Driving through the Concept Gridlock: Unraveling Explainability Bottlenecks in Automated Driving

Concept bottleneck models have been successfully used for explainable machine learning by encoding information within the model with a set of human-defined concepts. In the context of human-assisted or autonomous driving, explainability models can help user acceptance and understanding of decisions made by the autonomous vehicle, which can be used to rationalize and explain driver or vehicle behavior. We propose a new approach using concept bottlenecks as visual features for control command predictions and explanations of user and vehicle behavior. We learn a human-understandable concept layer that we use to explain sequential driving scenes while learning vehicle control commands. This approach can then be used to determine whether a change in a preferred gap or steering commands from a human (or autonomous vehicle) is led by an external stimulus or change in preferences. We achieve competitive performance to latent visual features while gaining interpretability within our model setup

MedEval: A Multi-Level, Multi-Task, and Multi-Domain Medical Benchmark for Language Model Evaluation

Curated datasets for healthcare are often limited due to the need of human annotations from experts. In this paper, we present MedEval, a multi-level, multi-task, and multi-domain medical benchmark to facilitate the development of language models for healthcare. MedEval is comprehensive and consists of data from several healthcare systems and spans 35 human body regions from 8 examination modalities. With 22,779 collected sentences and 21,228 reports, we provide expert annotations at multiple levels, offering a granular potential usage of the data and supporting a wide range of tasks. Moreover, we systematically evaluated 10 generic and domain-specific language models under zero-shot and finetuning settings, from domain-adapted baselines in healthcare to general-purposed state-of-the-art large language models (e.g., ChatGPT). Our evaluations reveal varying effectiveness of the two categories of language models across different tasks, from which we notice the importance of instruction tuning for few-shot usage of large language models. Our investigation paves the way toward benchmarking language models for healthcare and provides valuable insights into the strengths and limitations of adopting large language models in medical domains, informing their practical applications and future advancements.Comment: Accepted to EMNLP 2023. Camera-ready version: updated IRB, added more evaluation results on LLMs such as GPT4, LLaMa2, and LLaMa2-cha

Does chytridiomycosis affect tree frog attachment?

The pandemic disease chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), is a major threat to amphibian biodiversity. For most species, the exact mechanisms of chytridiomycosis that lead to negative population dynamics remain uncertain, though mounting evidence suggests that sublethal effects could be an important driver. In this review, we propose that tree frog attachment is a promising case to study the sublethal effects of a Bd infection on amphibians. A synthesis of the current knowledge on the functional morphology of the adhesive toe pads of tree frogs, on the underlying mechanisms of tree frog attachment, and on the epidermal pathology of chytridiomycosis substantiates the hypothesis that Bd-induced epidermal alterations have the potential to disrupt tree frog attachment. We highlight a series of (biomechanical) experiments to test this hypothesis and to shed some light on the sublethal disease mechanisms of chytridiomycosis. The knowledge generated from such an approach could contribute to future research on Bd epidemiology and ultimately to the conservation of the biodiversity of arboreal anurans

Calcium signals are necessary to establish auxin transporter polarity in a plant stem cell niche

In plants mechanical signals pattern morphogenesis through the polar transport of the hormone auxin and through regulation of interphase microtubule (MT) orientation. To date, the mechanisms by which such signals induce changes in cell polarity remain unknown. Through a combination of time-lapse imaging, and chemical and mechanical perturbations, we show that mechanical stimulation of the SAM causes transient changes in cytoplasmic calcium ion concentration (Ca^(2+)) and that transient Ca^(2+) response is required for downstream changes in PIN-FORMED 1 (PIN1) polarity. We also find that dynamic changes in Ca^(2+) occur during development of the SAM and this Ca^(2+) response is required for changes in PIN1 polarity, though not sufficient. In contrast, we find that Ca^(2+) is not necessary for the response of MTs to mechanical perturbations revealing that Ca^(2+) specifically acts downstream of mechanics to regulate PIN1 polarity response

ABA inhibits myristoylation and induces shuttling of the RGLG1 E3 ligase to promote nuclear degradation of PP2CA

