BigHat Biosciences Software Engineer Interview Guide

The 60-second brief

As a Software Engineer at BigHat Biosciences, you are at the intersection of cutting-edge software engineering and synthetic biology. Your work directly contributes to the development of a platform that designs better antibodies for patients through high-speed characterization and AI-driven design. This is not a standard SaaS role; you are building the digital infrastructure that enables scientists to engineer life-saving therapeutics faster and more effectively. You will face challenges involving complex data integration, high-throughput experimentation workflows, and the need for robust, scalable software systems. Because BigHat Biosciences operates at the bleeding edge of biotechnology, your code will directly impact the speed and accuracy of the drug discovery process.

This guide is scoped to a Software Engineer candidate at BigHat Biosciences.

Focus areas

• Take-home Coding Assignment
• Coding Exercises
• Software Engineering (General)

Where to focus your preparation

No round sequence has been reported for BigHat Biosciences. Confirm the format with your recruiter.

Preparation focus

No round sequence has been reported for this company, so confirm the format with your recruiter and work the reported questions below.

What to demonstrate

• Breadth across the topics this company reports testing
• Whether you confirm the format before preparing for it

How to prepare

• Ask the recruiter for the sequence, the duration of each stage and whether you will be writing code
• Work the reported questions below and time yourself

Where candidates lose points

Prioritize the Take-Home

This is your primary opportunity to showcase your engineering standards. Treat it like a production pull request.

Be Ready to Explain the "Why

In technical interviews, the reasoning behind your choice is often more important than the choice itself.

Prepare for Panel Interviews

You will meet people from other departments. Have your "elevator pitch" ready and practice explaining your technical work in simple, accessible terms.

Engage with the Recruiter

The recruiting team at BigHat Biosciences is known to be communicative and helpful. Use them as a resource to clarify expectations for each round.

Questions & practice

Walk me through your approach to the take-home technical assignment and the trade-offs you made.

Medium · Technical Proficiency and Problem Solvin

Approach

1. Restate the input: its shape, its size, and what is guaranteed about it.
2. Name the brute-force solution and its complexity before improving on it.
3. Choose the data structure from the access pattern, not from familiarity.
4. State the target complexity and say which constraint rules the naive version out.

Follow-up

• How does this change if the input no longer fits in memory?
• What is the worst case, and how likely is it on real data?

Explain a challenging technical bug you encountered recently and the steps you took to resolve it.

Medium · Technical Proficiency and Problem Solvin

Approach

1. Restate the input: its shape, its size, and what is guaranteed about it.
2. Name the brute-force solution and its complexity before improving on it.
3. Choose the data structure from the access pattern, not from familiarity.
4. State the target complexity and say which constraint rules the naive version out.

Follow-up

• How does this change if the input no longer fits in memory?
• What is the worst case, and how likely is it on real data?

Track a rolling failure rate per destination for circuit decisions

Easy · sliding window · ring buffer · circuit breaker

The egress service delivers about 1,500 webhooks per second across roughly 40,000 destinations, each call bounded by a 10 second timeout. Maintain, per destination, the failure rate over the trailing 60 seconds so a caller can ask before dispatch whether the circuit should open. Attempts arrive as (destination_id, finished_at_ms, outcome). Requirement: amortised O(1) per attempt, with total memory bounded by the destination count rather than by traffic. Give the structure, its exact memory, and the rule that stops a destination with three attempts from opening a circuit.

Approach

1. Name the exact-deque version and then reject it as the default. Holding timestamps and advancing a tail pointer past anything older than now minus 60 seconds is a correct two-pointer window at amortised O(1) per attempt, but its memory tracks in-window traffic, so one destination in a retry storm holds hundreds of thousands of entries while thousands of quiet destinations hold none.
2. Use a ring of 60 one-second buckets per destination, each bucket a pair of counters for attempts and failures. On an attempt, advance the ring by the elapsed whole seconds, zeroing at most min(elapsed, 60) buckets, then increment the head. That is amortised O(1) with a fixed footprint per destination.
3. State the footprint: 60 buckets times two 4-byte counters is 480 bytes of payload per destination, so 40,000 destinations is roughly 20 to 25 MB with per-entry overhead, bounded by the catalogue rather than by the rate. The cost is granularity, since the oldest bucket ages out in whole seconds, which is far tighter than the decision needs.
4. Require a minimum sample before the circuit may open. A destination with three attempts and three failures reads as 100 percent and is not evidence; a floor of roughly 20 attempts in the window makes the ratio meaningful, and below that floor use a run of consecutive failures as the trigger instead.

