Zhening Li

Yujie Qian, Jiang Guo, Zhengkai Tu et al.

Molecular structure recognition is the task of translating a molecular image into its graph structure. Significant variation in drawing styles and conventions exhibited in chemical literature poses a significant challenge for automating this task. In this paper, we propose MolScribe, a novel image-to-graph generation model that explicitly predicts atoms and bonds, along with their geometric layouts, to construct the molecular structure. Our model flexibly incorporates symbolic chemistry constraints to recognize chirality and expand abbreviated structures. We further develop data augmentation strategies to enhance the model robustness against domain shifts. In experiments on both synthetic and realistic molecular images, MolScribe significantly outperforms previous models, achieving 76-93% accuracy on public benchmarks. Chemists can also easily verify MolScribe's prediction, informed by its confidence estimation and atom-level alignment with the input image. MolScribe is publicly available through Python and web interfaces: https://github.com/thomas0809/MolScribe.

Zhening Li, Gabriel Poesia, Omar Costilla-Reyes et al. · mit

Humans tame the complexity of mathematical reasoning by developing hierarchies of abstractions. With proper abstractions, solutions to hard problems can be expressed concisely, thus making them more likely to be found. In this paper, we propose Learning Mathematical Abstractions (LEMMA): an algorithm that implements this idea for reinforcement learning agents in mathematical domains. LEMMA augments Expert Iteration with an abstraction step, where solutions found so far are revisited and rewritten in terms of new higher-level actions, which then become available to solve new problems. We evaluate LEMMA on two mathematical reasoning tasks--equation solving and fraction simplification--in a step-by-step fashion. In these two domains, LEMMA improves the ability of an existing agent, both solving more problems and generalizing more effectively to harder problems than those seen during training.

Zhening Li, Armando Solar-Lezama, Yisong Yue et al.

We introduce a new approach to agent programming, the development of LLM-based agents. Current approaches to agent programming often entangle two aspects of agent design: the core workflow logic and the inference-time strategy (e.g., tree search). We introduce "probabilistic angelic nondeterminism" ("PAN"), a programming model that disentangles these two concerns, allowing the programmer to describe the agent workflow and independently experiment with different inference-time strategies by simply changing a few inputs. We provide an implementation of PAN in Python as the EnCompass framework, which uses a Python decorator to compile agent workflow programs into a search space. We present three case studies that demonstrate how the framework lets the programmer quickly improve the reliability of an agent and easily switch between different inference-time strategies, all with little additional coding.

Yujie Qian, Zhening Li, Zhengkai Tu et al.

This paper focuses on using natural language descriptions to enhance predictive models in the chemistry field. Conventionally, chemoinformatics models are trained with extensive structured data manually extracted from the literature. In this paper, we introduce TextReact, a novel method that directly augments predictive chemistry with texts retrieved from the literature. TextReact retrieves text descriptions relevant for a given chemical reaction, and then aligns them with the molecular representation of the reaction. This alignment is enhanced via an auxiliary masked LM objective incorporated in the predictor training. We empirically validate the framework on two chemistry tasks: reaction condition recommendation and one-step retrosynthesis. By leveraging text retrieval, TextReact significantly outperforms state-of-the-art chemoinformatics models trained solely on molecular data.

Renfei Dang, Zhening Li, Shujian Huang et al.

Reasoning models often exhibit overthinking, characterized by redundant reasoning steps. We identify \emph{internal bias} elicited by the input question as a key trigger of such behavior. Upon encountering a problem, the model immediately forms a preliminary guess about the answer, which we term an internal bias since it may not be explicitly generated, and it arises without systematic reasoning. When this guess conflicts with its subsequent reasoning, the model tends to engage in excessive reflection, resulting in wasted computation. We validate the association between internal bias and overthinking across multiple models and diverse reasoning tasks. To demonstrate the causal relationship more rigorously, we conduct two counterfactual interventions, showing that removing the input question after the model reduces the redundant reasoning across various complex reasoning tasks, and manually injecting bias affects overthinking accordingly. Further interpretability experiments suggest that excessive attention to the input question serves as a key mechanism through which internal bias influences subsequent reasoning trajectories. Finally, we evaluated several methods aimed at mitigating overthinking, yet the influence of internal bias persisted under all conditions.

Jasmine Shone, Shaden Alshammari, Mark Hamilton et al.

The Information Contrastive (I-Con) framework revealed that over 23 representation learning methods implicitly minimize KL divergence between data and learned distributions that encode similarities between data points. However, a KL-based loss may be misaligned with the true objective, and properties of KL divergence such as asymmetry and unboundedness may create optimization challenges. We present Beyond I-Con, a framework that enables systematic discovery of novel loss functions by exploring alternative statistical divergences and similarity kernels. Key findings: (1) on unsupervised clustering of DINO-ViT embeddings, we achieve state-of-the-art results by modifying the PMI algorithm to use total variation (TV) distance; (2) on supervised contrastive learning, we outperform the standard approach by using TV and a distance-based similarity kernel instead of KL and an angular kernel; (3) on dimensionality reduction, we achieve superior qualitative results and better performance on downstream tasks than SNE by replacing KL with a bounded f-divergence. Our results highlight the importance of considering divergence and similarity kernel choices in representation learning optimization.

Zhening Li, Gabriel Poesia, Armando Solar-Lezama

Skills are temporal abstractions that are intended to improve reinforcement learning (RL) performance through hierarchical RL. Despite our intuition about the properties of an environment that make skills useful, a precise characterization has been absent. We provide the first such characterization, focusing on the utility of deterministic skills in deterministic sparse-reward environments with finite action spaces. We show theoretically and empirically that RL performance gain from skills is worse in environments where solutions to states are less compressible. Additional theoretical results suggest that skills benefit exploration more than they benefit learning from existing experience, and that using unexpressive skills such as macroactions may worsen RL performance. We hope our findings can guide research on automatic skill discovery and help RL practitioners better decide when and how to use skills.