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Eric Wang

Publications and source records attributed to Eric Wang.

At least 37 records · Page 2Linked to original sources

Unfolding Boxes with Local Constraints

We consider the problem of finding and enumerating polyominos that can be folded into multiple non-isomorphic boxes. While several computational approaches have been proposed, including SAT, randomized algorithms, and decision diagrams, none has been able to perform at scale. We argue that existing SAT encodings are hindered by the presence of global constraints (e.g., graph connectivity or acyclicity), which are generally hard to encode effectively and hard for solvers to reason about. In this work, we propose a new SAT-based approach that replaces these global constraints with simple local constraints that have substantially better propagation properties. Our approach dramatically improves the scalability of both computing and enumerating common box unfoldings: (i) while previous approaches could only find common unfoldings of two boxes up to area 88, ours easily scales beyond 150, and (ii) while previous approaches were only able to enumerate common unfoldings up to area 30, ours scales up to 60. This allows us to rule out 46, 54, and 58 as the smallest areas allowing a common unfolding of three boxes, thereby refuting a conjecture of Xu et al. (2017).

cs.CG↗

CAST: Time-Varying Treatment Effects with Application to Chemotherapy and Radiotherapy on Head and Neck Squamous Cell Carcinoma

Causal machine learning (CML) enables individualized estimation of treatment effects, offering critical advantages over traditional correlation-based methods. However, existing approaches for medical survival data with censoring such as causal survival forests estimate effects at fixed time points, limiting their ability to capture dynamic changes over time. We introduce Causal Analysis for Survival Trajectories (CAST), a novel framework that models treatment effects as continuous functions of time following treatment. By combining parametric and non-parametric methods, CAST overcomes the limitations of discrete time-point analysis to estimate continuous effect trajectories. Using the RADCURE dataset [1] of 2,651 patients with head and neck squamous cell carcinoma (HNSCC) as a clinically relevant example, CAST models how chemotherapy and radiotherapy effects evolve over time at the population and individual levels. By capturing the temporal dynamics of treatment response, CAST reveals how treatment effects rise, peak, and decline over the follow-up period, helping clinicians determine when and for whom treatment benefits are maximized. This framework advances the application of CML to personalized care in HNSCC and other life-threatening medical conditions. Source code/data available at: https://github.com/CAST-FW/HNSCC

cs.LG↗

TxGemma: Efficient and Agentic LLMs for Therapeutics

Therapeutic development is a costly and high-risk endeavor that is often plagued by high failure rates. To address this, we introduce TxGemma, a suite of efficient, generalist large language models (LLMs) capable of therapeutic property prediction as well as interactive reasoning and explainability. Unlike task-specific models, TxGemma synthesizes information from diverse sources, enabling broad application across the therapeutic development pipeline. The suite includes 2B, 9B, and 27B parameter models, fine-tuned from Gemma-2 on a comprehensive dataset of small molecules, proteins, nucleic acids, diseases, and cell lines. Across 66 therapeutic development tasks, TxGemma achieved superior or comparable performance to the state-of-the-art generalist model on 64 (superior on 45), and against state-of-the-art specialist models on 50 (superior on 26). Fine-tuning TxGemma models on therapeutic downstream tasks, such as clinical trial adverse event prediction, requires less training data than fine-tuning base LLMs, making TxGemma suitable for data-limited applications. Beyond these predictive capabilities, TxGemma features conversational models that bridge the gap between general LLMs and specialized property predictors. These allow scientists to interact in natural language, provide mechanistic reasoning for predictions based on molecular structure, and engage in scientific discussions. Building on this, we further introduce Agentic-Tx, a generalist therapeutic agentic system powered by Gemini 2.5 that reasons, acts, manages diverse workflows, and acquires external domain knowledge. Agentic-Tx surpasses prior leading models on the Humanity's Last Exam benchmark (Chemistry & Biology) with 52.3% relative improvement over o3-mini (high) and 26.7% over o3-mini (high) on GPQA (Chemistry) and excels with improvements of 6.3% (ChemBench-Preference) and 2.4% (ChemBench-Mini) over o3-mini (high).

cs.AI↗

Liger at W.M. Keck Observatory: imager structural analysis, fabrication, and characterization plan

