Preemptively Pruning Clever-Hans Strategies in Deep Neural Networks

Robustness has become an important consideration in deep learning. With the help of explainable AI, mismatches between an explained model's decision strategy and the user's domain knowledge (e.g. Clever Hans effects) have been identified as a starting point for improving faulty models. However, it is less clear what to do when the user and the explanation agree. In this paper, we demonstrate that acceptance of explanations by the user is not a guarantee for a machine learning model to be robust against Clever Hans effects, which may remain undetected. Such hidden flaws of the model can nevertheless be mitigated, and we demonstrate this by contributing a new method, Explanation-Guided Exposure Minimization (EGEM), that preemptively prunes variations in the ML model that have not been the subject of positive explanation feedback. Experiments demonstrate that our approach leads to models that strongly reduce their reliance on hidden Clever Hans strategies, and consequently achieve higher accuracy on new data.Comment: 18 pages + supplemen

REVERSIBLE HEPARIN MOLECULES AND METHODS OF MAKING AND USING THE SAME

Methods and systems for synthesizing heparin compounds are provided . The chemoenzymatic synthesis of structurally homogeneous low molecular weight heparins that have a reversible anticoagulant activity is provided . Also disclosed are heparin compounds having anticoagulant activity , including a binding affinity to antithrombin and an anti - Xa activity , but no detectable anti - lla activity . Additionally , provided are synthetic , low - molecular weight heparin com pounds with reversible anticoagulant activity , where the anticoagulant activity is reversible by protamine

Engineering sulfate donor accumulation in Escherichia coli for synthesis of sulfated glycosaminoglycans

The model bacterium Escherichia coli has been extensively engineered for a variety of applications. However, sulfated biomolecules remain a relatively under-explored domain of biologics that can be synthesized using E. coli. An important class in this domain are sulfated glycosaminoglycans (GAGs) which are of great pharmaceutical/nutraceutical interest. On-going studies aim at developing efficient and scalable chemical and chemoenzymatic methods to produce these compounds. However, we propose that engineered E. coli capable of entirely in vivo synthesis of sulfated GAGs will serve as a great alternative to the current state-of-art. The biosynthesis of sulfated biomolecules relies on the universal sulfate donor, 3’-phosphoadenosine-5’-phosphosulfate (PAPS). PAPS plays the role of a co-enzyme in enzymatic sulfotransferase reactions and donates the sulfate to the substrate. In the first part of this study, we engineered the metabolism of E. coli to improve PAPS accumulation around 10000-fold. In the second part, we applied this engineered strain to in vitro biosynthesis of chondroitin sulfate (a sulfated GAG). Certain strains of E. coli possess the ability to biosynthesize unsulfated GAG backbones. These have been well-studied and optimized for GAG production. In vitro sulfation requires the addition of purified sulfotransferase and an excess of commercially obtained PAPS to the unsulfated GAG. By utilizing PAPS from our engineered strain in the existing setup, we improve the biotransformation method to one in which all components are synthesized from E. coli. We also use this system and its comparison to other in vitro systems to identify the bottlenecks for total in vivo synthesis of sulfated GAGs in E. coli. We show for the first time that with this system, we have achieved the synthesis of chondroitin sulfate A without the dependence on the commercially procured PAPS cofactor

Chemoenzymatic synthesis of heparan sulfate and heparin oligosaccharides and NMR analysis: Paving the way to a diverse library for glycobiologists

Heparin and heparan sulfate are sulfated carbohydrates that display a wide range of biological functions. A chemoenzymatic method is becoming a promising approach to synthesize heparin-like oligosaccharides with high efficiency

Human alignment of neural network representations

Today's computer vision models achieve human or near-human level performance across a wide variety of vision tasks. However, their architectures, data, and learning algorithms differ in numerous ways from those that give rise to human vision. In this paper, we investigate the factors that affect the alignment between the representations learned by neural networks and human mental representations inferred from behavioral responses. We find that model scale and architecture have essentially no effect on the alignment with human behavioral responses, whereas the training dataset and objective function both have a much larger impact. These findings are consistent across three datasets of human similarity judgments collected using two different tasks. Linear transformations of neural network representations learned from behavioral responses from one dataset substantially improve alignment with human similarity judgments on the other two datasets. In addition, we find that some human concepts such as food and animals are well-represented by neural networks whereas others such as royal or sports-related objects are not. Overall, although models trained on larger, more diverse datasets achieve better alignment with humans than models trained on ImageNet alone, our results indicate that scaling alone is unlikely to be sufficient to train neural networks with conceptual representations that match those used by humans.Comment: Accepted for publication at ICLR 202

Chloroquine reduces arylsulphatase B activity and increases chondroitin-4-sulphate: implications for mechanisms of action and resistance

