From Molecules to Materials: Pre-training Large Generalizable Models for Atomic Property Prediction

Foundation models have been transformational in machine learning fields such as natural language processing and computer vision. Similar success in atomic property prediction has been limited due to the challenges of training effective models across multiple chemical domains. To address this, we introduce Joint Multi-domain Pre-training (JMP), a supervised pre-training strategy that simultaneously trains on multiple datasets from different chemical domains, treating each dataset as a unique pre-training task within a multi-task framework. Our combined training dataset consists of $\sim$120M systems from OC20, OC22, ANI-1x, and Transition-1x. We evaluate performance and generalization by fine-tuning over a diverse set of downstream tasks and datasets including: QM9, rMD17, MatBench, QMOF, SPICE, and MD22. JMP demonstrates an average improvement of 59% over training from scratch, and matches or sets state-of-the-art on 34 out of 40 tasks. Our work highlights the potential of pre-training strategies that utilize diverse data to advance property prediction across chemical domains, especially for low-data tasks

Viral variants that initiate and drive maturation of V1V2-directed HIV-1 broadly neutralizing antibodies.

CAPRISA, 2015.Abstract available in pdf

Dynamics of Retinal Function After Multiple Photodynamic Therapies in Age-Related Macular Degeneration: A Report of Cases

PURPOSE: To monitor retinal function after multiple laser treatments by photodynamic therapy (PDT) with the multifocal electroretinogram (mfERG) in age-related macular degeneration (AMD). METHODS: Five eyes of five subjects with AMD were investigated before the first and 1 month after each of three PDT treatments. Function was assessed using the cone- and rod-mediated mfERG, high-contrast distance visual acuity, central visual fields and contrast sensitivity. For each subject the local first-order mfERG results before treatment were used as a template and fitted against the local post-treatment results (Matlab, Mathworks). RESULTS: We found transient reduction of the cone- and rod-mediated amplitudes between the first and second treatments but stable or improved mfERG function in four of five eyes for the cone-mediated mfERG and in all eyes for the rod-mediated mfERG after three treatments. Visual acuities and contrast sensitivities remained stable between treatments in four and two eyes respectively, whereas visual fields showed substantially higher mean defects in two subjects after all treatments. CONCLUSION: As found in previous studies of the cone-mediated mfERG after one PDT treatment, objective function was stabilized after multiple treatments in this case report. Similarly, although poor at baseline, rod-mediated function was not further compromised. Transiently reduced amplitudes after 1 month possibly reflected choroidal hypoperfusion. A larger sample size is needed to confirm if additional evaluation using electrophysiological criteria might be helpful in re-treatment decisions during PDT

Low vision assessment and training materials for use in developing countries

The problems faced by developing countries for low vision assessment and training include the size and distribution of the population in relation to available resources, the lack of appropriate assessment materials, and lack of skills and knowledge in the assessment and rehabilitation of low vision. This paper reports on tests and assessment procedures which have been designed utilising technology appropriate to developing countries. Manuals include information on low vision and suggestions for a vision training program. Together these form a multi-purpose kit. Relevant parts can be selected for screening, identification of children with low vision, a comprehensive assessment of functional vision, or a short assessment for a particular purpose such as mobility. The kit has been used and evaluated in many parts of the developing world to ensure its appropriateness

Cone– and rod–mediated retinal function before and after multiple laser therapies in age–related macular degeneration

Aim: To study the cumultative effect of laser treatments with photodynamic therapy (PDT) and transpupillary thermotherapy (TTT) on retinal function in eyes with age–related macular degeneration (AMD). \ud \ud Methods: Seven eyes of seven AMD subjects were investigated before and 4 weeks after each laser treatment during a follow up period of 6 months. Three eyes underwent three PDT treatments and two eyes underwent two PDT treatments. One eye was treated with two TTTs and another eye underwent one PDT and one TTT. We studied subjective macular function by testing visual acuities (VA), central visual fields (VF), contrast sensitivity (Pelli–Robson) and colour vision (sat–D15) as well as cone– and rod–mediated mfERGs (VERIS). The mfERG stimulus for the cones consisted of 103 scaled hexagons and we used the conventional method for deriving the responses. For the rod–mediated mfERG we used a 61 hexagon unscaled stimulus with 3 blank frames, a Wratten 47B filter and reduced the luminance and stray light influence by adding a neutral density filter (1.5 ND) and a surround respectively. For analysis of the mfERG amplitude and implicit time a computer fitting method was applied (Matlab). We compared each of the 103 and 61 local first–order kernel mfERG responses after treatment with those before treatment. \ud \ud Results:Four eyes showed stabilisation in some of the vision measures and three eyes showed impairment in all the psychophysical tests after the second treatment. This was significantly reflected in the cone–mediated mfERG in two eyes (p<0.01). Cone–mediated mfERG function significantly deteriorated in three eyes (p<0.01), improved in one (p<0.01) and remained stable in three eyes after all treatments. Rod–mediated function was significantly impaired in only one eye (p=0.02) and did not show any further deterioration in the other eyes after two treatments. Both eyes treated with TTT showed a significant cone–mediated amplitude reduction greater than 40% which was reflected in reduced subjective function tests in only one eye. Data collection is continuing. \ud \ud Conclusion:Consistent with previous studies with the mfERG after one PDT treatment, subjective and objective function measured by the mfERG appears to be stabilized after multiple PDT treatments. Similarly rod–mediated function seems not to be further compromised. In contrast TTT treated eyes showed greater cone–mediated functional deficits

Performances of Volume Phase Holographic grating for space applications: study of the radiation effect

The special properties of volume phase holographic gratings make them promising candidates for spectrometry applications where high spectral resolution, low levels of straylight, and low polarization sensitivity are required. Therefore it is of interest to assess the maturity and suitability of volume phase holographic gratings as enabling technologies for future space missions, with demanding requirements for spectrometry. One of the main areas of research is related to grating ageing under space radiation. In the present paper, two volume grating technologies are analyzed and compared under gamma irradiation. The performances of both technologies, the photo–thermo–refractive glass and the Dichromated Gelatin, are tested on samples and assessed in the and near-infrared bands. The diffraction efficiency degradation under gamma irradiation is assessed

Open Challenges in Developing Generalizable Large Scale Machine Learning Models for Catalyst Discovery

The development of machine learned potentials for catalyst discovery has predominantly been focused on very specific chemistries and material compositions. While effective in interpolating between available materials, these approaches struggle to generalize across chemical space. The recent curation of large-scale catalyst datasets has offered the opportunity to build a universal machine learning potential, spanning chemical and composition space. If accomplished, said potential could accelerate the catalyst discovery process across a variety of applications (CO2 reduction, NH3 production, etc.) without additional specialized training efforts that are currently required. The release of the Open Catalyst 2020 (OC20) has begun just that, pushing the heterogeneous catalysis and machine learning communities towards building more accurate and robust models. In this perspective, we discuss some of the challenges and findings of recent developments on OC20. We examine the performance of current models across different materials and adsorbates to identify notably underperforming subsets. We then discuss some of the modeling efforts surrounding energy-conservation, approaches to finding and evaluating the local minima, and augmentation of off-equilibrium data. To complement the community's ongoing developments, we end with an outlook to some of the important challenges that have yet to be thoroughly explored for large-scale catalyst discovery.Comment: submitted to ACS Catalysi