Liger is an adaptive optics (AO) fed imager and integral field spectrograph (IFS) designed to take advantage of the Keck All-sky Precision Adaptive-optics (KAPA) upgrade to the Keck I telescope. Liger adapts the design of the InfraRed Imaging Spectrograph (IRIS) for the Thirty Meter Telescope (TMT) to Keck by implementing a new imager and re-imaging optics. The performance of the imager is critical as it sequentially feeds the spectrograph and contains essential components such as the pupil wheel, filter wheel, and pupil viewing camera. We present the design and structural analysis of the Liger imager optical assembly including static, modal, and thermal simulations. We present the fabrication as well as the full assembly and characterization plan. The imager will be assembled bench-top in a clean room utilizing a coordinate-measuring machine (CMM) for warm alignment. To ensure optimal performance, the imager will be characterized in a test cryostat before integration with the full Liger instrument. This comprehensive approach to characterization ensures the precision and reliability of the imager, enhancing the observational capabilities of Liger and W.M. Keck Observatory.

astro-ph.IM↗

The Dynamic Sensorium competition for predicting large-scale mouse visual cortex activity from videos

Understanding how biological visual systems process information is challenging due to the complex nonlinear relationship between neuronal responses and high-dimensional visual input. Artificial neural networks have already improved our understanding of this system by allowing computational neuroscientists to create predictive models and bridge biological and machine vision. During the Sensorium 2022, we introduced benchmarks for vision models with static input. However, animals operate and excel in dynamic environments, making it crucial to study and understand how the brain functions under these conditions. Moreover, many biological theories, such as predictive coding, suggest that previous input is crucial for current input processing. Currently, there is no standardized benchmark to identify state-of-the-art dynamic models of the mouse visual system. To address this gap, we propose the Sensorium 2023 Benchmark Competition with dynamic input. It includes the collection of a new large-scale dataset from the primary visual cortex of ten mice, containing responses from over 78,000 neurons to over 2 hours of dynamic stimuli per neuron. Participants in the main benchmark track will compete to identify the best predictive models of neuronal responses for dynamic input. We will also host a bonus track in which submission performance will be evaluated on out-of-domain input, using withheld neuronal responses to dynamic input stimuli whose statistics differ from the training set. Both tracks will offer behavioral data along with video stimuli. As before, we will provide code, tutorials, and strong pre-trained baseline models to encourage participation. We hope this competition will continue to strengthen the accompanying Sensorium benchmarks collection as a standard tool to measure progress in large-scale neural system identification models of the entire mouse visual hierarchy and beyond.

q-bio.NC↗

Retrospective for the Dynamic Sensorium Competition for predicting large-scale mouse primary visual cortex activity from videos

Understanding how biological visual systems process information is challenging because of the nonlinear relationship between visual input and neuronal responses. Artificial neural networks allow computational neuroscientists to create predictive models that connect biological and machine vision. Machine learning has benefited tremendously from benchmarks that compare different model on the same task under standardized conditions. However, there was no standardized benchmark to identify state-of-the-art dynamic models of the mouse visual system. To address this gap, we established the Sensorium 2023 Benchmark Competition with dynamic input, featuring a new large-scale dataset from the primary visual cortex of ten mice. This dataset includes responses from 78,853 neurons to 2 hours of dynamic stimuli per neuron, together with the behavioral measurements such as running speed, pupil dilation, and eye movements. The competition ranked models in two tracks based on predictive performance for neuronal responses on a held-out test set: one focusing on predicting in-domain natural stimuli and another on out-of-distribution (OOD) stimuli to assess model generalization. As part of the NeurIPS 2023 competition track, we received more than 160 model submissions from 22 teams. Several new architectures for predictive models were proposed, and the winning teams improved the previous state-of-the-art model by 50%. Access to the dataset as well as the benchmarking infrastructure will remain online at www.sensorium-competition.net.