Follow-up

• The fleet is 30 instances and each sees roughly a thirtieth of a destination's traffic. Where does the rate actually live, and what does a per-instance answer get wrong?
• A destination answers in 9.5 seconds and succeeds. It is not failing but it is consuming your per-destination concurrency. What signal should open the circuit here?

Replace offset paging on the resource feed with keyset

Easy · keyset pagination · composite index · sort order

resource holds resource_id, tenant_id, owner_user_id, title, body_ref, version, status ('draft','active','archived','deleted'), created_at, updated_at, deleted_at, with an index on (tenant_id, status, updated_at DESC, resource_id DESC). The listing endpoint returns active resources for one tenant, newest update first, 50 per page, today with LIMIT 50 OFFSET n. Tenants reach page 400 and rows are created while they read. Write the keyset query, define what the cursor carries and how it is encoded, and say which part of the index each predicate uses. Assume PostgreSQL 16.

Approach

1. Name the two failures separately. OFFSET 20000 makes the server produce and discard 20,000 rows, so page cost grows with depth rather than with page size. Independently, any write that changes how many rows sort above the offset moves the window between two fetches, and the direction decides which anomaly you get: an insert lands at the head of updated_at DESC and pushes already-returned rows down past the boundary, so they are returned a second time; a delete above the offset, or a row whose updated_at is bumped above the cursor, pulls rows up and one is never returned at all. Nothing in the response reveals either.
2. Write the seek: WHERE tenant_id = $1 AND status = 'active' AND (updated_at, resource_id) < ($2, $3) ORDER BY updated_at DESC, resource_id DESC LIMIT 50. The row-value comparison is one index range rather than a disjunction, and both columns are NOT NULL, which is what makes that comparison well defined.
3. Map each predicate onto the index: tenant_id and status are equality on the leading columns, (updated_at, resource_id) is the range, and the ORDER BY matches the index order so no Sort node appears and the scan stops after 50 rows. The DESC in the definition only matters for mixed directions — a plain ascending btree on the same columns is read backwards for this query.
4. Put both sort columns in the cursor and nothing the client can tamper with into another tenant: base64 of (updated_at, resource_id), validated server-side, with tenant_id taken from the principal.

Follow-up

• The client asks for 'jump to page 400'. What do you offer instead, and what does the honest version cost?
• Sort order becomes user-selectable across four columns. How many indexes is that, and which would you refuse to add?

Keep soft-deleted accounts from blocking re-registration

Easy · soft delete · unique constraints · engine differences

app_user holds user_id, tenant_id, email CITEXT, password_hash (NULL for SSO principals), email_verified_at, auth_version, status ('invited','active','suspended','deactivated'), created_at, updated_at, deleted_at. Two live accounts for one address inside a tenant must be impossible, but an address freed by a soft delete must be reusable, and the same tenant may delete and re-register it repeatedly. Write the uniqueness DDL for PostgreSQL 16, then the equivalent for MySQL 8 where partial indexes do not exist, and say what each permits once three deleted rows already hold that address.

Approach

1. Start from what is actually unique: not (tenant_id, email), but (tenant_id, email) among live rows. PostgreSQL says that directly — CREATE UNIQUE INDEX app_user_live_email ON app_user (tenant_id, email) WHERE deleted_at IS NULL. A full constraint over the same two columns burns the address permanently the first time someone deletes an account.
2. Keep case-insensitivity in the type or the index, never in the application: CITEXT as given, or UNIQUE (tenant_id, lower(email)) as an expression index where the extension is unavailable. A case-sensitive unique column is exactly how two accounts for one human appear.
3. For MySQL 8 the predicate has to move inside the key: add a discriminator column that is a constant 0 while the row is live and is set to user_id on delete, with UNIQUE (tenant_id, email, deleted_marker). Live rows share the constant and still collide; deleted rows differ from each other and stop colliding.
4. State the NULL variant and its dependency: leaving the marker NULL for deleted rows also works, because a unique index treats NULLs as distinct — true in MySQL, and true in PostgreSQL only under the default NULLS DISTINCT, which PostgreSQL 15 lets you reverse. Check the polarity against the three existing deleted rows: constant-on-live is what preserves the collision you want, and reversing it silently admits duplicate live accounts.

