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Drug discovery typically consists of multiple steps, including identifying a target protein key to a disease's etiology, validating that interacting with this target could prevent symptoms or cure the disease, discovering a small molecule or biologic therapeutic to interact with it, and optimizing the candidate molecule through a complex landscape of required properties. Drug discovery related tasks often involve prediction and generation while considering multiple entities that potentially interact, which poses a challenge for typical AI models. For this purpose we present MAMMAL - Molecular Aligned Multi-Modal Architecture and Language - a method that we applied to create a versatile multi-task multi-align foundation model that learns from large-scale biological datasets (2 billion samples) across diverse modalities, including proteins, small molecules, and genes. We introduce a prompt syntax that supports a wide range of classification, regression, and generation tasks. It allows combining different modalities and entity types as inputs and/or outputs. Our model handles combinations of tokens and scalars and enables the generation of small molecules and proteins, property prediction, and transcriptomic lab test predictions. We evaluated the model on 11 diverse downstream tasks spanning different steps within a typical drug discovery pipeline, where it reaches new SOTA in 9 tasks and is comparable to SOTA in 2 tasks. This performance is achieved while using a unified architecture serving all tasks, in contrast to the original SOTA performance achieved using tailored architectures. The model code and pretrained weights are publicly available at https://github.com/BiomedSciAI/biomed-multi-alignment and https://huggingface.co/ibm/biomed.omics.bl.sm.ma-ted-458m.

Bayesian Optimization is ubiquitous in the field of experimental design and blackbox optimization for improving search efficiency, but has been traditionally restricted to regression models which are only applicable to fixed search spaces and tabular input features. We propose Embed-then-Regress, a paradigm for applying in-context regression over string inputs, through the use of string embedding capabilities of pretrained language models. By expressing all inputs as strings, we are able to perform general-purpose regression for Bayesian Optimization over various domains including synthetic, combinatorial, and hyperparameter optimization, obtaining comparable results to state-of-the-art Gaussian Process-based algorithms. Code can be found at https://github.com/google-research/optformer/tree/main/optformer/embed_then_regress.

The evolution of biological neural systems has led to both modularity and sparse coding, which enables efficiency in energy usage, and robustness across the diversity of tasks in the lifespan. In contrast, standard neural networks rely on dense, non-specialized architectures, where all model parameters are simultaneously updated to learn multiple tasks, leading to representation interference. Current sparse neural network approaches aim to alleviate this issue, but are often hindered by limitations such as 1) trainable gating functions that cause representation collapse; 2) non-overlapping experts that result in redundant computation and slow learning; and 3) reliance on explicit input or task IDs that impose significant constraints on flexibility and scalability. In this paper we propose Conditionally Overlapping Mixture of ExperTs (COMET), a general deep learning method that addresses these challenges by inducing a modular, sparse architecture with an exponential number of overlapping experts. COMET replaces the trainable gating function used in Sparse Mixture of Experts with a fixed, biologically inspired random projection applied to individual input representations. This design causes the degree of expert overlap to depend on input similarity, so that similar inputs tend to share more parameters. This facilitates positive knowledge transfer, resulting in faster learning and improved generalization. We demonstrate the effectiveness of COMET on a range of tasks, including image classification, language modeling, and regression, using several popular deep learning architectures.

Resolving knowledge conflicts is a crucial challenge in Question Answering (QA) tasks, as the internet contains numerous conflicting facts and opinions. While some research has made progress in tackling ambiguous settings where multiple valid answers exist, these approaches often neglect to provide source citations, leaving users to evaluate the factuality of each answer. On the other hand, existing work on citation generation has focused on unambiguous settings with single answers, failing to address the complexity of real-world scenarios. Despite the importance of both aspects, no prior research has combined them, leaving a significant gap in the development of QA systems. In this work, we bridge this gap by proposing the novel task of QA with source citation in ambiguous settings, where multiple valid answers exist. To facilitate research in this area, we create a comprehensive framework consisting of: (1) five novel datasets, obtained by augmenting three existing reading comprehension datasets with citation meta-data across various ambiguous settings, such as distractors and paraphrasing; (2) the first ambiguous multi-hop QA dataset featuring real-world, naturally occurring contexts; (3) two new metrics to evaluate models' performances; and (4) several strong baselines using rule-based, prompting, and finetuning approaches over five large language models. We hope that this new task, datasets, metrics, and baselines will inspire the community to push the boundaries of QA research and develop more trustworthy and interpretable systems., Comment: Accepted to EMNLP 2024

We present the updated design of HighSpec, a high-resolution $\mathcal{R} \sim 20,000$ spectrograph designed for the Multi Aperture Spectroscopic Telescope (MAST). HighSpec offers three observing modes centered at the Ca II H&K, Mg b triplet, and H$\alpha$ lines. Each mode is supported by a highly optimized ion-etched grating, contributing to an exceptional instrument peak efficiency of $\gtrsim85\%$ for the two latter bands ($\gtrsim55\%$ for the Ca II H&K band). Optimizing throughput over wavelength coverage ($\Delta \lambda=10-17$ nm), HighSpec enables the precise measurement of spectral lines from faint targets. This approach is especially relevant for stellar object studies, specifically of WDs, which are intrinsically faint and have few spectroscopic lines. Each observing mode was tailored to target spectral features essential for WD research. Its integration with MAST, an array of 20 custom-designed telescopes that can function as a single large telescope (equivalent to a $2.7$ m telescope in collecting area) or multiplexing over the entire sky, provides unique adaptability for extensive and effective spectroscopic campaigns. Currently in its final assembly and testing stages, HighSpec's on-sky commissioning is scheduled for 2025., Comment: SPIE Conference "Space Telescopes and Instrumentation 2024: Ground-based and Airborne Instrumentation for Astronomy X", Yokahama, Japan