q-bio.NC↗

Tx-LLM: A Large Language Model for Therapeutics

Developing therapeutics is a lengthy and expensive process that requires the satisfaction of many different criteria, and AI models capable of expediting the process would be invaluable. However, the majority of current AI approaches address only a narrowly defined set of tasks, often circumscribed within a particular domain. To bridge this gap, we introduce Tx-LLM, a generalist large language model (LLM) fine-tuned from PaLM-2 which encodes knowledge about diverse therapeutic modalities. Tx-LLM is trained using a collection of 709 datasets that target 66 tasks spanning various stages of the drug discovery pipeline. Using a single set of weights, Tx-LLM simultaneously processes a wide variety of chemical or biological entities(small molecules, proteins, nucleic acids, cell lines, diseases) interleaved with free-text, allowing it to predict a broad range of associated properties, achieving competitive with state-of-the-art (SOTA) performance on 43 out of 66 tasks and exceeding SOTA on 22. Among these, Tx-LLM is particularly powerful and exceeds best-in-class performance on average for tasks combining molecular SMILES representations with text such as cell line names or disease names, likely due to context learned during pretraining. We observe evidence of positive transfer between tasks with diverse drug types (e.g.,tasks involving small molecules and tasks involving proteins), and we study the impact of model size, domain finetuning, and prompting strategies on performance. We believe Tx-LLM represents an important step towards LLMs encoding biochemical knowledge and could have a future role as an end-to-end tool across the drug discovery development pipeline.

cs.CL↗

Semantic Loss Functions for Neuro-Symbolic Structured Prediction

Structured output prediction problems are ubiquitous in machine learning. The prominent approach leverages neural networks as powerful feature extractors, otherwise assuming the independence of the outputs. These outputs, however, jointly encode an object, e.g. a path in a graph, and are therefore related through the structure underlying the output space. We discuss the semantic loss, which injects knowledge about such structure, defined symbolically, into training by minimizing the network's violation of such dependencies, steering the network towards predicting distributions satisfying the underlying structure. At the same time, it is agnostic to the arrangement of the symbols, and depends only on the semantics expressed thereby, while also enabling efficient end-to-end training and inference. We also discuss key improvements and applications of the semantic loss. One limitations of the semantic loss is that it does not exploit the association of every data point with certain features certifying its membership in a target class. We should therefore prefer minimum-entropy distributions over valid structures, which we obtain by additionally minimizing the neuro-symbolic entropy. We empirically demonstrate the benefits of this more refined formulation. Moreover, the semantic loss is designed to be modular and can be combined with both discriminative and generative neural models. This is illustrated by integrating it into generative adversarial networks, yielding constrained adversarial networks, a novel class of deep generative models able to efficiently synthesize complex objects obeying the structure of the underlying domain.

cs.LG↗

Advancing Multimodal Medical Capabilities of Gemini

Many clinical tasks require an understanding of specialized data, such as medical images and genomics, which is not typically found in general-purpose large multimodal models. Building upon Gemini's multimodal models, we develop several models within the new Med-Gemini family that inherit core capabilities of Gemini and are optimized for medical use via fine-tuning with 2D and 3D radiology, histopathology, ophthalmology, dermatology and genomic data. Med-Gemini-2D sets a new standard for AI-based chest X-ray (CXR) report generation based on expert evaluation, exceeding previous best results across two separate datasets by an absolute margin of 1% and 12%, where 57% and 96% of AI reports on normal cases, and 43% and 65% on abnormal cases, are evaluated as "equivalent or better" than the original radiologists' reports. We demonstrate the first ever large multimodal model-based report generation for 3D computed tomography (CT) volumes using Med-Gemini-3D, with 53% of AI reports considered clinically acceptable, although additional research is needed to meet expert radiologist reporting quality. Beyond report generation, Med-Gemini-2D surpasses the previous best performance in CXR visual question answering (VQA) and performs well in CXR classification and radiology VQA, exceeding SoTA or baselines on 17 of 20 tasks. In histopathology, ophthalmology, and dermatology image classification, Med-Gemini-2D surpasses baselines across 18 out of 20 tasks and approaches task-specific model performance. Beyond imaging, Med-Gemini-Polygenic outperforms the standard linear polygenic risk score-based approach for disease risk prediction and generalizes to genetically correlated diseases for which it has never been trained. Although further development and evaluation are necessary in the safety-critical medical domain, our results highlight the potential of Med-Gemini across a wide range of medical tasks.

cs.CV↗

Security and Privacy Product Inclusion

In this paper, we explore the challenges of ensuring security and privacy for users from diverse demographic backgrounds. We propose a threat modeling approach to identify potential risks and countermeasures for product inclusion in security and privacy. We discuss various factors that can affect a user's ability to achieve a high level of security and privacy, including low-income demographics, poor connectivity, shared device usage, ML fairness, etc. We present results from a global security and privacy user experience survey and discuss the implications for product developers. Our work highlights the need for a more inclusive approach to security and privacy and provides a framework for researchers and practitioners to consider when designing products and services for a diverse range of users.