Follow-up

• A deleted account re-registers with the same address the next day. Do the old resource rows follow the new user_id, and how does the API keep the two principals apart?
• How do you honour an erasure request while resource_revision.actor_user_id still references this table?

How do you ensure your code is scalable when dealing with experimental biological data?

Medium · Technical Proficiency and Problem Solvin

Approach

1. Fix the scope first: who calls this, how often, and what they do when it fails.
2. Name the read and write paths separately; they rarely have the same bottleneck.
3. Choose a partition key and say what query it makes expensive.
4. State the consistency you need, and where you are willing to be stale.

Follow-up

• What breaks first when traffic grows ten times?
• How does this behave when that dependency is down for an hour?

Publish rate-limit and deadline semantics the edge actually enforces

Easy · rate limiting · backpressure · retries

The edge API serves about 3k requests/second steady and 9k at peak against a 400 ms p99 budget, with an explicit bounded concurrency limit per instance. Limits exist per principal and per tenant. Callers are a partner integration running nightly bulk loads and a browser app. Specify the counting algorithm and window, which limit a request is charged against, the headers a well-behaved client reads, the status and body when a limit is hit, how that differs from the response when an instance is shedding load, and what each caller does with each.

Approach

1. Choose the counter and name its failure mode. Fixed windows admit nearly twice the limit across a boundary - a full burst at the end of one window and another at the start of the next. A token bucket states sustained rate and burst separately, which is exactly what a nightly bulk load needs. A sliding-window counter is more faithful and costs more state per key. State the choice and the burst it permits.
2. Charge each request against both keys and reject on the stricter. The tenant limit protects the shared primary, which absorbs roughly 1.2k writes/second in total; the per-principal limit stops one credential inside a tenant from consuming that tenant's whole allowance. The tenant is the fairness unit for the same reason it is the leading column of every index.
3. Advertise limit, remaining and reset for the binding key on every response, not only on rejections, so a client can pace before it is refused. Pick one naming scheme - the RateLimit-* draft fields or an X-prefixed set - document the units, and never change them afterwards.
4. Separate two rejections that look identical to a naive client. 429 means this caller exceeded its own share and Retry-After is a real schedule it should obey. 503 means the instance is at its concurrency bound and shedding, which is a statement about the server; a fleet-wide 503 retried on a fixed delay resynchronises every client into one stampede, so full jitter is mandatory there and the delay is the client's guess, not ours.

Follow-up

• One tenant stays under its limit and still degrades everyone else during a backfill. What changes - the limiter, the worker concurrency caps, or both?
• How are counters kept correct across 20 to 40 stateless instances, and what does your answer cost per request?

p99 jumped on one listing filter while p50 stayed flat

Medium · query planning · composite index · percentiles

After a release that added an owner_user_id filter to the resource listing, p99 rose from 90 ms to 1.9 s while p50 stayed at 40 ms. Traffic and row counts are unchanged. resource carries the index (tenant_id, status, updated_at DESC, resource_id DESC). The new query filters tenant_id and owner_user_id, orders by updated_at DESC, resource_id DESC, and takes 20 rows. On PostgreSQL, explain the shape of the regression, prove it from a query plan, and give the index you would add.

Approach

1. Start from the shape. A flat p50 with a moved p99 means a subset of requests changed cost, not all of them, so the first job is naming the subset. Bucket the endpoint's latency by the tenant's row count; the natural hypothesis is that large tenants are a small share of requests and all of the tail.
2. Get the plan for the new query on a large tenant with EXPLAIN (ANALYZE, BUFFERS). Expect an index scan over the tenant's range, a filter discarding most of it, then a Sort feeding the Limit, possibly reporting Sort Method: external merge Disk. Read actual rows on the scan node, not estimated.
3. Explain why the existing index cannot serve it. A composite B-tree is seekable only as a left prefix, and with no equality predicate on status the scan cannot treat updated_at as an ordering, because rows in the tenant's range are ordered by status first. Everything matching must be read and sorted before LIMIT 20 can apply, so a tenant with 400,000 rows pays 400,000 rows to return 20.
4. Add (tenant_id, owner_user_id, updated_at DESC, resource_id DESC). Equality on the first two columns leaves the index ordered by updated_at within that pair, so the plan becomes an index scan that stops after 20 rows with no Sort node. PostgreSQL can scan a B-tree backwards, so the DESC markers matter only if the two sort columns ever disagree in direction; keeping them explicit documents the order the keyset cursor depends on.

