Reasoning large language models achieve impressive test-time scaling by thinking for longer, but this performance gain comes at significant compute cost.Directly limiting test-time budget hurts overall performance, but not all problems are equally difficult.We propose thought calibration to decide dynamically when thinking can be terminated.To calibrate our decision rule, we view a language model's growing body of thoughts as a nested sequence of reasoning trees, where the goal is to identify the point at which novel reasoning plateaus.We realize this framework through lightweight probes that operate on top of the language model's hidden representations, which are informative of both the reasoning structure and overall consistency of response.Based on three reasoning language models and four datasets, thought calibration preserves model performance with up to a 60% reduction in thinking tokens on in-distribution data, and up to 20% in out-of-distribution data. 1

High-content perturbation experiments allow scientists to probe biomolecular systems at unprecedented resolution, but experimental and analysis costs pose significant barriers to widespread adoption. Machine learning has the potential to guide efficient exploration of the perturbation space and extract novel insights from these data. However, current approaches neglect the semantic richness of the relevant biology, and their objectives are misaligned with downstream biological analyses. In this paper, we hypothesize that large language models (LLMs) present a natural medium for representing complex biological relationships and rationalizing experimental outcomes. We propose PerturbQA, a benchmark for structured reasoning over perturbation experiments. Unlike current benchmarks that primarily interrogate existing knowledge, PerturbQA is inspired by open problems in perturbation modeling: prediction of differential expression and change of direction for unseen perturbations, and gene set enrichment. We evaluate state-of-the-art machine learning and statistical approaches for modeling perturbations, as well as standard LLM reasoning strategies, and we find that current methods perform poorly on PerturbQA. As a proof of feasibility, we introduce Summer (SUMMarize, retrievE, and answeR, a simple, domain-informed LLM framework that matches or exceeds the current state-of-the-art. Our code and data are publicly available at https://github.com/genentech/PerturbQA.

Identifying variables responsible for changes to a biological system enables applications in drug target discovery and cell engineering. Given a pair of observational and interventional datasets, the goal is to isolate the subset of observed variables that were the targets of the intervention. Directly applying causal discovery algorithms is challenging: the data may contain thousands of variables with as few as tens of samples per intervention, and biological systems do not adhere to classical causality assumptions. We propose a causality-inspired approach to address this practical setting. First, we infer noisy causal graphs from the observational and interventional data. Then, we learn to map the differences between these graphs, along with additional statistical features, to sets of variables that were intervened upon. Both modules are jointly trained in a supervised framework, on simulated and real data that reflect the nature of biological interventions. This approach consistently outperforms baselines for perturbation modeling on seven single-cell transcriptomics datasets. We also demonstrate significant improvements over current causal discovery methods for predicting soft and hard intervention targets across a variety of synthetic data.

We propose a robust and accurate non-parametric method for single-view 3D face reconstruction (SVFR). While tremendous efforts have been devoted to parametric SVFR, a visible gap still lies between the result 3D shape and the ground truth. We believe there are two major obstacles: 1) the representation of the parametric model is limited to a certain face database; 2) 2D images and 3D shapes in the fitted datasets are distinctly misaligned. To resolve these issues, a large-scale pseudo 2D&3D dataset is created by first rendering the detailed 3D faces, then swapping the face in the wild images with the rendered face. These pseudo 2D&3D pairs are created from publicly available datasets which eliminate the gaps between 2D and 3D data while covering diverse appearances, poses, scenes, and illumination. We further propose a non-parametric scheme to learn a well-generalized SVFR model from the created dataset, and the proposed hierarchical signed distance function turns out to be effective in predicting middle-scale and small-scale 3D facial geometry. Our model outperforms previous methods on FaceScape-wild/lab and MICC benchmarks and is well generalized to various appearances, poses, expressions, and in-the-wild environments. The code is released at https://github.com/zhuhao-nju/rafare.

Synthesizing high-quality 3D face models from natural language descriptions is very valuable for many applications, including avatar creation, virtual reality, and telepresence. However, little research ever tapped into this task. We argue the major obstacle lies in 1) the lack of high-quality 3D face data with descriptive text annotation, and 2) the complex mapping relationship between descriptive language space and shape/appearance space. To solve these problems, we build Describe3D dataset, the first large-scale dataset with fine-grained text descriptions for text-to-3D face generation task. Then we propose a two-stage framework to first generate a 3D face that matches the concrete descriptions, then optimize the parameters in the 3D shape and texture space with abstract description to refine the 3D face model. Extensive experimental results show that our method can produce a faithful 3D face that conforms to the input descriptions with higher accuracy and quality than previous methods. The code and Describe3D dataset are released at https://github.com/zhuhao-nju/describe3D.

In this article, we present a large-scale detailed 3D face dataset, FaceScape, and the corresponding benchmark to evaluate single-view facial 3D reconstruction. By training on FaceScape data, a novel algorithm is proposed to predict elaborate riggable 3D face models from a single image input. FaceScape dataset releases 16,940 textured 3D faces, captured from 847 subjects and each with 20 specific expressions. The 3D models contain the pore-level facial geometry that is also processed to be topologically uniform. These fine 3D facial models can be represented as a 3D morphable model for coarse shapes and displacement maps for detailed geometry. Taking advantage of the large-scale and high-accuracy dataset, a novel algorithm is further proposed to learn the expression-specific dynamic details using a deep neural network. The learned relationship serves as the foundation of our 3D face prediction system from a single image input. Different from most previous methods, our predicted 3D models are riggable with highly detailed geometry under different expressions. We also use FaceScape data to generate the in-the-wild and in-the-lab benchmark to evaluate recent methods of single-view face reconstruction. The accuracy is reported and analyzed on the dimensions of camera pose and focal length, which provides a faithful and comprehensive evaluation and reveals new challenges. The unprecedented dataset, benchmark, and code have been released to the public for research purpose.