Google Vizier has performed millions of optimizations and accelerated numerous research and production systems at Google, demonstrating the success of Bayesian optimization as a large-scale service. Over multiple years, its algorithm has been improved considerably, through the collective experiences of numerous research efforts and user feedback. In this technical report, we discuss the implementation details and design choices of the current default algorithm provided by Open Source Vizier. Our experiments on standardized benchmarks reveal its robustness and versatility against well-established industry baselines on multiple practical modes., Comment: Google DeepMind Technical Report. Code can be found in https://github.com/google/vizier

This study explores the impact of class outliers on the effectiveness of example-based explainability methods for black-box machine learning models. We reformulate existing explainability evaluation metrics, such as correctness and relevance, specifically for example-based methods, and introduce a new metric, distinguishability. Using these metrics, we highlight the shortcomings of current example-based explainability methods, including those who attempt to suppress class outliers. We conduct experiments on two datasets, a text classification dataset and an image classification dataset, and evaluate the performance of four state-of-the-art explainability methods. Our findings underscore the need for robust techniques to tackle the challenges posed by class outliers., Comment: arXiv admin note: text overlap with arXiv:2407.16010

SOXS (Son Of X-Shooter) is the new single object spectrograph for the ESO New Technology Telescope (NTT) at the La Silla Observatory, able to cover simultaneously both the UV-VIS and NIR bands (350-2000 nm). The instrument is currently in the integration and test phase, approaching the Preliminary Acceptance in Europe (PAE) before shipment to Chile for commissioning. After the assembly and preliminary test of the control electronics at INAF - Astronomical Observatory of Capodimonte (Napoli), the two main control cabinets of SOXS are now hosted in Padova, connected to the real hardware. This contribution describes the final electronic cabinets layout, the control strategy and the different integration phases, waiting for the Preliminary Acceptance in Europe and the installation of the instrument in Chile.

The Son Of X-Shooter (SOXS) will be the specialized facility to observe any transient event with a flexible scheduler at the ESO New Technology Telescope (NTT) at La Silla, Chile. SOXS is a single object spectrograph offering simultaneous spectral coverage in UV-VIS (350-850 nm) and NIR (800-2000 nm) wavelength regimes with an average of R~4500 for a 1arcsec slit. SOXS also has imaging capabilities in the visible wavelength regime. Currently, SOXS is being integrated at the INAF-Astronomical Observatory of Padova. Subsystem- and system-level tests and verification are ongoing to ensure and confirm that every requirement and performance are met. In this paper, we report on the integration and verification of SOXS as the team and the instrument prepare for the Preliminary Acceptance Europe (PAE).

The Son Of X-Shooter (SOXS) is a single object spectrograph, built by an international consortium for the 3.58-m ESO New Technology Telescope at the La Silla Observatory [1]. It offers a simultaneous spectral coverage over 350-2000 nm, with two separate spectrographs. In this paper we present the status of the Near InfraRed (NIR) cryogenic echelle cross-dispersed spectrograph [1], in the range 0.80-2.00 {\mu}m with 15 orders, equipped with an 2k x 2k Hawaii H2RG IR array from Teledyne, working at 40K, that is currently assembled and tested on the SOXS instrument, in the premises of INAF in Padova. We describe the different tests and results of the cryo, vacuum, opto-mechanics and detector subsystems that finally will be part of the PAE by ESO., Comment: 8 Pages, 7 Figures, Astronomical Telescopes and Instrumentation, SPIE Proceedings 2024

We present the advancements in the development of the scheduler for the Son Of X-shooter instrument at the ESO-NTT 3.58-m telescope in La Silla, Chile. SOXS is designed as a single-object spectroscopic facility and features a high-efficiency spectrograph with two arms covering the spectral range of 350-2000 nm and a mean resolving power of approximately R=4500. It will conduct UV-visible and near-infrared follow-up observations of astrophysical transients, drawing from a broad pool of targets accessible through the streaming services of wide-field telescopes, both current and future, as well as high-energy satellites. The instrument will cater to various scientific objectives within the astrophysical community, each entailing specific requirements for observation planning. SOXS will operate at the European Southern Observatory (ESO) in La Silla, without the presence of astronomers on the mountain. This poses a unique challenge for the scheduling process, demanding a fully automated algorithm that is autonomously interacting with the appropriate databases and the La Silla Weather API, and is capable of presenting the operator not only with an ordered list of optimal targets (in terms of observing constraints) but also with optimal backups in the event of changing weather conditions. This imposes the necessity for a scheduler with rapid-response capabilities without compromising the optimization process, ensuring the high quality of observations and best use of the time at the telescope. We thus developed a new highly available and scalable architecture, implementing API Restful applications like Docker Containers, API Gateway, and Python-based Flask frameworks. We provide an overview of the current state of the scheduler, which is now ready for the approaching on-site testing during Commissioning phase, along with insights into its web interface and preliminary performance tests.