cs.CR↗

Speeding up and reducing memory usage for scientific machine learning via mixed precision

Scientific machine learning (SciML) has emerged as a versatile approach to address complex computational science and engineering problems. Within this field, physics-informed neural networks (PINNs) and deep operator networks (DeepONets) stand out as the leading techniques for solving partial differential equations by incorporating both physical equations and experimental data. However, training PINNs and DeepONets requires significant computational resources, including long computational times and large amounts of memory. In search of computational efficiency, training neural networks using half precision (float16) rather than the conventional single (float32) or double (float64) precision has gained substantial interest, given the inherent benefits of reduced computational time and memory consumed. However, we find that float16 cannot be applied to SciML methods, because of gradient divergence at the start of training, weight updates going to zero, and the inability to converge to a local minima. To overcome these limitations, we explore mixed precision, which is an approach that combines the float16 and float32 numerical formats to reduce memory usage and increase computational speed. Our experiments showcase that mixed precision training not only substantially decreases training times and memory demands but also maintains model accuracy. We also reinforce our empirical observations with a theoretical analysis. The research has broad implications for SciML in various computational applications.

cs.LG↗

Inferring the redshift of more than 150 GRBs with a Machine Learning Ensemble model

Gamma-Ray Bursts (GRBs), due to their high luminosities are detected up to redshift 10, and thus have the potential to be vital cosmological probes of early processes in the universe. Fulfilling this potential requires a large sample of GRBs with known redshifts, but due to observational limitations, only 11\% have known redshifts ($z$). There have been numerous attempts to estimate redshifts via correlation studies, most of which have led to inaccurate predictions. To overcome this, we estimated GRB redshift via an ensemble supervised machine learning model that uses X-ray afterglows of long-duration GRBs observed by the Neil Gehrels Swift Observatory. The estimated redshifts are strongly correlated (a Pearson coefficient of 0.93) and have a root mean square error, namely the square root of the average squared error $\langleΔz^2\rangle$, of 0.46 with the observed redshifts showing the reliability of this method. The addition of GRB afterglow parameters improves the predictions considerably by 63\% compared to previous results in peer-reviewed literature. Finally, we use our machine learning model to infer the redshifts of 154 GRBs, which increase the known redshifts of long GRBs with plateaus by 94\%, a significant milestone for enhancing GRB population studies that require large samples with redshift.

astro-ph.CO↗

The development of HISPEC for Keck and MODHIS for TMT: science cases and predicted sensitivities

HISPEC is a new, high-resolution near-infrared spectrograph being designed for the W.M. Keck II telescope. By offering single-shot, R=100,000 between 0.98 - 2.5 um, HISPEC will enable spectroscopy of transiting and non-transiting exoplanets in close orbits, direct high-contrast detection and spectroscopy of spatially separated substellar companions, and exoplanet dynamical mass and orbit measurements using precision radial velocity monitoring calibrated with a suite of state-of-the-art absolute and relative wavelength references. MODHIS is the counterpart to HISPEC for the Thirty Meter Telescope and is being developed in parallel with similar scientific goals. In this proceeding, we provide a brief overview of the current design of both instruments, and the requirements for the two spectrographs as guided by the scientific goals for each. We then outline the current science case for HISPEC and MODHIS, with focuses on the science enabled for exoplanet discovery and characterization. We also provide updated sensitivity curves for both instruments, in terms of both signal-to-noise ratio and predicted radial velocity precision.

astro-ph.IM↗

Multi-Rate VAE: Train Once, Get the Full Rate-Distortion Curve

Variational autoencoders (VAEs) are powerful tools for learning latent representations of data used in a wide range of applications. In practice, VAEs usually require multiple training rounds to choose the amount of information the latent variable should retain. This trade-off between the reconstruction error (distortion) and the KL divergence (rate) is typically parameterized by a hyperparameter $β$. In this paper, we introduce Multi-Rate VAE (MR-VAE), a computationally efficient framework for learning optimal parameters corresponding to various $β$ in a single training run. The key idea is to explicitly formulate a response function that maps $β$ to the optimal parameters using hypernetworks. MR-VAEs construct a compact response hypernetwork where the pre-activations are conditionally gated based on $β$. We justify the proposed architecture by analyzing linear VAEs and showing that it can represent response functions exactly for linear VAEs. With the learned hypernetwork, MR-VAEs can construct the rate-distortion curve without additional training and can be deployed with significantly less hyperparameter tuning. Empirically, our approach is competitive and often exceeds the performance of multiple $β$-VAEs training with minimal computation and memory overheads.