Follow-up

• The endpoint paginates with OFFSET. What does page 500 cost with your index, and what does the keyset version cost?
• How would you have caught this before release, given that a 10,000-row seed database produces the same plan shape at an unnoticeable cost?

Suggested practice checklist

Built from the topics and questions BigHat Biosciences candidates report; no round sequence has been reported.

Day 1 — Establish the BigHat Biosciences format

• No round sequence has been reported, so ask your recruiter for the sequence, the duration of each stage and whether you will write code.

Deliverable: A written reply from your recruiter confirming the format.

Day 2 — Work Take-home Coding Assignment

• Spend the session on Take-home Coding Assignment, which BigHat Biosciences candidates report being tested on.
• Write one worked example in Take-home Coding Assignment and time yourself on it.

Deliverable: One timed worked example in Take-home Coding Assignment.

Day 3 — Work Coding Exercises

• Spend the session on Coding Exercises, which BigHat Biosciences candidates report being tested on.
• Write one worked example in Coding Exercises and time yourself on it.

Deliverable: One timed worked example in Coding Exercises.

Day 4 — Work Software Engineering (General)

• Spend the session on Software Engineering (General), which BigHat Biosciences candidates report being tested on.
• Write one worked example in Software Engineering (General) and time yourself on it.

Deliverable: One timed worked example in Software Engineering (General).

Day 5 — Answer out loud: Technical Proficiency and Problem Solving

• Answer aloud, timed: Walk me through your approach to the take-home technical assignment and the trade-offs you made.
• Answer aloud, timed: How do you ensure your code is scalable when dealing with experimental biological data?

Deliverable: Spoken answers to 2 reported Technical Proficiency and Problem Solving question(s), under time.

Day 6 — Rehearse your own examples

• Prepare three examples from your own work where you made the decision, each with the outcome you can quantify.

Deliverable: Three examples written out, each with a number attached.

Day 7 — Dry run for BigHat Biosciences

• Run one full mock under time, then write down the two questions you most want to ask your interviewers.

Deliverable: A completed timed mock and two questions to ask.

Behavioural preparation

Behavioural rounds judge the decision you made and what it cost.

How do you handle edge cases when building data processing pipelines?

Medium · Technical Proficiency and Problem Solvin

Approach

1. Pick a story where you made the decision, not one where you watched it.
2. State the situation in two sentences and spend the rest on the reasoning.
3. Give the blast radius: what could have broken, and what you measured.
4. Name the disagreement and how you resolved it with evidence.

Follow-up

• What would you do differently if you ran that again?
• How did you know your change caused the improvement?

Describe a time you had to refactor a piece of legacy code to improve performance.

Medium · Technical Proficiency and Problem Solvin

Approach

1. Pick a story where you made the decision, not one where you watched it.
2. State the situation in two sentences and spend the rest on the reasoning.
3. Give the blast radius: what could have broken, and what you measured.
4. Name the disagreement and how you resolved it with evidence.

Follow-up

• What would you do differently if you ran that again?
• How did you know your change caused the improvement?

Tell callers you do not own that their integration breaks

Medium · deprecation · compatibility · stakeholders

A field in a write endpoint's response must change shape. You own the endpoint; you do not own the four internal callers or the outbound webhook consumers who read it. Describe a deprecation you were responsible for: what you shipped first, how you established who was actually reading the field, the window you gave and what set its length, what you did about the consumer who never moved, and how you decided removal was safe. Name the signal you used, not the announcement you sent.

Approach

1. Establish the reader set empirically rather than from a wiki of owners: per-field usage counters keyed by principal, or access logs attributed to a consumer. State the blind spot of whichever you pick, since a consumer that reads the field only on a monthly job will not appear in a week of logs.
2. Ship additive first. Populate the new field alongside the old one so no reader is forced to move, which is also what keeps a rolling deploy safe, because old and new instances answer the same requests at the same time and a rollback must still find the old shape present.
3. Set the window from the slowest legitimate consumer's release cadence, not from your calendar, and decide separately what to do for a consumer with no release process at all, such as an external webhook endpoint you can only email.
4. Convert silence into evidence before you rely on it: a short, low-traffic removal window that makes a still-dependent consumer fail visibly and loudly while you are watching, rather than at three in the morning after you have moved on.

Follow-up

• How would you detect a consumer that reads the field only during a monthly export?
• One caller refuses to move and has a commercial relationship behind it. What changes in your plan and what does not?