The SOXS spectrograph, designed for the ESO NTT telescope, operates in both the optical (UV-VIS: 350-850 nm) and NIR (800-2000 nm) bands. This article provides an overview of the final tests conducted on the UV-VIS camera system using a telescope simulator. It details the system's performance evaluation, including key metrics such as gain, readout noise, and linearity, and highlights the advancements made in the upgraded acquisition system. The testing process, conducted in the Padua laboratory, involved comprehensive simulations of the telescope environment to ensure the results closely resemble those expected at the ESO-NTT telescope. The successful completion of these tests confirms the system's readiness for deployment to Chile, where it will be installed on the NTT telescope, marking a significant milestone in the SOXS project., Comment: SPIE Proceedings Volume 13096, Ground-based and Airborne Instrumentation for Astronomy X; 130962U (2024)

The Instrument Control Software of SOXS (Son Of X-Shooter), the forthcoming spectrograph for the ESO New Technology Telescope at the La Silla Observatory, has reached a mature state of development and is approaching the crucial Preliminary Acceptance in Europe phase. Now that all the subsystems have been integrated in the laboratories of the Padova Astronomical Observatory, the team operates for testing purposes with the whole instrument at both engineering and scientific level. These activities will make use of a set of software peculiarities that will be discussed in this contribution. In particular, we focus on the synoptic panel, the co-rotator system special device, on the Active Flexure Compensation system which controls two separate piezo tip-tilt devices., Comment: 6 pages, 3 figures, SPIE conference

For many use-cases, it is often important to explain the prediction of a black-box model by identifying the most influential training data samples. Existing approaches lack customization for user intent and often provide a homogeneous set of explanation samples, failing to reveal the model's reasoning from different angles. In this paper, we propose AIDE, an approach for providing antithetical (i.e., contrastive), intent-based, diverse explanations for opaque and complex models. AIDE distinguishes three types of explainability intents: interpreting a correct, investigating a wrong, and clarifying an ambiguous prediction. For each intent, AIDE selects an appropriate set of influential training samples that support or oppose the prediction either directly or by contrast. To provide a succinct summary, AIDE uses diversity-aware sampling to avoid redundancy and increase coverage of the training data. We demonstrate the effectiveness of AIDE on image and text classification tasks, in three ways: quantitatively, assessing correctness and continuity; qualitatively, comparing anecdotal evidence from AIDE and other example-based approaches; and via a user study, evaluating multiple aspects of AIDE. The results show that AIDE addresses the limitations of existing methods and exhibits desirable traits for an explainability method.

A large population of intermediate-separation binaries, consisting of a main-sequence (MS) star and a white dwarf (WD), has recently emerged from Gaia's third data release (DR3), posing challenges to current models of binary evolution. Here we examine the $s$-process element abundances in these systems using data from GALAH DR3. Following refined sample analysis with parameter estimates based on GALAH spectra, we find a distinct locus where enhanced $s$-process elements depend on both the WD mass and metallicity, consistent with loci identified in previous asymptotic giant branch (AGB) nucleosynthesis studies with higher $s$-process yields. Notably, these enhanced abundances show no correlation with the systems' orbital parameters, supporting a history of accretion in intermediate-separation MS+WD systems. Consequently, our results form a direct observational evidence of a connection between AGB masses and $s$-process yields. We conclude by showing that the GALAH DR3 survey includes numerous Ba dwarf stars, within and beyond the mass range covered in our current sample, which can further elucidate $s$-process element distributions in MS+WD binaries., Comment: Published in ApJL; 12 pages, 10 figures

High kinetic inductance superconductors are gaining increasing interest for the realisation of qubits, amplifiers and detectors. Moreover, thanks to their high impedance, quantum buses made of such materials enable large zero-point fluctuations of the voltage, boosting the coupling rates to spin and charge qubits. However, fully exploiting the potential of disordered or granular superconductors is challenging, as their inductance and, therefore, impedance at high values are difficult to control. Here we have integrated a granular aluminium resonator, having a characteristic impedance exceeding the resistance quantum, with a germanium double quantum dot and demonstrate strong charge-photon coupling with a rate of $g_\text{c}/2\pi= (566 \pm 2)$ MHz. This was achieved due to the realisation of a wireless ohmmeter, which allows \emph{in situ} measurements during film deposition and, therefore, control of the kinetic inductance of granular aluminium films. Reproducible fabrication of circuits with impedances (inductances) exceeding 13 k$\Omega$ (1 nH per square) is now possible. This broadly applicable method opens the path for novel qubits and high-fidelity, long-distance two-qubit gates.

Vastextures is a vast repository of 500,000 textures and PBR materials extracted from real-world images using an unsupervised process. The extracted materials and textures are extremely diverse and cover a vast range of real-world patterns, but at the same time less refined compared to existing repositories. The repository is composed of 2D textures cropped from natural images and SVBRDF/PBR materials generated from these textures. Textures and PBR materials are essential for CGI. Existing materials repositories focus on games, animation, and arts, that demand a limited amount of high-quality assets. However, virtual worlds and synthetic data are becoming increasingly important for training A.I systems for computer vision. This application demands a huge amount of diverse assets but at the same time less affected by noisy and unrefined assets. Vastexture aims to address this need by creating a free, huge, and diverse assets repository that covers as many real-world materials as possible. The materials are automatically extracted from natural images in two steps: 1) Automatically scanning a giant amount of images to identify and crop regions with uniform textures. This is done by splitting the image into a grid of cells and identifying regions in which all of the cells share a similar statistical distribution. 2) Extracting the properties of the PBR material from the cropped texture. This is done by randomly guessing every correlation between the properties of the texture image and the properties of the PBR material. The resulting PBR materials exhibit a vast amount of real-world patterns as well as unexpected emergent properties. Neutral nets trained on this repository outperformed nets trained using handcrafted assets., Comment: Vastexture was published as part of Learning Zero-Shot Material States Segmentation, by Implanting Natural Image Patterns in Synthetic Data, refer to this work in citations. This document gives a more detailed and technical discussion of this repository

