in vitro and in piglets. This infectious clone can be used both to study the genetics, virulence, and transmission of PEDV coronavirus and to inform the creation of a live attenuated PEDV vaccine

Designing Low-PAPR Waveform for OFDM-Based RadCom Systems

This paper is focused on the fusion of radar and wireless communication, called RadCom, which has been extensively studied in recent years for future intelligent transportation systems. We propose a new waveform design algorithm for reducing peak-to-average power ratio (PAPR) in OFDM-based RadCom systems. We consider a flexible and generic RadCom structure in which a number of non-contiguous sub-bands for data transmission are located within a large contiguous spectrum band for radar detection/sensing. New RadCom waveforms with low PAPR are obtained by carrying out optimization over those subcarriers which are complementary to the communication bands. As an application of the majorization-minimization (MM) optimization method, our major contribution is an l -norm cyclic algorithm which is capable of efficiently reducing the maximum PAPR of RadCom waveforms. We show by numerical simulation results that significant performance enhancements can be achieved compared to OFDM RadCom waveforms from legacy approaches

Critical Intersections through Poetry in a TESOL & World Language Graduate Education Program

In this studio submission, Language Education students who took one or more poetry writing courses along with their instructor share one poem draft and critical reflection, noting the political climate of the work co-produced and inquiry regarding the impact of producing creative work as reflexive, critical teacher education scholarship. Together they draw a context and implications for creative and critical teacher education through shared poetry writing

Longitudinal morphological and functional characterization of human heart organoids using optical coherence tomography

Organoids play an increasingly important role as in vitro models for studying organ development, disease mechanisms, and drug discovery. Organoids are self-organizing, organ-like three-dimensional (3D) cell cultures developing organ-specific cell types and functions. Recently, three groups independently developed self-assembling human heart organoids (hHOs) from human pluripotent stem cells (hPSCs). In this study, we utilized a customized spectral-domain optical coherence tomography (SD-OCT) system to characterize the growth of hHOs. Development of chamber structures and beating patterns of the hHOs were observed via OCT and calcium imaging. We demonstrated the capability of OCT to produce 3D images in a fast, label-free, and non-destructive manner. The hHOs formed cavities of various sizes, and complex interconnections were observed as early as on day 4 of differentiation. The hHOs models and the OCT imaging system showed promising insights as an in vitro platform for investigating heart development and disease mechanisms

Training Sequence Design for Efficient Channel Estimation in MIMO-FBMC Systems

This paper is focused on training sequence design for efficient channel estimation in multiple-input multiple-output filterbank multicarrier (MIMO-FBMC) communications using offset quadrature amplitude modulation (OQAM). MIMO-FBMC is a promising technique to achieve high spectrum efficiency as well as strong robustness against dispersive channels due to its feature of time-frequency localization. A salient drawback of FBMC/OQAM signals is that only real-field orthogonality can be kept, leading to the intrinsic imaginary interference being a barrier for high-performance channel estimations. Also, conventional channel estimations in the MIMO-FBMC systems mostly suffer from high training overhead especially for large number of transmit antennas. Motivated by these problems, in this paper, we propose a new class of training sequences, which are formed by concatenation of two identical zero-correlation zone sequences whose auto-correlation and cross correlation are zero within a time-shift window around the in-phase position. Since only real-valued symbols can be transmitted in MIMO-FBMC systems, we propose “complex training sequence decomposition (CTSD)” to facilitate the reconstruction of the complex-field orthogonality of MIMO-FBMC signals. Our simulations validate that the proposed CTSD is an efficient channel estimation approach for practical preamble-based MIMO-FBMC systems

Deletion of a 197-Amino-Acid Region in the N-Terminal Domain of Spike Protein Attenuates Porcine Epidemic Diarrhea Virus in Piglets

ABSTRACT We previously isolated a porcine epidemic diarrhea virus (PEDV) strain, PC177, by blind serial passaging of the intestinal contents of a diarrheic piglet in Vero cell culture. Compared with the highly virulent U.S. PEDV strain PC21A, the tissue culture-adapted PC177 (TC-PC177) contains a 197-amino-acid (aa) deletion in the N-terminal domain of the spike (S) protein. We orally inoculated neonatal, conventional suckling piglets with TC-PC177 or PC21A to compare their pathogenicities. Within 7 days postinoculation, TC-PC177 caused mild diarrhea and lower fecal viral RNA shedding, with no mortality, whereas PC21A caused severe clinical signs and 55% mortality. To investigate whether infection with TC-PC177 can induce cross-protection against challenge with a highly virulent PEDV strain, all the surviving piglets were challenged with PC21A at 3 weeks postinoculation. Compared with 100% protection in piglets initially inoculated with PC21A, 88% and 100% TC-PC177- and mock-inoculated piglets had diarrhea following challenge, respectively, indicating incomplete cross-protection. To investigate whether this 197-aa deletion was the determinant for the attenuation of TC-PC177, we generated a mutant (icPC22A-S1Δ197) bearing the 197-aa deletion from an infectious cDNA clone of the highly virulent PEDV PC22A strain (infectious clone PC22A, icPC22A). In neonatal gnotobiotic pigs, the icPC22A-S1Δ197 virus caused mild to moderate diarrhea, lower titers of viral shedding, and no mortality, whereas the icPC22A virus caused severe diarrhea and 100% mortality. Our data indicate that deletion of this 197-aa fragment in the spike protein can attenuate a highly virulent PEDV, but the virus may lose important epitopes for inducing robust protective immunity. IMPORTANCE The emerging, highly virulent PEDV strains have caused substantial economic losses worldwide. However, the virulence determinants are not established. In this study, we found that a 197-aa deletion in the N-terminal region of the S protein did not alter virus (TC-PC177) tissue tropism but reduced the virulence of the highly virulent PEDV strain PC22A in neonatal piglets. We also demonstrated that the primary infection with TC-PC177 failed to induce complete cross-protection against challenge by the highly virulent PEDV PC21A, suggesting that the 197-aa region may contain important epitopes for inducing protective immunity. Our results provide an insight into the role of this large deletion in virus propagation and pathogenicity. In addition, the reverse genetics platform of the PC22A strain was further optimized for the rescue of recombinant PEDV viruses in vitro . This breakthrough allows us to investigate other virulence determinants of PEDV strains and will provide knowledge leading to better control PEDV infections

Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude

Crucihimalaya himalaica is a close relative of Arabidopsis with typical Qinghai–Tibet Plateau (QTP) distribution. Here, by combining short- and long-read sequencing technologies, we provide a de novo genome sequence of C. himalaica. Our results suggest that the quick uplifting of the QTP coincided with the expansion of repeat elements. Gene families showing dramatic contractions and expansions, as well as genes showing clear signs of natural selection, were likely responsible for C. himalaica’s specific adaptation to the harsh environment of the QTP. We also show that the transition to self-pollination of C. himalaica might have enabled its occupation of the QTP. This study provides insights into how plants might adapt to extreme environmental conditions