cs.LG↗

Design of SCALES: A 2-5 Micron Coronagraphic Integral Field Spectrograph for Keck Observatory

We present the design of SCALES (Slicer Combined with Array of Lenslets for Exoplanet Spectroscopy) a new 2-5 micron coronagraphic integral field spectrograph under construction for Keck Observatory. SCALES enables low-resolution (R~50) spectroscopy, as well as medium-resolution (R~4,000) spectroscopy with the goal of discovering and characterizing cold exoplanets that are brightest in the thermal infrared. Additionally, SCALES has a 12x12" field-of-view imager that will be used for general adaptive optics science at Keck. We present SCALES's specifications, its science case, its overall design, and simulations of its expected performance. Additionally, we present progress on procuring, fabricating and testing long lead-time components.

astro-ph.IM↗

Design of an IR Imaging Channel for the Keck Observatory SCALES Instrument

A next-generation instrument named, Slicer Combined with Array of Lenslets for Exoplanet Spectroscopy (SCALES), is being planned for the W. M. Keck Observatory. SCALES will have an integral field spectrograph (IFS) and a diffraction-limited imaging channel to discover and spectrally characterize the directly imaged exoplanets. Operating at thermal infrared wavelengths (1-5 micron, and a goal of 0.6-5 micron), the imaging channel of the SCALES is designed to cover a 12"x 12" field of view with low distortions and high throughput. Apart from expanding the mid-infrared science cases and providing a potential upgrade/alternative for the NIRC2, the H2RG detector of the imaging channel can take high-resolution images of the pupil to aid the alignment process.Further, the imaging camera would also assist in small field acquisition for the IFS arm. In this work, we present the optomechanical design of the imager and evaluate its capabilities and performances.

astro-ph.IM↗

Liger at Keck Observatory: Design of Imager Optical Assembly and Spectrograph Re-Imaging Optics

Liger is an adaptive optics (AO) fed imager and integral field spectrograph (IFS) designed to take advantage of the Keck All-sky Precision Adaptive-optics (KAPA) upgrade for the W.M. Keck Observatory. We present the design and analysis of the imager optical assembly including the spectrograph Re-Imaging Optics (RIO) which transfers the beam path from the imager focal plane to the IFS slicer module and lenslet array. Each imager component and the first two RIO mechanisms are assembled and individually aligned on the same optical plate. Baffling suppresses background radiation and scattered light, and a pupil viewing camera allows the imager detector to focus on an image of the telescope pupil. The optical plate mounts on an adapter frame for alignment of the overall system. The imager and RIO will be characterized in a cryogenic test chamber before installation in the final science cryostat.

astro-ph.IM↗

Liger at Keck Observatory: Imager Detector and IFS Pick-off Mirror Assembly

Liger is a next-generation near-infrared imager and integral field spectrograph (IFS) planned for the W.M. Keck Observatory. Liger is designed to take advantage of improved adaptive optics (AO) from the Keck All-Sky Precision Adaptive Optics (KAPA) upgrade currently underway. Liger operates at 0.84-2.45 $μ$m with spectral resolving powers of R$\sim$4,000-10,000. Liger makes use of a sequential imager and spectrograph design allowing for simultaneous observations. There are two spectrograph modes: a lenslet with high spatial sampling of 14 and 31 mas, and a slicer with 75 and 150 mas sampling with an expanded field of view. Two pick-off mirrors near the imager detector direct light to these two IFS channels. We present the design and structural analysis for the imager detector and IFS pick-off mirror mounting assembly that will be used to align and maintain stability throughout its operation. A piezoelectric actuator will be used to step through $\rm3\,mm$ of travel during alignment of the instrument to determine the optimal focus for both the detector and pick-off mirrors which will be locked in place during normal operation. We will demonstrate that the design can withstand the required gravitational and shipping loads and can be aligned within the positioning tolerances for the optics.

astro-ph.IM↗