Analyzing Vision Transformers for Image Classification in Class Embedding Space

Despite the growing use of transformer models in computer vision, a mechanistic understanding of these networks is still needed. This work introduces a method to reverse-engineer Vision Transformers trained to solve image classification tasks. Inspired by previous research in NLP, we demonstrate how the inner representations at any level of the hierarchy can be projected onto the learned class embedding space to uncover how these networks build categorical representations for their predictions. We use our framework to show how image tokens develop class-specific representations that depend on attention mechanisms and contextual information, and give insights on how self-attention and MLP layers differentially contribute to this categorical composition. We additionally demonstrate that this method (1) can be used to determine the parts of an image that would be important for detecting the class of interest, and (2) exhibits significant advantages over traditional linear probing approaches. Taken together, our results position our proposed framework as a powerful tool for mechanistic interpretability and explainability research.Comment: NeurIPS 202

Survival of spin state in magnetic porphyrins contacted by graphene nanoribbons

We report on the construction and magnetic characterization of a fully functional hybrid molecular system composed of a single magnetic porphyrin molecule bonded to graphene nanoribbons with atomically precise contacts. We use on-surface synthesis to direct the hybrid creation by combining two molecular precursors on a gold surface. High-resolution imaging with a scanning tunneling microscope finds that the porphyrin core fuses into the graphene nanoribbons through the formation of new carbon rings at chemically predefined positions. These ensure the stability of the hybrid and the extension of the conjugated character of the ribbon into the molecule. By means of inelastic tunneling spectroscopy, we prove the survival of the magnetic functionality of the contacted porphyrin. The molecular spin appears unaffected by the graphenoid electrodes, and we simply observe that the magnetic anisotropy appears modified depending on the precise structure of the contacts.We acknowledge the financial support from Spanish Agencia Estatal de Investigación (AEI) (project nos. MAT2016-78293-C6 and FIS2015-62538-ERC, and the Maria de Maeztu Units of Excellence Programme MDM-2016-0618), the Basque Government (Department Industry, grant no. PI-2015-1-42), the European project PAMS (610446), the Xunta de Galicia (Centro singular de investigación de Galicia accreditation 2016 to 2019, ED431G/09), the European Research Council (grant agreement no. 635919), and the European Regional Development FundS

Unraveling the electronic structure of narrow atomically precise chiral graphene nanoribbons

This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposesRecent advances in graphene-nanoribbon-based research have demonstrated the controlled synthesis of chiral graphene nanoribbons (chGNRs) with atomic precision using strategies of on-surface chemistry. However, their electronic characterization, including typical figures of merit like band gap or frontier band's effective mass, has not yet been reported. We provide a detailed characterization of (3,1)-chGNRs on Au(111). The structure and epitaxy, as well as the electronic band structure of the ribbons, are analyzed by means of scanning tunneling microscopy and spectroscopy, angle-resolved photoemission, and density functional theoryThe project leading to this publication has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 635919), from the Spanish Ministry of Economy, Industry and Competitiveness (MINECO, grant nos. MAT2016-78293-C6, FIS2015-62538-ERC), from the Basque Government (grant nos. IT-621-13, PI-2015-1-42, PI-2016-1-0027), from the European Commission in FP7 FET-ICT “Planar Atomic and Molecular Scale Devices” (PAMS) project (contract no. 610446), from the Xunta de Galicia (Centro singular de investigación de Galicia accreditation 2016−2019, ED431G/09), and from the European Regional Development Fund (ERDF