Natural language processing has seen rapid progress over the past decade. Due to the speed of developments, some practices get established without proper evaluation. Considering one such case and focusing on reading comprehension, we ask our first research question: 1) How does the order of inputs -- i.e., question and context -- affect model performance? Additionally, given recent advancements in input emphasis, we ask a second research question: 2) Does emphasizing either the question, the context, or both enhance performance? Experimenting with 9 large language models across 3 datasets, we find that presenting the context before the question improves model performance, with an accuracy increase of up to $31\%$. Furthermore, emphasizing the context yields superior results compared to question emphasis, and in general, emphasizing parts of the input is particularly effective for addressing questions that models lack the parametric knowledge to answer. Experimenting with both prompt-based and attention-based emphasis methods, we additionally find that the best method is surprisingly simple: it only requires concatenating a few tokens to the input and results in an accuracy improvement of up to $36\%$, allowing smaller models to outperform their significantly larger counterparts., Comment: Accepted to ACL Findings

Atomic interferometers measure phase differences along paths with exceptional precision. Tweezer interferometry represents a novel approach for this measurement by guiding particles along predefined trajectories. This study explores the feasibility of using condensed bosons in tweezer interferometry. Unlike the factor $\sqrt{N}$ enhancement expected with classical ensembles, using NOON state interferometry can yield an enhancement by a factor of $N$. We consider a protocol for a tweezer-based NOON state interferometer that includes adiabatic splitting and merging of condensed bosons, followed by adiabatic branching for phase encoding. Our theoretical analysis focuses on the conditions necessary to achieve adiabaticity and avoid spontaneous symmetry breaking. Additionally, we demonstrate the feasibility of the proposed scheme and estimate the time required to perform these sweep processes., Comment: 14 pages, 10 figures

Gate-tunable transmons (gatemons) employing semiconductor Josephson junctions have recently emerged as building blocks for hybrid quantum circuits. In this study, we present a gatemon fabricated in planar Germanium. We induce superconductivity in a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which separates the superconductor from the Ge quantum well. The Josephson junction is then integrated into an Xmon circuit and capacitively coupled to a transmission line resonator. We showcase the qubit tunability in a broad frequency range with resonator and two-tone spectroscopy. Time-domain characterizations reveal energy relaxation and coherence times up to 75 ns. Our results, combined with the recent advances in the spin qubit field, pave the way towards novel hybrid and protected qubits in a group IV, CMOS-compatible material.

Addressing the so-called ``Red-AI'' trend of rising energy consumption by large-scale neural networks, this study investigates the actual energy consumption, as measured by node-level watt-meters, of training various fully connected neural network architectures. We introduce the BUTTER-E dataset, an augmentation to the BUTTER Empirical Deep Learning dataset, containing energy consumption and performance data from 63,527 individual experimental runs spanning 30,582 distinct configurations: 13 datasets, 20 sizes (number of trainable parameters), 8 network ``shapes'', and 14 depths on both CPU and GPU hardware collected using node-level watt-meters. This dataset reveals the complex relationship between dataset size, network structure, and energy use, and highlights the impact of cache effects. We propose a straightforward and effective energy model that accounts for network size, computing, and memory hierarchy. Our analysis also uncovers a surprising, hardware-mediated non-linear relationship between energy efficiency and network design, challenging the assumption that reducing the number of parameters or FLOPs is the best way to achieve greater energy efficiency. Highlighting the need for cache-considerate algorithm development, we suggest a combined approach to energy efficient network, algorithm, and hardware design. This work contributes to the fields of sustainable computing and Green AI, offering practical guidance for creating more energy-efficient neural networks and promoting sustainable AI., Comment: 25 pages, 8 figures, for associated dataset see https://data.openei.org/submissions/5991

Visual recognition of materials and their states is essential for understanding the physical world, from identifying wet regions on surfaces or stains on fabrics to detecting infected areas on plants or minerals in rocks. Collecting data that captures this vast variability is complex due to the scattered and gradual nature of material states. Manually annotating real-world images is constrained by cost and precision, while synthetic data, although accurate and inexpensive, lacks real-world diversity. This work aims to bridge this gap by infusing patterns automatically extracted from real-world images into synthetic data. Hence, patterns collected from natural images are used to generate and map materials into synthetic scenes. This unsupervised approach captures the complexity of the real world while maintaining the precision and scalability of synthetic data. We also present the first comprehensive benchmark for zero-shot material state segmentation, utilizing real-world images across a diverse range of domains, including food, soils, construction, plants, liquids, and more, each appears in various states such as wet, dry, infected, cooked, burned, and many others. The annotation includes partial similarity between regions with similar but not identical materials and hard segmentation of only identical material states. This benchmark eluded top foundation models, exposing the limitations of existing data collection methods. Meanwhile, nets trained on the infused data performed significantly better on this and related tasks. The dataset, code, and trained model are available. We also share 300,000 extracted textures and SVBRDF/PBR materials to facilitate future datasets generation.