<p>Abstract</p> <p>Background</p> <p>The receptors for adhesion of <it>Plasmodium falciparum</it>-infected red blood cells (RBC) in the placenta have been identified as chondroitin-4-sulphate (C4S) proteoglycans, and the more sulphate-rich chondroitin oligosaccharides have been reported to inhibit adhesion. Since the anti-malarial drug chloroquine accumulates in lysosomes and alters normal lysosomal processes, the effects of chloroquine on the lysosomal enzyme arylsulphatase B (ASB, N-acetylgalactosamine-4-sulphatase), which removes 4-sulphate groups from chondroitin-4-sulphate, were addressed. The underlying hypothesis derived from the recognized impairment of attachment of parasite-infected erythrocytes in the placenta, when chondroitin-4-sulphation was increased. If chloroquine reduced ASB activity, leading to increased chondroitin-4-sulphation, it was hypothesized that the anti-malarial mechanism of chloroquine might derive, at least in part, from suppression of ASB.</p> <p>Methods</p> <p>Experimental methods involved cell culture of human placental, bronchial epithelial, and cerebrovascular cells, and the <it>in vitro </it>exposure of the cells to chloroquine at increasing concentrations and durations. Measurements of arylsulphatase B enzymatic activity, total sulphated glycosaminoglycans (sGAG), and chondroitin-4-sulphate (C4S) were performed using <it>in vitro </it>assays, following exposure to chloroquine and in untreated cell preparations. Fluorescent immunostaining of ASB was performed to determine the effect of chloroquine on cellular ASB content and localization. Mass spectrometry and high performance liquid chromatography were performed to document and to quantify the changes in chondroitin disaccharides following chloroquine exposure.</p> <p>Results</p> <p>In the human placental, bronchial epithelial, and cerebrovascular cells, exposure to increasing concentrations of chloroquine was associated with reduced ASB activity and with increased concentrations of sGAG, largely attributable to increased C4S. The study data demonstrated: 1) decline in ASB activity following chloroquine exposure; 2) inverse correlation between ASB activity and C4S content; 3) increased content of chondroitin-4-sulphate disaccharides following chloroquine exposure; and 4) decline in extent of chloroquine-induced ASB reduction with lower baseline ASB activity. Confocal microscopy demonstrated the presence of ASB along the cell periphery, indicating extra-lysosomal localization.</p> <p>Conclusions</p> <p>The study data indicate that the therapeutic mechanism of chloroquine action may be attributable, at least in part, to reduction of ASB activity, leading to increased chondroitin-4-sulphation in human placental, bronchial epithelial, and cerebrovascular cells. In vivo, increased chondroitin-4-sulphation may reduce the attachment of <it>P. falciparum</it>-infected erythrocytes to human cells. Extra-lysosomal localization of ASB and reduced impact of chloroquine when baseline ASB activity is less suggest possible mechanisms of resistance to the effects of chloroquine.</p

Negative ion fast-atom bombardment tandem mass spectrometry to determine sulfate and linkage position in glycosaminoglycan-derived disaccharides

AbstractNegative ion fast-atom bombardment tandem mass spectrometry has been used in the analysis of monosulfated disaccharides. These commercially obtained disaccharides have been enzymatically prepared from glycosaminoglycans using polysaccharide lyases. Three disaccharides from chondroitin sulfate and dermatan sulfate and two disaccharides from heparan sulfate and chemically derivatized heparin were analyzed. All five disaccharides were isomeric, with differences in sulfate position and linkage position. The full-scan mass spectra are useful in differentiating isomers when the sulfate group resides on different saccharide units. This structural information was obtained from fragment ions produced through cleavage at the glycosidic linkage. the full-scan mass spectra of each monosulfated disaccharide also produced intense molecular anions having long lifetimes. Collisional activation of these resulted in tandem mass spectra rich in significant product ions. Some of these fragment ions were formed through ring cleavage and were useful in the determination of both sulfate and linkage position

Electron-Induced Dissociation of Glycosaminoglycan Tetrasaccharides

Electron detachment dissociation (EDD) Fourier transform mass spectrometry has recently been shown to be a powerful tool for examining the structural features of sulfated glycosaminoglycans (GAGs). The characteristics of GAG fragmentation by EDD include abundant cross-ring fragmentation primarily on hexuronic acid residues, cleavage of all glycosidic bonds, and the formation of even- and odd-electron product ions. GAG dissociation by EDD has been proposed to occur through the formation of an excited species that can undergo direct decomposition or ejects an electron and then undergoes dissociation. In this work, we perform electron-induced dissociation (EID) on singly charged GAGs to identify products that form via direct decomposition by eliminating the pathway of electron detachment. EID of GAG tetrasaccharides produces cleavage of all glycosidic bonds and abundant cross-ring fragmentation primarily on hexuronic acid residues, producing fragmentation similar to EDD of the same molecules, but distinctly different from the products of infrared multiphoton dissociation or collisionally activated decomposition. These results suggest that observed abundant fragmentation of hexuronic acid residues occurs as a result of their increased lability when they undergo electronic excitation. EID fragmentation of GAG tetrasaccharides results in both even- and odd-electron products. EID of heparan sulfate tetrasaccharide epimers produces identical fragmentation, in contrast to EDD, in which the epimers can be distinguished by their fragment ions. These data suggest that for EDD, electron detachment plays a significant role in distinguishing glucuronic acid from iduronic acid

Enzymatic Synthesis of Glycosaminoglycan Heparin

Heparin and its low molecular weight heparin derivatives, widely used as clinical anticoagulants, are acidic polysaccharide members of a family of biomacromolecules called glycosaminoglycans (GAGs). Heparin and the related heparan sulfate are biosynthesized in the Golgi apparatus of eukaryotic cells. Heparin is a polycomponent drug that currently is prepared for clinical use by extraction from animal tissues. A heparin pentasaccharide, fondaparinux, has also been prepared through chemical synthesis for use as a homogenous anticoagulant drug. Recent enabling technologies suggest that it may now be possible to synthesize heparin and its derivatives enzymatically. Moreover, new technologies including advances in synthetic carbohydrate synthesis, enzyme-based GAG synthesis, micro- and nano-display of GAGs, rapid on-line structural analysis, and microarray/microfluidic technologies might be applied to the enzymatic synthesis of heparins with defined structures and exhibiting selected activities. The advent of these new technologies also makes it possible to consider the construction of an artificial Golgi to increase our understanding of the cellular control of GAG biosyntheses in this organelle