Understanding polysemanticity in neural networks through coding theory

Despite substantial efforts, neural network interpretability remains an elusive goal, with previous research failing to provide succinct explanations of most single neurons' impact on the network output. This limitation is due to the polysemantic nature of most neurons, whereby a given neuron is involved in multiple unrelated network states, complicating the interpretation of that neuron. In this paper, we apply tools developed in neuroscience and information theory to propose both a novel practical approach to network interpretability and theoretical insights into polysemanticity and the density of codes. We infer levels of redundancy in the network's code by inspecting the eigenspectrum of the activation's covariance matrix. Furthermore, we show how random projections can reveal whether a network exhibits a smooth or non-differentiable code and hence how interpretable the code is. This same framework explains the advantages of polysemantic neurons to learning performance and explains trends found in recent results by Elhage et al.~(2022). Our approach advances the pursuit of interpretability in neural networks, providing insights into their underlying structure and suggesting new avenues for circuit-level interpretability

Development of a stereovision-based technique to measure the spread patterns of granular fertilizer spreaders

Centrifugal fertilizer spreaders are by far the most commonly used granular fertilizer spreader type in Europe. Their spread pattern however is error-prone, potentially leading to an undesired distribution of particles in the field and losses out of the field, which is often caused by poor calibration of the spreader for the specific fertilizer used. Due to the large environmental impact of fertilizer use, it is important to optimize the spreading process and minimize these errors. Spreader calibrations can be performed by using collection trays to determine the (field) spread pattern, but this is very time-consuming and expensive for the farmer and hence not common practice. Therefore, we developed an innovative multi-camera system to predict the spread pattern in a fast and accurate way, independent of the spreader configuration. Using high-speed stereovision, ejection parameters of particles leaving the spreader vanes were determined relative to a coordinate system associated with the spreader. The landing positions and subsequent spread patterns were determined using a ballistic model incorporating the effect of tractor motion and wind. Experiments were conducted with a commercial spreader and showed a high repeatability. The results were transformed to one spatial dimension to enable comparison with transverse spread patterns determined in the field and showed similar results

Cell Population Dynamics in Wound-Induced Hair Follicle Neogenesis Model

Hair follicle (HF) regeneration can be achieved in the center of large full-thickness wounds on mouse backs (wound-induced HF neogenesis model, WIHN). Investigations with this model have allowed for the identification of some of the factors limiting the extent of fibrosis, which creates a permissive environment for the reposition of HF. For WIHN, specific subpopulations of cells rather than cell types are permissive to this process. Detailed information on the cellular composition in WIHN is not available. Here, we provide a description of changes in cell numbers of fibroblasts, HF dermal papilla, endothelial cells, keratinocytes (interfollicular epidermis, HF-infundibulum, HF-isthmus, HF-bulge (basal and suprabasal), HF-hair germ) and immune cells (macrophages, monocytes, dendritic cells, T cells (CD4+ , CD8+ , CD4+/CD8+ , regulatory T cells) and neutrophils) based on flow cytometric analysis. We compared unwounded skin with large wounds (1.5 × 1.5 cm) at different time points after wounding. We found that non-immune dermal cells have the largest share in the skin at all time points studied, and that the number of epidermal cells started increasing nine days after wounding, which precede isthmus cells and bulge cells, mirroring the development of hair follicles. Monocytes and neutrophils represent most myeloid cells in wounds and remain in wounds even beyond the inflammatory phase of wound healing. Macrophages can be identified as inflammatory and alternative cells and are also found in wounds even in the late remodeling phase of wound healing. Lastly, we provide information about T cells in large wounds. Most T cells in the wounds were CD8+ at all time points and expressed γδTCR, which was previously thought to be expressed mainly on CD4+ . We also report the existence of double positive CD4/CD8. Our study provides a guide in terms of time points suitable for the further study of cell subpopulations aiming to dissect the cellular heterogeneity in WIHN. Our results might set the base for the comparison of WIHN between control mice and animals manipulated to influence HF neogenesis and the full understanding of the responsible actors allowing for HF regeneration

Precision and Personalized Medicine and anti-TB treatment:Is TDM feasible for programmatic use?

Therapeutic Drug Monitoring (TDM) is increasingly recommended to ensure the correct drug dose thereby minimizing adverse events and maximizing regimen efficacy. To facilitate implementation in TB programs, a framework for TDM is urgently needed. TDM is only useful for dose optimization if a patient is on an appropriate regimen guided by drug susceptibility testing. TDM using a targeted approach selecting patients with risk factors for suboptimal drug exposure (e.g. diabetes) or not responding to treatment for drugs with a clear concentration-response relationship may provide the best value for money. Semiquantitative point-of-care tests for detection of low or high drug concentration should be implemented at community level while quantitative assays can be performed at regional or central level. Expanding PK/PD research followed by clinical trials including both clinical outcome as well as cost-effectiveness will increase the level of evidence supporting TDM

Molecular Simulation Study on the Influence of the Scratching Velocity on Nanoscopic Contact Processes

The influence of the scratching velocity on mechanical and thermal properties of a nanoscopic contact process was studied by molecular dynamics simulations. Simulations with different scratching velocities were conducted in dry and lubricated systems. The contact process consisted of a lateral scratching of a spherical indenter on a planar substrate. All molecular interactions were described by the Lennard-Jones truncated and shifted potential. The forces on the indenter, the coefficient of friction and the work done by the indenter as well as the power applied on the indenter were sampled. Furthermore, an analysis of thermal properties was conducted: The change of the energy of the substrate, the indenter and the fluid was evaluated and the local temperature field was determined. The forces, the coefficient of friction and the work done by the indenter show practically no influence of the scratching velocity. The work done by the indenter was found to be the same for all velocities. As a consequence, the power supplied to the system depends linearly on the scratching velocity, which affects the temperature of the contact zone. As expected, the presence of a lubricant reduces the temperature of the substrate in the vicinity of the contact

Identification of Seasonal Variations of Antibodies against PR-10-Specific Epitopes Can Be Improved Using Peptide-Phage Display

Background: In pollinosis patients, allergen-specific antibody titers show seasonal variations. Little is known about these variations at the epitope level. Objectives: We aimed at investigating seasonal variations on the level of allergen epitope recognition in patients with Bet v 1-related food allergy using a peptide phage display approach. Methods: Serum samples collected over 1 year from 4 patients of the placebo arm of the birch-associated soya allergy immunotherapy trial were included. To identify epitopes from Bet v 1-related food allergens, patient sera were used in peptide phage display experiments. In silico analysis of enriched allergen-related motifs was performed. Results: We identified epitope motifs related to Bet v 1 and its homologs in soya and hazelnut (Gly m 4 and Cor a 1, respectively) that were enriched in accordance with birch and hazel pollen exposure. Within several weeks after the birch pollen season peak, the pattern of identified epitope motifs differed considerably among patients. Data for amino acid preferences in homologous Bet v 1 and Cor a 1 epitope motifs identified for one of the investigated patients suggest changes in concentration or specificity of serum antibodies for the Cor a 1 epitope motif. Conclusions: Peptide phage display data suggest an impact of birch and hazel pollen exposure on the recognition pattern of Bet v 1-like allergen epitopes. Epitope-oriented analyses could provide deeper, personalized details regarding the allergen epitope recognition influenced by pollen exposure beyond the capability of current method