Over the broad landscape of experimental design, regression has been a powerful tool to accurately predict the outcome metrics of a system or model given a set of parameters, but has been traditionally restricted to methods which are only applicable to a specific task. In this paper, we propose OmniPred, a framework for training language models as universal end-to-end regressors over $(x,y)$ evaluation data from diverse real world experiments. Using data sourced from Google Vizier, one of the largest blackbox optimization databases in the world, our extensive experiments demonstrate that through only textual representations of mathematical parameters and values, language models are capable of very precise numerical regression, and if given the opportunity to train over multiple tasks, can significantly outperform traditional regression models., Comment: 24 pages, 10 figures. Code can be found in https://github.com/google-research/optformer/tree/main/optformer/omnipred

Clock interferometry refers to the coherent splitting of a clock into two different paths and recombining in a way that reveals the proper time difference between them. Unlike the comparison of two separate clocks, this approach allows testing how non-flat spacetime influences quantum coherence. Atomic clocks are currently the most accurate time keeping devices. Here we propose using optical tweezers to implement clock interferometry. Our proposed clock interferometer employs an alkaline-earth-like atom held in an optical trap at the magic wavelength. Through a combination of adiabatic, tweezer-based, splitting and recombining schemes and a modified Ramsey sequence on the clock states, we achieve a linear sensitivity to the gravitational time dilation. Moreover, the measurement of the time dilation is insensitive to relative fluctuations in the intensity of the tweezer beams. We analyze the tweezer clock interferometer and show that it is feasible with current technological capabilities. The proposed interferometer could test the effect of gravitational redshift on quantum coherence, and implement the quantum twin paradox., Comment: 10 pages, 3 figures, accepted to Physical Review A

The differences between cloze-task language model (LM) probing with 1) expert-made templates and 2) naturally-occurring text have often been overlooked. Here, we evaluate 16 different LMs on 10 probing English datasets -- 4 template-based and 6 template-free -- in general and biomedical domains to answer the following research questions: (RQ1) Do model rankings differ between the two approaches? (RQ2) Do models' absolute scores differ between the two approaches? (RQ3) Do the answers to RQ1 and RQ2 differ between general and domain-specific models? Our findings are: 1) Template-free and template-based approaches often rank models differently, except for the top domain-specific models. 2) Scores decrease by up to 42% Acc@1 when comparing parallel template-free and template-based prompts. 3) Perplexity is negatively correlated with accuracy in the template-free approach, but, counter-intuitively, they are positively correlated for template-based probing. 4) Models tend to predict the same answers frequently across prompts for template-based probing, which is less common when employing template-free techniques., Comment: Accepted to EACL 2024

Prior work has uncovered a set of common problems in state-of-the-art context-based question answering (QA) systems: a lack of attention to the context when the latter conflicts with a model's parametric knowledge, little robustness to noise, and a lack of consistency with their answers. However, most prior work focus on one or two of those problems in isolation, which makes it difficult to see trends across them. We aim to close this gap, by first outlining a set of -- previously discussed as well as novel -- desiderata for QA models. We then survey relevant analysis and methods papers to provide an overview of the state of the field. The second part of our work presents experiments where we evaluate 15 QA systems on 5 datasets according to all desiderata at once. We find many novel trends, including (1) systems that are less susceptible to noise are not necessarily more consistent with their answers when given irrelevant context; (2) most systems that are more susceptible to noise are more likely to correctly answer according to a context that conflicts with their parametric knowledge; and (3) the combination of conflicting knowledge and noise can reduce system performance by up to 96%. As such, our desiderata help increase our understanding of how these models work and reveal potential avenues for improvements., Comment: Accepted to EACL 2024

Bioactivity data plays a key role in drug discovery and repurposing. The resource-demanding nature of \textit{in vitro} and \textit{in vivo} experiments, as well as the recent advances in data-driven computational biochemistry research, highlight the importance of \textit{in silico} drug target interaction (DTI) prediction approaches. While numerous large public bioactivity data sources exist, research in the field could benefit from better standardization of existing data resources. At present, different research works that share similar goals are often difficult to compare properly because of different choices of data sources and train/validation/test split strategies. Additionally, many works are based on small data subsets, leading to results and insights of possible limited validity. In this paper we propose a way to standardize and represent efficiently a very large dataset curated from multiple public sources, split the data into train, validation and test sets based on different meaningful strategies, and provide a concrete evaluation protocol to accomplish a benchmark. We analyze the proposed data curation, prove its usefulness and validate the proposed benchmark through experimental studies based on an existing neural network model.