Electronic consequences of chemical doping of 7-Armchair Graphene Nanoribbons

Resumen del trabajo presentado a la International Conference on Nanoscience + Technology (ICN+T), celebrada en Brno (Czech Republic) del 22 al 27 de julio de 2018.The tunable electronic structure of Graphene Nanoribbons (GNRs) with different edge types has provoked great interest due to potential applications in electronic devices as molecular diodes or transistors. Thanks to the on-surface synthesis of chemically customized molecular precursors, nanoribbons with atomically defined structure can be grown. This high precision in their bottom-up growth allows to tune their electronic structure via width control or chemical doping. Here we use two different strategies to chemically modify 7-armchair GNRs (7-AGNRs) to clarify how the chemical modifications on the nanoribbons’ structure affect their electronic properties. By means of Scanning Tunneling Spectroscopy we tackle with atomic precision this issue on 7-AGNRs with substitutional nitrile functional groups at the ribbons’ edges and on 7-AGNRs with substitutional boron atoms within the ribbons’ backbone. We find that in the first case the CN groups lead to an efficient n-like doping of the ribbon, while in the second case B atoms induce the formation of a new acceptor band and bandgap renormalization.Peer Reviewe

Magnetic interactions between radical pairs in chiral graphene nanoribbons

Open-shell graphene nanoribbons have become promising candidates for future applications, including quantum technologies. Here, we characterize magnetic states hosted by chiral graphene nanoribbons (chGNRs). The substitution of a hydrogen atom at the chGNR edge by a ketone effectively adds one pz electron to the π-electron network, producing an unpaired π-radical. A similar scenario occurs for regular ketone-functionalized chGNRs in which one ketone is missing. Two such radical states can interact via exchange coupling, and we study those interactions as a function of their relative position, which includes a remarkable dependence on the chirality, as well as on the nature of the surrounding ribbon, that is, with or without ketone functionalization. Besides, we determine the parameters whereby this type of system with oxygen heteroatoms can be adequately described within the widely used mean-field Hubbard model. Altogether, we provide insight to both theoretically model and devise GNR-based nanostructures with tunable magnetic properties.We acknowledge financial support from the MCIN/AEI/10.13039/501100011033 (Grants PID2019-107338RB-C62, PID2019-107338RB-C63, PID2020-115406GB-I00, PCI2019-111933-2 (FLAG-ERA grant LEGOCHIP), and Juan de la Cierva Grant FJC2019-041202-I), the European Union’s Horizon 2020 research and innovation program (FET-OPEN project SPRING, Grant No. 863098 and Marie Skłodowska-Curie Actions Individual Fellowship No. 101022150), the Xunta de Galicia (Centro Singular de Investigación de Galicia, 2019-2022, Grant ED431G2019/03), the European Regional Development Fund, the Basque Government (IT-1255-19), the Basque Government (PIBA Grant PI_2020_1_0014), the Basque Departamento de Educación through the Ph.D. scholarship No. PRE_2020_2_0049 (S.S.), the Spanish Research Council (LINKC20002).Peer reviewe

Circumventing the stability problems of graphene nanoribbon zigzag edges

Carbon nanostructures with zigzag edges exhibit unique properties—such as localized electronic states and spins—with exciting potential applications. Such nanostructures however are generally synthesized under vacuum because their zigzag edges are unstable under ambient conditions: a barrier that must be surmounted to achieve their scalable integration into devices for practical purposes. Here we show two chemical protection/deprotection strategies, demonstrated on labile, air-sensitive chiral graphene nanoribbons. Upon hydrogenation, the chiral graphene nanoribbons survive exposure to air, after which they are easily converted back to their original structure by annealing. We also approach the problem from another angle by synthesizing a form of the chiral graphene nanoribbons that is functionalized with ketone side groups. This oxidized form is chemically stable and can be converted to the pristine hydrocarbon form by hydrogenation and annealing. In both cases, the deprotected chiral graphene nanoribbons regain electronic properties similar to those of the pristine nanoribbons. We believe both approaches may be extended to other graphene nanoribbons and carbon-based nanostructures.Research was supported by MCIN/AEI/10.13039/501100011033 (grant nos PID2019-107338RB-C62 (D.P.), PID2019-107338RB-C63 (M.C. and D.G.d.O.) and FJC2019-041202-I (F.S.)); the European Union’s Horizon 2020 programme (grant nos 863098 (D.P.) and 635919 (D.G.d.O.), and Marie Skłodowska-Curie Actions Individual Fellowship no. 101022150 (T.W.)); the Gobierno Vasco (grant no. PIBA_2020_1_0036 (D.G.d.O.)); the Xunta de Galicia (Centro Singular de Investigación de Galicia, 2019–2022, grant no. ED431G2019/03 (D.P.)); the European Regional Development Fund; the Praemium Academie of the Academy of Science of the Czech Republic (GACR project no. 20-13692X (P.J.)); the Czech Nanolab Research Infrastructure supported by MEYS CR (project no. LM2018110 (P.J.)); and the Operational Programme for Research, Development and Education of the European Regional Development Fund (project no. CZ.02.1.01/0.0/0.0/16_019/0000754 (P.J.)).Peer reviewe