[EN] Hormone- and stress-induced shuttling of signaling or regulatory proteins is an important cellular mechanism to modulate hormone signaling and cope with abiotic stress. Hormone-induced ubiquitination plays a crucial role to determine half-life of key negative regulators of hormone signaling. For ABA signaling, degradation of clade A PP2Cs, such as PP2CA or ABI1, is a complementary mechanism to PYR/PYL/RCAR-mediated inhibition of PP2C activity. ABA promotes the degradation of PP2CA through the RGLG1 E3 ligase, although it is not known how ABA enhances the interaction of RGLG1 with PP2CA given they are predominantly found in plasma membrane and nucleus, respectively. We demonstrate that ABA modifies the subcellular localization of RGLG1 and promotes nuclear interaction with PP2CA. We found RGLG1 is myristoylated in vivo, which facilitates its attachment to plasma membrane. ABA inhibits myristoylation of RGLG1 through downregulation of Nmyristoyltransferase1 (NMT1) and promotes nuclear translocation of RGLG1 in a cycloheximide-insensitive manner. Enhanced nuclear recruitment of the E3 ligase was also promoted by increasing PP2CA protein levels and the formation of RGLG1-receptor-phosphatase complexes. We show that RGLG1Gly2Ala -mutated in the Nterminal myristoylation site- shows constitutive nuclear localization and causes enhanced response to ABA and salt/osmotic stress. RGLG1/5 can interact with certain monomeric ABA receptors, which facilitates the formation of nuclear complexes such as RGLG1-PP2CA-PYL8. In summary, we provide evidence that an E3 ligase can dynamically re-localize in response to both ABA and increased levels of its target, which reveals a mechanism to explain how ABA enhances RGLG1-PP2CA interaction and hence PP2CA degradation.Work in P.L.R.'s laboratory was supported by the Ministerio de Ciencia e Innovacion, Fondo Europeo de Desarrollo Regional and Consejo Superior de Investigaciones Cientificas through grants BIO2014-52537-R and BIO2017-82503-R. This work was also funded by grants from the Deutsche Forschungsgemeinschaft (DFG) Ku931/4-1 to J. K., and BA4742/1-2 to O.B. B.B. was funded by Programa VALi+ d GVA APOSTD/2017/039. J.J. was supported by an FPI contract from MINECOBelda Palazón, B.; Julian, J.; Coego, A.; Wu, Q.; Zhang, X.; Batistic, O.; Alquraishi, SA.... (2019). ABA inhibits myristoylation and induces shuttling of the RGLG1 E3 ligase to promote nuclear degradation of PP2CA. 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The Plant Cell, 27(12), 3425-3438. doi:10.1105/tpc.15.00371Leitner, J., Petrasek, J., Tomanov, K., Retzer, K., Parezova, M., Korbei, B., … Luschnig, C. (2012). Lysine63-linked ubiquitylation of PIN2 auxin carrier protein governs hormonally controlled adaptation of Arabidopsis root growth. Proceedings of the National Academy of Sciences, 109(21), 8322-8327. doi:10.1073/pnas.1200824109Li, W., & Schmidt, W. (2010). A lysine-63-linked ubiquitin chain-forming conjugase, UBC13, promotes the developmental responses to iron deficiency in Arabidopsis roots. The Plant Journal, 62(2), 330-343. doi:10.1111/j.1365-313x.2010.04150.xLumba, S., Cutler, S., & McCourt, P. (2010). Plant Nuclear Hormone Receptors: A Role for Small Molecules in Protein-Protein Interactions. Annual Review of Cell and Developmental Biology, 26(1), 445-469. doi:10.1146/annurev-cellbio-100109-103956Lynch, T., Erickson, B. J., & Finkelstein, R. R. (2012). 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Structure of Ligand-Bound Intermediates of Crop ABA Receptors Highlights PP2C as Necessary ABA Co-receptor. Molecular Plant, 10(9), 1250-1253. doi:10.1016/j.molp.2017.07.004NAKAGAWA, T., SUZUKI, T., MURATA, S., NAKAMURA, S., HINO, T., MAEO, K., … ISHIGURO, S. (2007). Improved Gateway Binary Vectors: High-Performance Vectors for Creation of Fusion Constructs in Transgenic Analysis of Plants. Bioscience, Biotechnology, and Biochemistry, 71(8), 2095-2100. doi:10.1271/bbb.70216Peirats-Llobet, M., Han, S.-K., Gonzalez-Guzman, M., Jeong, C. W., Rodriguez, L., Belda-Palazon, B., … Rodriguez, P. L. (2016). A Direct Link between Abscisic Acid Sensing and the Chromatin-Remodeling ATPase BRAHMA via Core ABA Signaling Pathway Components. Molecular Plant, 9(1), 136-147. doi:10.1016/j.molp.2015.10.003Pierre, M., Traverso, J. A., Boisson, B., Domenichini, S., Bouchez, D., Giglione, C., & Meinnel, T. (2007). N-Myristoylation Regulates the SnRK1 Pathway inArabidopsis. 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Two Novel RING-Type Ubiquitin Ligases, RGLG3 and RGLG4, Are Essential for Jasmonate-Mediated Responses in Arabidopsis      . Plant Physiology, 160(2), 808-822. doi:10.1104/pp.112.20342

GPT-4V in Wonderland: Large Multimodal Models for Zero-Shot Smartphone GUI Navigation

We present MM-Navigator, a GPT-4V-based agent for the smartphone graphical user interface (GUI) navigation task. MM-Navigator can interact with a smartphone screen as human users, and determine subsequent actions to fulfill given instructions. Our findings demonstrate that large multimodal models (LMMs), specifically GPT-4V, excel in zero-shot GUI navigation through its advanced screen interpretation, action reasoning, and precise action localization capabilities. We first benchmark MM-Navigator on our collected iOS screen dataset. According to human assessments, the system exhibited a 91\% accuracy rate in generating reasonable action descriptions and a 75\% accuracy rate in executing the correct actions for single-step instructions on iOS. Additionally, we evaluate the model on a subset of an Android screen navigation dataset, where the model outperforms previous GUI navigators in a zero-shot fashion. Our benchmark and detailed analyses aim to lay a robust groundwork for future research into the GUI navigation task. The project page is at https://github.com/zzxslp/MM-Navigator.Comment: Work in progres

Vanishing Minors in the Neutrino Mass Matrix from Abelian Gauge Symmetries

Augmenting the Standard Model by three right-handed neutrinos allows for an anomaly-free gauge group extension G_max = U(1)_(B-L) x U(1)_(L_e-L_mu) x U(1)_(L_mu-L_tau). While simple U(1) subgroups of G_max have already been discussed in the context of approximate flavor symmetries, we show how two-zero textures in the right-handed neutrino Majorana mass matrix can be enforced by the flavor symmetry, which is spontaneously broken very economically by singlet scalars. These zeros lead to two vanishing minors in the low-energy neutrino mass matrix after the seesaw mechanism. This study may provide a new testing ground for a zero-texture approach: the different classes of two-zero textures with almost identical neutrino oscillation phenomenology can in principle be distinguished by their different Z' interactions at colliders.Comment: 12 pages; Extended and clarified discussion; comments on finetuning in the textures; matches published versio