The third data release of Gaia introduced a large catalog of astrometric binaries, out of which about 3,200 are likely main-sequence stars with a white-dwarf (WD) companion. These binaries are typically found with orbital separations of ~1 AU, a separation range that was largely unexplored due to observational challenges. Such systems are likely to have undergone a phase of stable mass transfer while the WD progenitor was on the asymptotic giant branch. Here we study the WD mass distribution of a volume-complete sample of binaries with K/M-dwarf primaries and orbital separations ~1 AU. We find that the number of massive WDs relative to the total number of WDs in these systems is smaller by an order of magnitude compared to their occurrence among single WDs in the field. One possible reason can be an implicit selection of the WD mass range if these are indeed post-stable-mass-transfer systems. Another reason can be the lack of merger products in our sample compared to the field, due to the relatively tight orbital separations of these systems. In addition, we find that about 14% of these systems have distant tertiary companions within 1 pc., Comment: Submitted to ApJL, revised version

In recent years, certain luminous extragalactic optical transients have been observed to last only a few days. Their short observed duration implies a different powering mechanism from the most common luminous extragalactic transients (supernovae) whose timescale is weeks. Some short-duration transients, most notably AT2018cow, display blue optical colours and bright radio and X-ray emission. Several AT2018cow-like transients have shown hints of a long-lived embedded energy source, such as X-ray variability, prolonged ultraviolet emission, a tentative X-ray quasiperiodic oscillation, and large energies coupled to fast (but subrelativistic) radio-emitting ejecta. Here we report observations of minutes-duration optical flares in the aftermath of an AT2018cow-like transient, AT2022tsd (the "Tasmanian Devil"). The flares occur over a period of months, are highly energetic, and are likely nonthermal, implying that they arise from a near-relativistic outflow or jet. Our observations confirm that in some AT2018cow-like transients the embedded energy source is a compact object, either a magnetar or an accreting black hole., Comment: 79 pages, 3 figures (main text) + 7 figures (extended data) + 2 figures (supplementary information). Published online in Nature on 15 November 2023

Automatic hate speech detection using deep neural models is hampered by the scarcity of labeled datasets, leading to poor generalization. To mitigate this problem, generative AI has been utilized to generate large amounts of synthetic hate speech sequences from available labeled examples, leveraging the generated data in finetuning large pre-trained language models (LLMs). In this chapter, we provide a review of relevant methods, experimental setups and evaluation of this approach. In addition to general LLMs, such as BERT, RoBERTa and ALBERT, we apply and evaluate the impact of train set augmentation with generated data using LLMs that have been already adapted for hate detection, including RoBERTa-Toxicity, HateBERT, HateXplain, ToxDect, and ToxiGen. An empirical study corroborates our previous findings, showing that this approach improves hate speech generalization, boosting recall performance across data distributions. In addition, we explore and compare the performance of the finetuned LLMs with zero-shot hate detection using a GPT-3.5 model. Our results demonstrate that while better generalization is achieved using the GPT-3.5 model, it achieves mediocre recall and low precision on most datasets. It is an open question whether the sensitivity of models such as GPT-3.5, and onward, can be improved using similar techniques of text generation.

Ontologies play a crucial role in organizing and representing knowledge. However, even current ontologies do not encompass all relevant concepts and relationships. Here, we explore the potential of large language models (LLM) to expand an existing ontology in a semi-automated fashion. We demonstrate our approach on the biomedical ontology SNOMED-CT utilizing semantic relation types from the widely used UMLS semantic network. We propose a method that uses conversational interactions with an LLM to analyze clinical practice guidelines (CPGs) and detect the relationships among the new medical concepts that are not present in SNOMED-CT. Our initial experimentation with the conversational prompts yielded promising preliminary results given a manually generated gold standard, directing our future potential improvements., Comment: Presented as a short paper at the Knowledge Representation for Healthcare 2023 workshop

Both standalone language models (LMs) as well as LMs within downstream-task systems have been shown to generate statements which are factually untrue. This problem is especially severe for low-resource languages, where training data is scarce and of worse quality than for high-resource languages. In this opinion piece, we argue that LMs in their current state will never be fully trustworthy in critical settings and suggest a possible novel strategy to handle this issue: by building LMs such that can cite their sources - i.e., point a user to the parts of their training data that back up their outputs. We first discuss which current NLP tasks would or would not benefit from such models. We then highlight the expected benefits such models would bring, e.g., quick verifiability of statements. We end by outlining the individual tasks that would need to be solved on the way to developing LMs with the ability to cite. We hope to start a discussion about the field's current approach to building LMs, especially for low-resource languages, and the role of the training data in explaining model generations., Comment: Accepted to IJCNLP-AACL 2023

State-of-the-art question answering (QA) models exhibit a variety of social biases (e.g., with respect to sex or race), generally explained by similar issues in their training data. However, what has been overlooked so far is that in the critical domain of biomedicine, any unjustified change in model output due to patient demographics is problematic: it results in the unfair treatment of patients. Selecting only questions on biomedical topics whose answers do not depend on ethnicity, sex, or sexual orientation, we ask the following research questions: (RQ1) Do the answers of QA models change when being provided with irrelevant demographic information? (RQ2) Does the answer of RQ1 differ between knowledge graph (KG)-grounded and text-based QA systems? We find that irrelevant demographic information change up to 15% of the answers of a KG-grounded system and up to 23% of the answers of a text-based system, including changes that affect accuracy. We conclude that unjustified answer changes caused by patient demographics are a frequent phenomenon, which raises fairness concerns and should be paid more attention to., Comment: Accepted to IJCNLP-AACL 2023

Recent works have shown that depth information can be obtained from Dual-Pixel (DP) sensors. A DP arrangement provides two views in a single shot, thus resembling a stereo image pair with a tiny baseline. However, the different point spread function (PSF) per view, as well as the small disparity range, makes the use of typical stereo matching algorithms problematic. To address the above shortcomings, we propose a Continuous Cost Aggregation (CCA) scheme within a semi-global matching framework that is able to provide accurate continuous disparities from DP images. The proposed algorithm fits parabolas to matching costs and aggregates parabola coefficients along image paths. The aggregation step is performed subject to a quadratic constraint that not only enforces the disparity smoothness but also maintains the quadratic form of the total costs. This gives rise to an inherently efficient disparity propagation scheme with a pixel-wise minimization in closed-form. Furthermore, the continuous form allows for a robust multi-scale aggregation that better compensates for the varying PSF. Experiments on DP data from both DSLR and phone cameras show that the proposed scheme attains state-of-the-art performance in DP disparity estimation.