Good scientific practice in MEEG Research: Progress and Perspectives

Good Scientific Practice (GSP) refers to both explicit and implicit rules, recommendations, and guidelines that help scientists to produce work that is of the highest quality at any given time, and to efficiently share that work with the community for further scrutiny or utilization.For experimental research using magneto- and electroencephalography (MEEG), GSP includes specific standards and guidelines for technical competence, which are periodically updated and adapted to new findings. However, GSP also needs to be periodically revisited in a broader light. At the LiveMEEG 2020 conference, a reflection on GSP was fostered that included explicitly documented guidelines and technical advances, but also emphasized intangible GSP: a general awareness of personal, organizational, and societal realities and how they can influence MEEG research.This article provides an extensive report on most of the LiveMEEG contributions and new literature, with the additional aim to synthesize ongoing cultural changes in GSP. It first covers GSP with respect to cognitive biases and logical fallacies, pre-registration as a tool to avoid those and other early pitfalls, and a number of resources to enable collaborative and reproducible research as a general approach to minimize misconceptions. Second, it covers GSP with respect to data acquisition, analysis, reporting, and sharing, including new tools and frameworks to support collaborative work. Finally, GSP is considered in light of ethical implications of MEEG research and the resulting responsibility that scientists have to engage with societal challenges.Considering among other things the benefits of peer review and open access at all stages, the need to coordinate larger international projects, the complexity of MEEG subject matter, and today's prioritization of fairness, privacy, and the environment, we find that current GSP tends to favor collective and cooperative work, for both scientific and for societal reasons

Stroke genetics informs drug discovery and risk prediction across ancestries

Previous genome-wide association studies (GWASs) of stroke — the second leading cause of death worldwide — were conducted predominantly in populations of European ancestry1,2. Here, in cross-ancestry GWAS meta-analyses of 110,182 patients who have had a stroke (five ancestries, 33% non-European) and 1,503,898 control individuals, we identify association signals for stroke and its subtypes at 89 (61 new) independent loci: 60 in primary inverse-variance-weighted analyses and 29 in secondary meta-regression and multitrait analyses. On the basis of internal cross-ancestry validation and an independent follow-up in 89,084 additional cases of stroke (30% non-European) and 1,013,843 control individuals, 87% of the primary stroke risk loci and 60% of the secondary stroke risk loci were replicated (P < 0.05). Effect sizes were highly correlated across ancestries. Cross-ancestry fine-mapping, in silico mutagenesis analysis3, and transcriptome-wide and proteome-wide association analyses revealed putative causal genes (such as SH3PXD2A and FURIN) and variants (such as at GRK5 and NOS3). Using a three-pronged approach4, we provide genetic evidence for putative drug effects, highlighting F11, KLKB1, PROC, GP1BA, LAMC2 and VCAM1 as possible targets, with drugs already under investigation for stroke for F11 and PROC. A polygenic score integrating cross-ancestry and ancestry-specific stroke GWASs with vascular-risk factor GWASs (integrative polygenic scores) strongly predicted ischaemic stroke in populations of European, East Asian and African ancestry5. Stroke genetic risk scores were predictive of ischaemic stroke independent of clinical risk factors in 52,600 clinical-trial participants with cardiometabolic disease. Our results provide insights to inform biology, reveal potential drug targets and derive genetic risk prediction tools across ancestries

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children