Heng Ji
Publications
Protein Language Models Diverge from Natural Language: Comparative Analysis and Improved Inference
Modern Protein Language Models (PLMs) apply transformer-based model architectures from natural language processing to biological sequences, predicting a variety of protein functions and properties. However, protein language has key differences from natural language, such as a rich functional space despite a vocabulary of only 20 amino acids. These differences motivate research into how transformer-based architectures operate differently in the protein domain and how we can better leverage PLMs to solve protein-related tasks. In this work, we begin by directly comparing how the distribution of information stored across layers of attention heads differs between the protein and natural language domain. Furthermore, we adapt a simple early-exit technique-originally used in the natural language domain to improve efficiency at the cost of performance-to achieve both increased accuracy and substantial efficiency gains in protein non-structural property prediction by allowing the model to automatically select protein representations from the intermediate layers of the PLMs for the specific task and protein at hand. We achieve performance gains ranging from 0.4 to 7.01 percentage points while simultaneously improving efficiency by over 10 percent across models and non-structural prediction tasks. Our work opens up an area of research directly comparing how language models change behavior when moved into the protein domain and advances language modeling in biological domains.
ReIn: Conversational Error Recovery with Reasoning Inception
Conversational agents powered by large language models (LLMs) with tool integration achieve strong performance on fixed task-oriented dialogue datasets but remain vulnerable to unanticipated, user-induced errors. Rather than focusing on error prevention, this work focuses on error recovery, which necessitates the accurate diagnosis of erroneous dialogue contexts and execution of proper recovery plans. Under realistic constraints precluding model fine-tuning or prompt modification due to significant cost and time requirements, we explore whether agents can recover from contextually flawed interactions and how their behavior can be adapted without altering model parameters and prompts. To this end, we propose Reasoning Inception (ReIn), a test-time intervention method that plants an initial reasoning into the agent's decision-making process. Specifically, an external inception module identifies predefined errors within the dialogue context and generates recovery plans, which are subsequently integrated into the agent's internal reasoning process to guide corrective actions, without modifying its parameters or system prompts. We evaluate ReIn by systematically simulating conversational failure scenarios that directly hinder successful completion of user goals: user's ambiguous and unsupported requests. Across diverse combinations of agent models and inception modules, ReIn substantially improves task success and generalizes to unseen error types. Moreover, it consistently outperforms explicit prompt-modification approaches, underscoring its utility as an efficient, on-the-fly method. In-depth analysis of its operational mechanism, particularly in relation to instruction hierarchy, indicates that jointly defining recovery tools with ReIn can serve as a safe and effective strategy for improving the resilience of conversational agents without modifying the backbone models or system prompts.
Toward Cognitive Supersensing in Multimodal Large Language Model
Multimodal Large Language Models (MLLMs) have achieved remarkable success in open-vocabulary perceptual tasks, yet their ability to solve complex cognitive problems remains limited, especially when visual details are abstract and require visual memory. Current approaches primarily scale Chain-of-Thought (CoT) reasoning in the text space, even when language alone is insufficient for clear and structured reasoning, and largely neglect visual reasoning mechanisms analogous to the human visuospatial sketchpad and visual imagery. To mitigate this deficiency, we introduce Cognitive Supersensing, a novel training paradigm that endows MLLMs with human-like visual imagery capabilities by integrating a Latent Visual Imagery Prediction (LVIP) head that jointly learns sequences of visual cognitive latent embeddings and aligns them with the answer, thereby forming vision-based internal reasoning chains. We further introduce a reinforcement learning stage that optimizes text reasoning paths based on this grounded visual latent. To evaluate the cognitive capabilities of MLLMs, we present CogSense-Bench, a comprehensive visual question answering (VQA) benchmark assessing five cognitive dimensions. Extensive experiments demonstrate that MLLMs trained with Cognitive Supersensing significantly outperform state-of-the-art baselines on CogSense-Bench and exhibit superior generalization on out-of-domain mathematics and science VQA benchmarks, suggesting that internal visual imagery is potentially key to bridging the gap between perceptual recognition and cognitive understanding. We will open-source the CogSense-Bench and our model weights.
Towards Agentic Intelligence for Materials Science
The convergence of artificial intelligence and materials science presents a transformative opportunity, but achieving true acceleration in discovery requires moving beyond task-isolated, fine-tuned models toward agentic systems that plan, act, and learn across the full discovery loop. This survey advances a unique pipeline-centric view that spans from corpus curation and pretraining, through domain adaptation and instruction tuning, to goal-conditioned agents interfacing with simulation and experimental platforms. Unlike prior reviews, we treat the entire process as an end-to-end system to be optimized for tangible discovery outcomes rather than proxy benchmarks. This perspective allows us to trace how upstream design choices-such as data curation and training objectives-can be aligned with downstream experimental success through effective credit assignment. To bridge communities and establish a shared frame of reference, we first present an integrated lens that aligns terminology, evaluation, and workflow stages across AI and materials science. We then analyze the field through two focused lenses: From the AI perspective, the survey details LLM strengths in pattern recognition, predictive analytics, and natural language processing for literature mining, materials characterization, and property prediction; from the materials science perspective, it highlights applications in materials design, process optimization, and the acceleration of computational workflows via integration with external tools (e.g., DFT, robotic labs). Finally, we contrast passive, reactive approaches with agentic design, cataloging current contributions while motivating systems that pursue long-horizon goals with autonomy, memory, and tool use. This survey charts a practical roadmap towards autonomous, safety-aware LLM agents aimed at discovering novel and useful materials.