The cornerstone of structural biology is the unique relationship between protein sequence and the 3D structure at equilibrium. Although intrinsically disordered proteins (IDPs) do not fold into a specific 3D structure, breaking this paradigm, some IDPs exhibit large-scale organization, such as liquid-liquid phase separation. In such cases, the structural plasticity has the potential to form numerous self-assembled structures out of thermal equilibrium. Here, we report that high-temperature incubation time is a defining parameter for micro and nanoscale self-assembly of resilin-like IDPs. Interestingly, high-resolution scanning electron microscopy micrographs reveal that an extended incubation time leads to the formation of micron-size rods and ellipsoids that depend on the amino acid sequence. More surprisingly, a prolonged incubation time also induces amino acid composition-dependent formation of short-range nanoscale order, such as periodic lamellar nanostructures. We can correlate the lamellar structures to \b{eta}-sheet formation and demonstrate similarities between the observed nanoscopic structural arrangement and spider silk. We, therefore, suggest that regulating the period of high-temperature incubation, in the one-phase regime, can serve as a unique method of controlling the hierarchical self-assembly mechanism of structurally disordered proteins., Comment: 27pages, 8 figures

Atomic interferometers measure forces and acceleration with exceptional precision. The conventional approach to atomic interferometry is to launch an atomic cloud into a ballistic trajectory and perform the wave-packet splitting in momentum space by Raman transitions. This places severe constraints on the possible atomic trajectory, positioning accuracy and probing duration. Here, we propose and analyze a novel atomic interferometer that uses micro-optical traps (optical tweezers) to manipulate and control the motion of atoms. The new interferometer allows long probing time, sub micrometer positioning accuracy, and utmost flexibility in shaping of the atomic trajectory. The cornerstone of the tweezer interferometer are the coherent atomic splitting and combining schemes. We present two adiabatic schemes with two or three tweezers that are robust to experimental imperfections and work simultaneously with many vibrational states. The latter property allows for multi-atom interferometry in a single run. We also highlight the advantage of using fermionic atoms to obtain single-atom occupation of vibrational states and to eliminate mean-field shifts. We examine the impact of tweezer intensity noise and demonstrate that, when constrained by shot noise, the interferometer can achieve a relative accuracy better than $10^{-11}$ in measuring Earth's gravitational acceleration. The sub-micrometer resolution and extended measurement duration offer promising opportunities for exploring fundamental physical laws in new regimes. We discuss two applications well-suited for the unique capabilities of the tweezer interferometer: the measurement of gravitational forces and the study of Casimir-Polder forces between atoms and surfaces. Crucially, our proposed tweezer interferometer is within the reach of current technological capabilities., Comment: 14 pages, 7 figures

The upcoming Extremely Large Telescopes (ELTs) are expected to have the collecting area required to detect potential biosignature gases such as molecular oxygen, $\mathrm{O_2}$, in the atmosphere of terrestrial planets around nearby stars. One of the most promising detection methods is transmission spectroscopy. To maximize our capability to detect $\mathrm{O_2}$ using this method, spectral resolutions $\mathrm{R}\geq 300,000$ are required to fully resolve the absorption lines in an Earth-like exoplanet atmosphere and disentangle the signal from telluric lines. Current high-resolution spectrographs typically achieve a spectral resolution of $\mathrm{R}\sim100,000$. Increasing the resolution in seeing limited observations/instruments requires drastically larger optical components, making these instruments even more expensive and hard to fabricate and assemble. Instead, we demonstrate a new approach to high-resolution spectroscopy. We implemented an ultra-high spectral resolution booster to be coupled in front of a high-resolution spectrograph. The instrument is based on a chained Fabry Perot array which generates a hyperfine spectral profile. We present on-sky telluric observations with a lab demonstrator. Depending on the configuration, this two-arm prototype reaches a resolution of R=250,000-350,000. After carefully modeling the prototype's behavior, we propose a Fabry Perot Interferometer (FPI) design for an eight-arm array configuration aimed at ELTs capable of exceeding R=300,000. The novel FPI resolution booster can be plugged in at the front end of an existing R=100,000 spectrograph to overwrite the spectral profile with a higher resolution for exoplanet atmosphere studies., Comment: Accepted for publication in A&A; 12 pages, 13 figures

The task of textual geolocation - retrieving the coordinates of a place based on a free-form language description - calls for not only grounding but also natural language understanding and geospatial reasoning. Even though there are quite a few datasets in English used for geolocation, they are currently based on open-source data (Wikipedia and Twitter), where the location of the described place is mostly implicit, such that the location retrieval resolution is limited. Furthermore, there are no datasets available for addressing the problem of textual geolocation in morphologically rich and resource-poor languages, such as Hebrew. In this paper, we present the Hebrew Geo-Location (HeGeL) corpus, designed to collect literal place descriptions and analyze lingual geospatial reasoning. We crowdsourced 5,649 literal Hebrew place descriptions of various place types in three cities in Israel. Qualitative and empirical analysis show that the data exhibits abundant use of geospatial reasoning and requires a novel environmental representation., Comment: Accepted for ACL findings 2023

