Bioinformatics Agents
LLM-agent benchmarks for computational biology — exploring datasets, running multi-step analyses, and interpreting biological results.
Bioinformatics Agents is a key task in agentic ai. Below you will find the standard benchmarks used to evaluate models, along with current state-of-the-art results.
Benchmarks & SOTA
Related Tasks
HCAST
HCAST (Human-Calibrated Autonomy Software Tasks) is a 90-task benchmark from METR designed to measure AI autonomy with human-calibrated baselines — every task has known completion times from professional software engineers, enabling direct human-vs-AI comparison. Tasks span realistic software engineering scenarios at varying difficulty levels, from simple bug fixes to complex architectural changes. The human calibration is what makes HCAST distinctive: instead of just pass/fail, it reveals whether AI agents are 10x slower, equally fast, or approaching superhuman speed on specific task types.
Tool Use
Benchmarks measuring AI agents ability to use tools and APIs to complete real-world tasks across domains like retail and airline customer service.
Autonomous Coding
Autonomous coding — AI systems that write, debug, and ship software without human guidance — is the most commercially immediate agentic capability. Benchmarks range from function-level synthesis (HumanEval, MBPP) to full-repository tasks (SWE-bench), and the field moved from autocomplete to genuine software engineering when Cognition's Devin (2024) and open alternatives like SWE-Agent and OpenHands demonstrated multi-file, multi-step coding workflows. The frontier is extended autonomy: can an agent maintain a codebase over days, not just resolve a single issue?
SWE-bench
SWE-bench — resolving real GitHub issues from popular Python repositories — became the defining benchmark for AI software engineering after its 2023 release by Princeton. The verified subset (500 curated problems) went from ~4% resolution rate with raw GPT-4 to over 50% with agentic scaffolds like SWE-Agent and Amazon Q Developer by mid-2025. What makes it uniquely challenging is the need to navigate large codebases, write tests, and produce patches that pass CI — skills that require genuine multi-file reasoning, not just code generation.
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