M-dwarfs are common stellar hosts of habitable-zone exoplanets. NUV radiation can severely impact the atmospheric and surface conditions of such planets, making characterization of NUV flaring activity a key aspect in determining habitability. We use archival data from the GALEX and XMM-Newton telescopes to study the flaring activity of M-dwarfs in the NUV. The GALEX observations form the most extensive dataset of M-dwarfs in the NUV to date, with exploitation of this data possible due to the new gPhoton2 pipeline. We run a dedicated algorithm to detect flares in the pipeline produced lightcurves and find some of the most energetic flares observed to date within the NUV bandpass, with energies of $\sim 10^{34}$ ergs. Using GALEX data, we constrain flare frequency distributions for stars from M0 to M6 in the NUV up to $10^5$ s in equivalent duration and $10^{34}$ ergs in energy, orders of magnitude above any previous study in the UV. We estimate the combined effect of NUV luminosities and flare rates of stars later than M2 to be sufficient for abiogenesis on habitable zone exoplanets orbiting them. As a counterpoint, we speculate the high frequencies of energetic UV flares and associated coronal mass ejections would inhibit the formation of an ozone layer, possibly preventing genesis of complex Earth-like lifeforms due to sterilizing levels of surface UV radiation. We also provide a framework for future observations of M-dwarfs with ULTRASAT, a wide FoV NUV telescope to be launched in 2026., Comment: 30 pages, 27 figures. Accepted for publication in The Astrophysical Journal

Superconductor/semiconductor hybrid devices have attracted increasing interest in the past years. Superconducting electronics aims to complement semiconductor technology, while hybrid architectures are at the forefront of new ideas such as topological superconductivity and protected qubits. In this work, we engineer the induced superconductivity in two-dimensional germanium hole gas by varying the distance between the quantum well and the aluminum. We demonstrate a hard superconducting gap and realize an electrically and flux tunable superconducting diode using a superconducting quantum interference device (SQUID). This allows to tune the current phase relation (CPR), to a regime where single Cooper pair tunneling is suppressed, creating a $\sin \left( 2 \varphi \right)$ CPR. Shapiro experiments complement this interpretation and the microwave drive allows to create a diode with 100% efficiency. The reported results open up the path towards integration of spin qubit devices, microwave resonators and (protected) superconducting qubits on a silicon technology compatible platform.

Spatial adiabatic passage (SAP) is a process that facilitates the transfer of a wave packet between two localized modes that are not directly coupled, but rather interact through an intermediate third mode. By employing a counter-intuitive adiabatic pulse sequence, this technique achieves minimal population in the intermediate state and high transfer efficiency. Here, we report the implementation of SAP for transferring massive particles between three micro-optical traps. We begin by preparing ultracold fermionic atoms in low vibrational eigenstates of one trap and then manipulate the distance between the three traps to execute the SAP protocol. We observe a smooth transfer of atoms between the two outer traps, accompanied by a low population in the central trap. We validate our findings and underscore the significance of the counter-intuitive sequence by reversing the order of the pulse sequence. Additionally, we investigate the influence of the tunneling rate and the time delay between the motion of the two external tweezers on the fidelity of the process. Our results open up new possibilities for advanced control and manipulation schemes in optical tweezer array platforms., Comment: 6 pages, 4 figures

The rise of social media has been argued to intensify uncivil and hostile online political discourse. Yet, to date, there is a lack of clarity on what incivility means in the political sphere. In this work, we utilize a multidimensional perspective of political incivility, developed in the fields of political science and communication, that differentiates between impoliteness and political intolerance. We present state-of-the-art incivility detection results using a large dataset of 13K political tweets, collected and annotated per this distinction. Applying political incivility detection at large-scale, we observe that political incivility demonstrates a highly skewed distribution over users, and examine social factors that correlate with incivility at subpopulation and user-level. Finally, we propose an approach for modeling social context information about the tweet author alongside the tweet content, showing that this leads to improved performance on the task of political incivility detection. We believe that this latter result holds promise for socially-informed text processing in general.

Measuring the size distribution of small (km-scale) KBOs can help constrain models of Solar System formation and planetary migration. Such small, distant bodies are hard to detect with current or planned telescopes, but can be identified as sub-second occultations of background stars. We present the analysis of data from the Weizmann Fast Astronomical Survey Telescope (W-FAST), consisting of fast photometry of ~10^6 star hours at a frame rate of 10-25 Hz. Our pipeline utilizes a matched-filter approach with a large template bank, including red-noise treatment, and injection of simulated events for estimating the detection efficiency. The KBO radius at which our survey is 10% (50%) efficient is 1.1 (2.0) km. The data from 2020-2021 observing seasons were analyzed and no occultations were identified. We discuss a sample of sub-second false-positive events, both occultation-like and flare-like, which are still not fully understood but could be instructive for future surveys looking for short-duration events. We use our null-detection result to set limits on the km-scale KBO number density. Our individual radius bin limits are consistent with most previous works, with N(r>1km) <=10^6 deg^-2 (95% confidence limit). Our integrated (all size) limits, assuming a power law normalized to large (~45 km) KBOs gives a power law index q<3.93 (95% confidence limit). Finally, our results are in tension with a recently reported KBO detection from the ground, at the p=4x10^-4 level.